# Generated by fetch_yeastpathways_biopax.py from YeastPathways BioPAX L3 exports; do not edit. ACETATEUTIL2-PWY: all_genes: - &id001 orf: YAL054C symbol: ACS1 uniprot: UniProtKB:Q01574 - &id002 orf: YLR153C symbol: ACS2 uniprot: UniProtKB:P52910 comment: 'In S. cerevisiae, mitochondrial acetyl-CoA reserves are biochemically isolated and cannot be transported to the cytosol to support processes such as protein acetylation and fatty acid biosynthesis. Instead, S. cerevisiae obtains cytosolic acetyl-CoA through the activation of acetate. Acetate activation to acetyl-CoA occurs via the enzyme acetyl-CoA synthetase, which catalyzes the ATP-dependent ligation of acetate and coenzyme A to form acetyl-CoA. Two genes encode for acetyl-CoA synthetase in S. cerevisiae: ACS1 and ACS2. ACS1 is a glucose-repressed gene required for growth on acetate during glucose starvation, while ACS2 is a constitutively expressed gene essential for cell viability in glucose medium. ACS1 is repressed by Ume6p and is activated by Adr1p and Cat8p in the absence of glucose. Double mutants of acs1 and acs2 are inviable, suggesting that acetate activation by acetyl-CoA synthetase is an essential source of acetyl-CoA in S. cerevisiae. Likewise, acs2 mutants are inviable when grown on glucose medium due to repression of ACS1. References: |CITS: [25326522]||CITS: [16857587]||CITS: [8910545]||CITS: [22876324]||CITS: [7649171]||CITS: [15743812]||CITS: [9427394]|' name: acetate utilization pmids: - '15743812' - '16857587' - '22876324' - '25326522' - '7649171' - '8910545' - '9427394' reactions: - ec: - 6.2.1.1 genes: - *id001 - *id002 left: - ATP - acetate - coenzyme A name: acetate + ATP + coenzyme A -> acetyl-CoA + AMP + diphosphate pmids: [] rhea: [] right: - AMP - acetyl-CoA - diphosphate yeastcyc_id: ACETATE--COA-LIGASE-RXN yeastcyc_id: ACETATEUTIL2-PWY AERO-GLYCEROL-CAT-PWY: all_genes: - &id003 orf: YHL032C symbol: GUT1 uniprot: UniProtKB:P32190 - &id004 orf: YIL155C symbol: GUT2 uniprot: UniProtKB:P32191 comment: 'Under aerobic conditions, S. cerevisiae is able to utilize glycerol as a sole carbon and energy source. Glycerol degradation is a two-step process; the first step of glycerol phosphorylation occurs in the cytosol, then glycerol-3-phosphate enters the motichondrion where the second step of conversion to dihydroxyacetone is catalyzed |CITS:[191434]|. Dihydroxyacetone is then returned to the cytosol where it enters into either glycolysis or gluconeogenesis. The genes encoding the enzymes catalyzing glycerol catabolism, GUT1 and GUT2, are carbon source regulated; gene expression is repressed when cells are grown on fermentable carbon sources such as glucose and upregulated on non-fermentable carbon sources such as glycerol or ethanol |CITS:[191434]|, |CITS:[10536147]|, |CITS:[11142398]|. On non-fermentable carbon sources, GUT1 transcription is induced by the transcriptional activators Adr1p, Ino2p and Ino4p |CITS:[10536147]|, while GUT2 regulation requires the protein kinase Snf1p and the transcriptional activating Hap2p/Hap3p/Hap4p/Hap5p complex |CITS:[11142398]|. Conversely, the negative regulator Opi1p facilitates GUT1 and GUT2 repression |CITS:[10536147]|, |CITS:[11142398]|. ' name: glycerol degradation pmids: - '191434' reactions: - ec: - 2.7.1.30 genes: - *id003 left: - ATP - glycerol name: glycerol + ATP -> sn-glycerol 3-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - sn-glycerol 3-phosphate yeastcyc_id: GLYCEROL-KIN-RXN - ec: - 1.1.5.3 genes: - *id004 left: - sn-glycerol 3-phosphate - ubiquinone-6 name: sn-glycerol 3-phosphate + ubiquinone-6 -> glycerone phosphate + ubiquinol-6 pmids: [] rhea: [] right: - glycerone phosphate - ubiquinol-6 yeastcyc_id: RXN3O-9815 yeastcyc_id: AERO-GLYCEROL-CAT-PWY ALANINE-DEG3-PWY: all_genes: - &id005 orf: YLR089C symbol: ALT1 uniprot: UniProtKB:P52893 name: L-alanine degradation III pmids: [] reactions: - ec: - 2.6.1.2 genes: - *id005 left: - 2-oxoglutarate - L-alanine name: 2-oxoglutarate + L-alanine <-> L-glutamate + pyruvate pmids: [] rhea: [] right: - L-glutamate - pyruvate yeastcyc_id: ALANINE-AMINOTRANSFERASE-RXN yeastcyc_id: ALANINE-DEG3-PWY ALANINE-SYN2-PWY: all_genes: - *id005 comment: 'Alanine is an essential component of protein (as L-alpha-alanine). alt1 null mutations demonstrated that under respiratory conditions, the alanine aminotransferase encoded by ALT1 plays a central role in arginine biosynthesis and degradation in Saccharomyces cerevisiae |CITS: [19396236]|. Under fermentative conditions, Saccharomyces cerevisiae appears to synthesize alanine by an alternative pathway that is independent of Alt1p, but it degrades alanine by the same Alt1p-dependent pathway as used during respiration |CITS: [19396236]|.' name: L-alanine biosynthesis II pmids: - '19396236' reactions: - ec: - 2.6.1.2 genes: - *id005 left: - 2-oxoglutarate - L-alanine name: 2-oxoglutarate + L-alanine <-> L-glutamate + pyruvate pmids: [] rhea: [] right: - L-glutamate - pyruvate yeastcyc_id: ALANINE-AMINOTRANSFERASE-RXN yeastcyc_id: ALANINE-SYN2-PWY ALL-CHORISMATE-PWY-1: all_genes: - &id014 orf: YNR033W symbol: ABZ1 uniprot: UniProtKB:P37254 - &id009 orf: YMR289W symbol: ABZ2 uniprot: UniProtKB:Q03266 - &id021 orf: YGR204W symbol: ADE3 uniprot: UniProtKB:P07245 - &id008 orf: YDR127W symbol: ARO1 uniprot: UniProtKB:P08566 - &id011 orf: YGL148W symbol: ARO2 uniprot: UniProtKB:P28777 - &id035 orf: YDR035W symbol: ARO3 uniprot: UniProtKB:P14843 - &id036 orf: YBR249C symbol: ARO4 uniprot: UniProtKB:P32449 - &id029 orf: YPR060C symbol: ARO7 uniprot: UniProtKB:P32178 - &id015 orf: YGL202W symbol: ARO8 uniprot: UniProtKB:P53090 - &id017 orf: YHR137W symbol: ARO9 uniprot: UniProtKB:P38840 - &id026 orf: YOR074C symbol: CDC21 uniprot: UniProtKB:P06785 - &id027 orf: YOR236W symbol: DFR1 uniprot: UniProtKB:P07807 - &id010 orf: YNL256W symbol: FOL1 uniprot: UniProtKB:P53848 - &id012 orf: YGR267C symbol: FOL2 uniprot: UniProtKB:P51601 - &id013 orf: YMR113W symbol: FOL3 uniprot: UniProtKB:Q12676 - &id031 orf: YDR019C symbol: GCV1 uniprot: UniProtKB:P48015 - &id032 orf: YMR189W symbol: GCV2 uniprot: UniProtKB:P49095 - &id033 orf: YAL044C symbol: GCV3 uniprot: UniProtKB:P39726 - &id016 orf: YIL116W symbol: HIS5 uniprot: UniProtKB:P07172 - &id034 orf: YFL018C symbol: LPD1 uniprot: UniProtKB:P09624 - &id023 orf: YPL023C symbol: MET12 uniprot: UniProtKB:P46151 - &id024 orf: YGL125W symbol: MET13 uniprot: UniProtKB:P53128 - &id022 orf: YBR084W symbol: MIS1 uniprot: UniProtKB:P09440 - &id025 orf: YKR080W symbol: MTD1 uniprot: UniProtKB:Q02046 - &id037 orf: YNL316C symbol: PHA2 uniprot: UniProtKB:P32452 - &id018 orf: YBR263W symbol: SHM1 uniprot: UniProtKB:P37292 - &id019 orf: YLR058C symbol: SHM2 uniprot: UniProtKB:P37291 - &id020 orf: YDR007W symbol: TRP1 uniprot: UniProtKB:P00912 - &id030 orf: YER090W symbol: TRP2 uniprot: UniProtKB:P00899 - &id007 orf: YKL211C symbol: TRP3 uniprot: UniProtKB:P00937 - &id028 orf: YDR354W symbol: TRP4 uniprot: UniProtKB:P07285 - &id006 orf: YGL026C symbol: TRP5 uniprot: UniProtKB:P00931 - &id038 orf: YBR166C symbol: TYR1 uniprot: UniProtKB:P20049 comment: Chorismate is an intermediate in the synthesis of the aromatic amino acids tyrosine, phenylalanine, and tryptophan and the vitamins, p-aminobenzoate and p-hydroxybenzoate |CITS:[Jones]|. The series of reactions to chorismate, called the shikimate pathway, are common for all of the aforementioned compounds, at which point the pathway branches |CITS:[Jones][1943992]|. One branch proceeds to tryptophan, one to phenylalanine and tyrosine, one to p-aminobenzoate, and one to p-hydroxybenzoate |CITS:[Jones][ 1943992]|. Aromatic amino acid biosynthesis in S. cerevisiae is controlled by a combination of feedback inhibition, activation of enzyme activity, and regulation of enzyme synthesis |CITS:[Jones][1943992]|. The carbon flow through the pathways is regulated primarily at the initial step and the branching points by the terminal end-products. The initial step of chorismate biosynthesis can be catalyzed by two isoenzymes, one of which (ARO3) is inhibited by phenylalanine, and the other (ARO4) by tyrosine |CITS:[Jones][1943992]|. The first step in the phenylalanine-tyrosine branch is feedback inhibited by tyrosine and activated by tryptophan |CITS:[1943992]|, and the first step in the tryptophan branch is feedback inhibited by tryptophan. The transcriptional activator GCN4 regulates most of the genes encoding for the aromatic amino acid biosynthetic enzymes. name: superpathway of chorismate metabolism pmids: [] reactions: - ec: - 4.2.1.20 genes: - *id006 left: - (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate - L-serine name: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine -> L-tryptophan + D-glyceraldehyde 3-phosphate + H2O pmids: [] rhea: [] right: - D-glyceraldehyde 3-phosphate - H2O - L-tryptophan yeastcyc_id: TRYPSYN-RXN - ec: - 4.1.1.48 genes: - *id007 left: - 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate - H+ name: 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate + H+ -> (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O pmids: [] rhea: [] right: - (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate - CO2 - H2O yeastcyc_id: IGPSYN-RXN - ec: - 4.2.1.10 genes: - *id008 left: - 3-dehydroquinate name: 3-dehydroquinate <-> 3-dehydroshikimate + H2O pmids: [] rhea: [] right: - 3-dehydroshikimate - H2O yeastcyc_id: 3-DEHYDROQUINATE-DEHYDRATASE-RXN - ec: - 4.2.3.4 genes: - *id008 left: - 3-deoxy-D-arabino-heptulosonate 7-phosphate name: 3-deoxy-D-arabino-heptulosonate 7-phosphate -> 3-dehydroquinate + phosphate pmids: [] rhea: [] right: - 3-dehydroquinate - phosphate yeastcyc_id: 3-DEHYDROQUINATE-SYNTHASE-RXN - ec: - 4.1.3.38 genes: - *id009 left: - 4-amino-4-deoxychorismate name: 4-amino-4-deoxychorismate -> 4-aminobenzoate + pyruvate + H+ pmids: [] rhea: [] right: - 4-aminobenzoate - H+ - pyruvate yeastcyc_id: ADCLY-RXN - ec: - 2.5.1.15 genes: - *id010 left: - (7,8-dihydropterin-6-yl)methyl diphosphate - 4-aminobenzoate name: 4-aminobenzoate + (7,8-dihydropterin-6-yl)methyl diphosphate -> 7,8-dihydropteroate + diphosphate pmids: [] rhea: [] right: - 7,8-dihydropteroate - diphosphate yeastcyc_id: H2PTEROATESYNTH-RXN - ec: - 4.2.3.5 genes: - *id011 left: - 5-enolpyruvoyl-shikimate 3-phosphate name: 5-enolpyruvoyl-shikimate 3-phosphate -> chorismate + phosphate pmids: [] rhea: [] right: - chorismate - phosphate yeastcyc_id: CHORISMATE-SYNTHASE-RXN - ec: - 2.7.6.3 genes: - *id010 left: - 6-(hydroxymethyl)-7,8-dihydropterin - ATP name: 6-(hydroxymethyl)-7,8-dihydropterin + ATP -> (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H+ pmids: [] rhea: [] right: - (7,8-dihydropterin-6-yl)methyl diphosphate - AMP - H+ yeastcyc_id: H2PTERIDINEPYROPHOSPHOKIN-RXN - ec: - 4.1.2.25 genes: - *id010 left: - 7,8-dihydroneopterin name: 7,8-dihydroneopterin -> glycolaldehyde + 6-(hydroxymethyl)-7,8-dihydropterin pmids: [] rhea: [] right: - 6-(hydroxymethyl)-7,8-dihydropterin - glycolaldehyde yeastcyc_id: H2NEOPTERINALDOL-RXN - ec: - 3.6.1.- genes: [] left: - 7,8-dihydroneopterin 3'-phosphate - H2O name: 7,8-dihydroneopterin 3'-phosphate + H2O -> 7,8-dihydroneopterin + phosphate pmids: [] rhea: [] right: - 7,8-dihydroneopterin - phosphate yeastcyc_id: DIHYDRONEOPTERIN-MONO-P-DEPHOS-RXN - ec: - 3.6.1.67 genes: [] left: - 7,8-dihydroneopterin 3'-triphosphate - H2O name: 7,8-dihydroneopterin 3'-triphosphate + H2O -> 7,8-dihydroneopterin 3'-phosphate + diphosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydroneopterin 3'-phosphate - H+ - diphosphate yeastcyc_id: H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN - ec: - 3.5.4.16 genes: - *id012 left: - GTP - H2O name: GTP + H2O -> formate + 7,8-dihydroneopterin 3'-triphosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydroneopterin 3'-triphosphate - H+ - formate yeastcyc_id: GTP-CYCLOHYDRO-I-RXN - ec: - 6.3.2.12 genes: - *id013 left: - 7,8-dihydropteroate - ATP - L-glutamate name: L-glutamate + 7,8-dihydropteroate + ATP -> ADP + 7,8-dihydrofolate monoglutamate + phosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydrofolate monoglutamate - ADP - H+ - phosphate yeastcyc_id: DIHYDROFOLATESYNTH-RXN - ec: - 2.6.1.85 genes: - *id014 left: - L-glutamine - chorismate name: L-glutamine + chorismate <-> 4-amino-4-deoxychorismate + L-glutamate pmids: [] rhea: [] right: - 4-amino-4-deoxychorismate - L-glutamate yeastcyc_id: PABASYN-RXN - ec: - 2.6.1.1 - 2.6.1.27 - 2.6.1.57 - 2.6.1.9 genes: - *id015 - *id016 left: - 2-oxoglutarate - L-phenylalanine name: L-phenylalanine + 2-oxoglutarate <-> 3-phenyl-2-oxopropanoate + L-glutamate pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-phenyl-2-oxopropanoate - L-glutamate yeastcyc_id: RXN-10814 - ec: - 2.6.1.58 genes: - *id017 left: - L-phenylalanine - pyruvate name: L-phenylalanine + pyruvate <-> 3-phenyl-2-oxopropanoate + L-alanine pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-phenyl-2-oxopropanoate - L-alanine yeastcyc_id: 2.6.1.58-RXN - ec: - 2.1.2.1 genes: - *id018 - *id019 left: - L-serine - a tetrahydrofolate name: L-serine + a tetrahydrofolate <-> glycine + a 5,10-methylenetetrahydrofolate + H2O pmids: [] rhea: [] right: - H2O - a 5,10-methylenetetrahydrofolate - glycine yeastcyc_id: GLYOHMETRANS-RXN - ec: - 2.6.1.27 - 2.6.1.5 - 2.6.1.57 genes: - *id015 left: - 2-oxoglutarate - L-tyrosine name: L-tyrosine + 2-oxoglutarate <-> 3-(4-hydroxyphenyl)pyruvate + L-glutamate pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - L-glutamate yeastcyc_id: TYROSINE-AMINOTRANSFERASE-RXN - ec: - 2.6.1.58 genes: - *id017 left: - L-tyrosine - pyruvate name: L-tyrosine + pyruvate <-> 3-(4-hydroxyphenyl)pyruvate + L-alanine pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - L-alanine yeastcyc_id: RXN3O-4157 - ec: - 5.3.1.24 genes: - *id020 left: - N-(5-phosphoribosyl)-anthranilate name: N-(5-phosphoribosyl)-anthranilate -> 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate pmids: [] rhea: [] right: - 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate yeastcyc_id: PRAISOM-RXN - ec: - 3.5.4.9 genes: - *id021 - *id022 left: - H2O - a 5,10-methenyltetrahydrofolate name: a 5,10-methenyltetrahydrofolate + H2O <-> a 10-formyltetrahydrofolate + H+ pmids: [] rhea: [] right: - H+ - a 10-formyltetrahydrofolate yeastcyc_id: METHENYLTHFCYCLOHYDRO-RXN - ec: - 1.5.1.20 genes: - *id023 - *id024 left: - H+ - NAD(P)H - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NAD(P)H + H+ -> a 5-methyltetrahydrofolate + NAD(P)+ pmids: [] rhea: [] right: - NAD(P)+ - a 5-methyltetrahydrofolate yeastcyc_id: RXN3O-9789 - ec: - 1.5.1.15 genes: - *id025 left: - NAD+ - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NAD+ -> a 5,10-methenyltetrahydrofolate + NADH pmids: - '8608153' rhea: [] right: - NADH - a 5,10-methenyltetrahydrofolate yeastcyc_id: 1.5.1.15-RXN - ec: - 1.5.1.5 genes: - *id021 - *id022 left: - NADP+ - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NADP+ <-> a 5,10-methenyltetrahydrofolate + NADPH pmids: [] rhea: [] right: - NADPH - a 5,10-methenyltetrahydrofolate yeastcyc_id: METHYLENETHFDEHYDROG-NADP-RXN - ec: - 2.1.1.45 genes: - *id026 left: - a 5,10-methylenetetrahydrofolate - dUMP name: a 5,10-methylenetetrahydrofolate + dUMP -> dTMP + a 7,8-dihydrofolate pmids: [] rhea: [] right: - a 7,8-dihydrofolate - dTMP yeastcyc_id: THYMIDYLATESYN-RXN - ec: - 6.3.4.3 genes: - *id021 - *id022 left: - ATP - a tetrahydrofolate - formate name: a tetrahydrofolate + ATP + formate <-> a 10-formyltetrahydrofolate + ADP + phosphate pmids: - '1916088' rhea: [] right: - ADP - a 10-formyltetrahydrofolate - phosphate yeastcyc_id: FORMATETHFLIG-RXN - ec: - 1.5.1.3 genes: - *id027 left: - NADP+ - a tetrahydrofolate name: a tetrahydrofolate + NADP+ <- a 7,8-dihydrofolate + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 7,8-dihydrofolate yeastcyc_id: DIHYDROFOLATEREDUCT-RXN - ec: - 2.4.2.18 genes: - *id028 left: - 5-phospho-α-D-ribose 1-diphosphate - anthranilate name: anthranilate + 5-phospho-α-D-ribose 1-diphosphate -> N-(5-phosphoribosyl)-anthranilate + diphosphate pmids: [] rhea: [] right: - N-(5-phosphoribosyl)-anthranilate - diphosphate yeastcyc_id: PRTRANS-RXN - ec: - 5.4.99.5 genes: - *id029 left: - chorismate name: chorismate <-> prephenate pmids: [] rhea: [] right: - prephenate yeastcyc_id: CHORISMATEMUT-RXN - ec: - 4.1.3.27 genes: - *id030 - *id007 left: - L-glutamine - chorismate name: chorismate + L-glutamine -> anthranilate + L-glutamate + pyruvate + H+ pmids: [] rhea: [] right: - H+ - L-glutamate - anthranilate - pyruvate yeastcyc_id: ANTHRANSYN-RXN - ec: [] genes: - *id031 - *id032 - *id033 - *id034 left: - NAD+ - a tetrahydrofolate - glycine name: glycine + a tetrahydrofolate + NAD+ -> a 5,10-methylenetetrahydrofolate + ammonium + CO2 + NADH pmids: - '1916088' rhea: [] right: - CO2 - NADH - a 5,10-methylenetetrahydrofolate - ammonium yeastcyc_id: GCVMULTI-RXN - ec: - 2.5.1.54 genes: - *id035 - *id036 left: - D-erythrose 4-phosphate - H2O - phosphoenolpyruvate name: phosphoenolpyruvate + D-erythrose 4-phosphate + H2O <-> 3-deoxy-D-arabino-heptulosonate 7-phosphate + phosphate pmids: [] rhea: [] right: - 3-deoxy-D-arabino-heptulosonate 7-phosphate - phosphate yeastcyc_id: DAHPSYN-RXN - ec: - 4.2.1.51 genes: - *id037 left: - H+ - prephenate name: prephenate + H+ <-> 3-phenyl-2-oxopropanoate + CO2 + H2O pmids: [] rhea: [] right: - 3-phenyl-2-oxopropanoate - CO2 - H2O yeastcyc_id: PREPHENATEDEHYDRAT-RXN - ec: - 1.3.1.13 genes: - *id038 left: - NADP+ - prephenate name: prephenate + NADP+ -> CO2 + 3-(4-hydroxyphenyl)pyruvate + NADPH pmids: [] rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - CO2 - NADPH yeastcyc_id: PREPHENATE-DEHYDROGENASE-NADP+-RXN - ec: - 2.7.1.71 genes: - *id008 left: - ATP - shikimate name: shikimate + ATP <-> shikimate 3-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - shikimate 3-phosphate yeastcyc_id: SHIKIMATE-KINASE-RXN - ec: - 1.1.1.25 genes: - *id008 left: - NADP+ - shikimate name: shikimate + NADP+ <- 3-dehydroshikimate + NADPH + H+ pmids: [] rhea: [] right: - 3-dehydroshikimate - H+ - NADPH yeastcyc_id: SHIKIMATE-5-DEHYDROGENASE-RXN - ec: - 2.5.1.19 genes: - *id008 left: - phosphoenolpyruvate - shikimate 3-phosphate name: shikimate 3-phosphate + phosphoenolpyruvate <-> 5-enolpyruvoyl-shikimate 3-phosphate + phosphate pmids: [] rhea: [] right: - 5-enolpyruvoyl-shikimate 3-phosphate - phosphate yeastcyc_id: 2.5.1.19-RXN yeastcyc_id: ALL-CHORISMATE-PWY-1 ALLANTOINDEG-PWY: all_genes: - &id039 orf: YIR027C symbol: DAL1 uniprot: UniProtKB:P32375 - &id042 orf: YIR029W symbol: DAL2 uniprot: UniProtKB:P25335 - &id040 orf: YIR032C symbol: DAL3 uniprot: UniProtKB:P32459 - &id041 orf: YBR208C symbol: DUR1,2 uniprot: UniProtKB:P32528 comment: 'The allantoin degradation pathway, which converts allantoin to ammonia and carbon dioxide, allows S. cerevisiae to use allantoin as a sole nitrogen source. Conversion of allantoin to ammonia is carried out by the DAL1, DAL2, and DAL3 gene products, which work sequentially to generate urea |CITS: [3915539]|. Urea is then degraded to ammonia in a two-step process by the DUR1,2 protein, a multifunctional single enzyme originally thought to be encoded by two tightly-linked genes (hence the name DUR1,2; |CITS: [6105114]|. The allantoin catabolic pathway genes are regulated by a general signal that responds to the availability of readily utilizable nitrogen sources, and also by pathway-specific induction by allantoin or the intermediate allophanate. These regulatory effects are mediated by cis-acting DNA elements and the trans-acting factors Gln3p, Gat1p, Dal80p, Dal81p, and Dal82p |CITS: [10488154]||CITS: [12062797]||CITS: [10702289]||CITS: [7899074]|.' name: superpathway of allantoin degradation in yeast pmids: - '6105114' reactions: - ec: - 3.5.2.5 genes: - *id039 left: - (S)-(+)-allantoin - H2O name: (S)-(+)-allantoin + H2O -> allantoate + H+ pmids: [] rhea: [] right: - H+ - allantoate yeastcyc_id: ALLANTOINASE-RXN - ec: - 4.3.2.3 genes: - *id040 left: - (S)-ureidoglycolate name: (S)-ureidoglycolate -> urea + glyoxylate pmids: [] rhea: [] right: - glyoxylate - urea yeastcyc_id: UREIDOGLYCOLATE-LYASE-RXN - ec: - 6.3.4.6 genes: - *id041 left: - ATP - CO2 - H2O - urea name: CO2 + urea + ATP + H2O -> ADP + urea-1-carboxylate + phosphate + 2 H+ pmids: [] rhea: [] right: - ADP - H+ - phosphate - urea-1-carboxylate yeastcyc_id: UREA-CARBOXYLASE-RXN - ec: - 3.5.3.4 genes: - *id042 left: - H2O - allantoate name: allantoate + H2O -> (S)-ureidoglycolate + urea pmids: [] rhea: [] right: - (S)-ureidoglycolate - urea yeastcyc_id: ALLANTOICASE-RXN - ec: - 3.5.1.54 genes: - *id041 left: - H+ - H2O - urea-1-carboxylate name: urea-1-carboxylate + 3 H+ + H2O -> 2 ammonium + 2 CO2 pmids: [] rhea: [] right: - CO2 - ammonium yeastcyc_id: ALLOPHANATE-HYDROLASE-RXN yeastcyc_id: ALLANTOINDEG-PWY ARG-PRO-PWY: all_genes: - &id043 orf: YPL111W symbol: CAR1 uniprot: UniProtKB:P00812 - &id044 orf: YLR438W symbol: CAR2 uniprot: UniProtKB:P07991 - &id045 orf: YER023W symbol: PRO3 uniprot: UniProtKB:P32263 comment: 'Under conditions where optimal sources of nitrogen are unavailable, S. cerevisiae is able to utilize arginine as its sole nitrogen source. Arginine catabolism occurs in the cytosol with the hydrolysis of arginine to proline, releasing three nitrogen atoms that can be used by the cell |CITS: [14263163]|, |CITS: [1592829]|. In the absence of oxygen, the proline ring is unable to be further degraded |CITS: [1592829]|. The utilization of arginine as a nitrogen source is repressed if better nitrogen compounds such as ammonia, asparagine or glutamine are present. This is known as nitrogen catabolite repression (NCR) |CITS: [10640599]|. The CAR1 gene is subject to the effect of this repression which is mediated by the negative regulator Ure2p |CITS: [8622686]|, |CITS: [7891726]|. In the presence of arginine and the absence of a preferred nitrogen source, NCR is released by the GATA transcriptional activators Gln3p and Gat1p |CITS:[7568152]|, |CITS: [8816501]|, |CITS: [12796300]|. Unrelated to NCR, the presence of arginine also induces CAR1 and CAR2 expression by the regulators Arg80p, Arg81p and Mcm1p |CITS:[9065690]|, |CITS: [11119723]|. The CAR genes are also activated by the globally acting transcription factors Rap1p and Abf1p |CITS: [10559172]|, |CITS: [8816501]|. Conversely, CAR1 and CAR2 experssion is repressed by the Ume6p-Sin2p-Rpd3p complex |CITS: [10809695]|. Additionally, CAR2 expression is unduced by the two positive regulators Dal81p and Dal82p as well as allophanate, a degradation product of urea |CITS:[10559172]|. Wild type S. cerevisiae cells normally synthesize proline by a pathway involving the gene products of PRO1, PRO2, and PRO3. However, strains that are mutant for pro1 and pro2 are able to bypass the early steps of proline biosynthesis and satisfy their requirement for proline via the arginine degradation pathway. Although the pro mutants can grow both anaerobically and aerobically, they cannot grow on optimal nitrogen sources due to the repression of the genes necessart for arginine and ornithine degradation to glutamate semialdehyde |CITS:[2824433]|. ' name: L-arginine degradation VI (arginase 2 pathway) pmids: - '12620851' reactions: - ec: [] genes: [] left: - (S)-1-pyrroline-5-carboxylate - H+ - H2O name: (S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde pmids: [] rhea: [] right: - L-glutamate-5-semialdehyde yeastcyc_id: SPONTPRO-RXN - ec: - 3.5.3.1 genes: - *id043 left: - H2O - L-arginine name: L-arginine + H2O -> urea + L-ornithine pmids: - '14263163' rhea: [] right: - L-ornithine - urea yeastcyc_id: ARGINASE-RXN - ec: - 2.6.1.13 genes: - *id044 left: - 2-oxoglutarate - L-ornithine name: L-ornithine + 2-oxoglutarate -> L-glutamate + L-glutamate-5-semialdehyde pmids: [] rhea: [] right: - L-glutamate - L-glutamate-5-semialdehyde yeastcyc_id: ORNITHINE-GLU-AMINOTRANSFERASE-RXN - ec: - 1.5.1.2 genes: - *id045 left: - L-proline - NAD(P)+ name: L-proline + NAD(P)+ <- (S)-1-pyrroline-5-carboxylate + NAD(P)H + 2 H+ pmids: - '6997271' rhea: [] right: - (S)-1-pyrroline-5-carboxylate - H+ - NAD(P)H yeastcyc_id: PYRROLINECARBREDUCT-RXN yeastcyc_id: ARG-PRO-PWY ARGDEG-YEAST-PWY: all_genes: - *id043 - *id044 - *id045 - &id046 orf: YLR142W symbol: PUT1 uniprot: UniProtKB:P09368 comment: 'Under conditions where optimal sources of nitrogen are unavailable, S. cerevisiae is able to utilize arginine as its sole nitrogen source. Arginine catabolism begins in the cytosol with the hydrolysis of arginine to proline |CITS:[14263163]|, |CITS: [1592829]|. Under aerobic condition, the arginine and proline degradation pathways converge; resulting in the conversion of proline to L-glutamate in the mitochondria |CITS: [6997271]|. The utilization of arginine as nitrogen source is repressed if better nitrogen compounds such as ammonia, asparagine or glutamine are present. This is known as nitrogen catabolite repression (NCR) |CITS:[10640599]|. The CAR1, PUT1 and PUT2 genes are subject to the effect of this repression which is mediated by the negative regulator Ure2p |CITS:[8622686]|, |CITS: [7891726]|. In the presence of arginine and the absence of a preferred nitrogen sources, NCR is released by the GATA transcriptional activators Gln3p and Gat1p |CITS: [7568152]|, |CITS: [8816501]|, |CITS:[12796300]|. The genes encoding the arginine degradation enzymes are also regulated by factors not involved in NCR. The CAR genes are activated by the globally acting transcription factors Rap1p and Abf1p |CITS: [10559172]|, |CITS: [8816501]| and repressed by the Ume6p-Sin2p-Rpd3p complex |CITS: [10809695]|. The presence of arginine induces CAR1 and CAR2 expression by the regulators Arg80p, Arg81p, and Mcm1p |CITS:[9065690]|, |CITS:[11119723]|. Similarly, the presence of proline leads to the upregulation of the proline degradation enzymes PUT1 and PUT2 by the transcription factor Put3p |CITS: [10629046]|. Also unrelated to NCR, CAR2 expression is induced by allophanate, a degradation product of urea, as well as the two positive regulators Dal181p, Dal82p |CITS:[10559172]|. ' name: arginine degradation (aerobic) pmids: [] reactions: - ec: [] genes: [] left: - (S)-1-pyrroline-5-carboxylate - H+ - H2O name: (S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde pmids: [] rhea: [] right: - L-glutamate-5-semialdehyde yeastcyc_id: SPONTPRO-RXN - ec: - 3.5.3.1 genes: - *id043 left: - H2O - L-arginine name: L-arginine + H2O -> urea + L-ornithine pmids: - '14263163' rhea: [] right: - L-ornithine - urea yeastcyc_id: ARGINASE-RXN - ec: - 1.2.1.88 genes: [] left: - H2O - L-glutamate-5-semialdehyde - NAD+ name: L-glutamate-5-semialdehyde + NAD+ + H2O -> L-glutamate + NADH + 2 H+ pmids: [] rhea: [] right: - H+ - L-glutamate - NADH yeastcyc_id: RXN-14116 - ec: - 2.6.1.13 genes: - *id044 left: - 2-oxoglutarate - L-ornithine name: L-ornithine + 2-oxoglutarate -> L-glutamate + L-glutamate-5-semialdehyde pmids: [] rhea: [] right: - L-glutamate - L-glutamate-5-semialdehyde yeastcyc_id: ORNITHINE-GLU-AMINOTRANSFERASE-RXN - ec: - 1.5.1.2 genes: - *id045 left: - L-proline - NAD(P)+ name: L-proline + NAD(P)+ <- (S)-1-pyrroline-5-carboxylate + NAD(P)H + 2 H+ pmids: - '6997271' rhea: [] right: - (S)-1-pyrroline-5-carboxylate - H+ - NAD(P)H yeastcyc_id: PYRROLINECARBREDUCT-RXN - ec: - 1.5.5.2 genes: - *id046 left: - L-proline - an electron-transfer quinone name: L-proline[in] + an electron-transfer quinone[membrane] -> (S)-1-pyrroline-5-carboxylate[in] + an electron-transfer quinol[membrane] + H+[in] pmids: - '387737' rhea: [] right: - (S)-1-pyrroline-5-carboxylate - H+ - an electron-transfer quinol yeastcyc_id: RXN-14903 yeastcyc_id: ARGDEG-YEAST-PWY ARGSPECAT-PWY: all_genes: - &id047 orf: YOL052C symbol: SPE2 uniprot: UniProtKB:P21182 - &id048 orf: YLR146C symbol: SPE4 uniprot: UniProtKB:Q12455 name: spermine biosynthesis pmids: [] reactions: - ec: - 4.1.1.50 genes: - *id047 left: - H+ - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + H+ -> CO2 + S-adenosyl 3-(methylsulfanyl)propylamine pmids: [] rhea: [] right: - CO2 - S-adenosyl 3-(methylsulfanyl)propylamine yeastcyc_id: SAMDECARB-RXN - ec: - 2.5.1.22 genes: - *id048 left: - S-adenosyl 3-(methylsulfanyl)propylamine - spermidine name: spermidine + S-adenosyl 3-(methylsulfanyl)propylamine -> spermine + S-methyl-5'-thioadenosine + H+ pmids: [] rhea: [] right: - H+ - S-methyl-5'-thioadenosine - spermine yeastcyc_id: SPERMINE-SYNTHASE-RXN yeastcyc_id: ARGSPECAT-PWY ARGSYNBSUB-PWY: all_genes: - &id054 orf: YOL058W symbol: ARG1 uniprot: UniProtKB:P22768 - &id056 orf: YJL071W symbol: ARG2 uniprot: UniProtKB:P40360 - &id057 orf: YJL088W symbol: ARG3 uniprot: UniProtKB:P05150 - &id053 orf: YHR018C symbol: ARG4 uniprot: UniProtKB:P04076 - &id058 orf: YER069W symbol: ARG5,6 uniprot: UniProtKB:Q01217 - &id055 orf: YMR062C symbol: ARG7 uniprot: UniProtKB:Q04728 - &id052 orf: YOL140W symbol: ARG8 uniprot: UniProtKB:P18544 - &id049 orf: YOR303W symbol: CPA1 uniprot: UniProtKB:P07258 - &id050 orf: YJR109C symbol: CPA2 uniprot: UniProtKB:P03965 - &id051 orf: YJL130C symbol: URA2 uniprot: UniProtKB:P07259 comment: 'The first five steps of arginine biosynthesis in S. cerevisiae take place in the mitochondrion |CITS: [11553611]||CITS: [Hinnebusch]|. This part of the pathway is known as the acetylated derivatives cycle because the acetyl group that is added to L-glutamate in the first step of the pathway is recycled via N-acetylglutamate generated in the fifth step. The enzymes that catalyze the second and third steps are encoded by a single gene (ARG5,6) that is translated into a pre-protein which is imported into mitochondria and cleaved there to yield two enzymes, N-acetylglutamate kinase and N-acetylglutamyl-phosphate reductase |CITS: [1649049]|. These enzymes form a complex with each other and with N-acetylglutamate synthase, the first enzyme in the pathway, which may have implications for regulation of their activity |CITS: [11553611]|. The mitochondrial steps of the arginine biosynthesis pathway result in the formation of ornithine, which is exported to the cytoplasm by the transporter Ort1p |CITS: [8798783]|. In the cytoplasm, L-ornithine is converted to L-arginine in three reactions mediated by ornithine carbamoyltransferase, arginosuccinate synthase, and argininosuccinate lyase. Transcription of genes of the arginine biosynthetic pathway, as well as of other amino acid biosynthetic pathways, is activated by the transcription factor Gcn4p under conditions of amino acid starvation |CITS: [11390663]||CITS: [Hinnebusch]|. Transcription of ARG1, ARG3, ARG5,6, and ARG8 is also repressed in the presence of arginine by the ArgR/Mcm1p complex, which consists of Arg80p, Arg81p, Arg82p, and Mcm1p |CITS: [14563547]|. The transcriptional activator Gcn4p interacts with subunits of the ArgR/Mcm1p repressor, allowing for fine-tuning of transcriptional control in response to arginine availability |CITS: [15289616]|. General Background (from MetaCyc) Arginine biosynthesis is notable for its complexity and variability at the genetic level, and by its connection with several other pathways, such as pyrimidine and polyamine biosynthesis, and certain degradative pathways. The initial steps of the arginine biosynthetic pathways proceed via N-acetylated intermediates. The presumed reason for this is that the acetylation prevents the spontaneous cyclization of glutamate derivatives, which leads to proline biosynthesis, thus keeping the two pathways separate (|CITS: [12633501]| and references therein). About This Pathway (from MetaCyc) The cyclic pathway for arginine biosynthesis has been demonstrated in many organisms, including the prokaryotes Bacillaceae, pseudomonads, cyanobacteria, photosynthetic bacteria and archaebacteria, as well as eukaryotic organisms such as Saccharomyces cerevisiae, Neurospora sp., and Chlamydomonas sp. Organisms that employ this pathway possess the argJ gene, which encodes the enzyme ornithine acetyltransferase (OAT). OAT catalyzes the transfer of the acetyl group from N--acetyl-ornithine to glutamate, generating ornithine and N-acetyl-glutamate (NAG). Since the later is the substrate for another enzyme in this pathway, N-acetyl-glutamate kinase (encoded by argB), which catalyzes a previous step, this reaction effectively converts the otherwise linear pathway to a cyclical pathway |CITS: [8025667 ]|. While most of the NAG in these organisms is generated by OAT, some of it is still generated by N-acetyl-ornithine synthase (NAGS, EC 2.3.1.1, encoded by argA), which fulfils an anaplerotic (replenishment of pathway intermediates) role to replenish NAG that is lost due to degradation or cell division |CITS: [12633501 ]|. In some bacteria, such as Bacillus sp. |CITS: [8473852 ]|, Nisseria gonorrhoeae |CITS: [1339419 ]|, Thermotoga neapolitana |CITS: [10931207 ] | and in yeast (Saccharomyces cerevisiae) |CITS: [9428669 ]|, OAT can have a dual enzymic function. In these organisms, either N-acetylornithine or acetyl-CoA can be used as acetyl donors for formation of NAG. argJ genes from such organisms can complement both argE and argA m' name: L-arginine biosynthesis II (acetyl cycle) pmids: - '11553611' - '12603335' - '205532' reactions: - ec: - 6.3.5.5 genes: - *id049 - *id050 - *id051 left: - ATP - H2O - L-glutamine - hydrogencarbonate name: 2 ATP + L-glutamine + hydrogencarbonate + H2O -> L-glutamate + carbamoyl phosphate + 2 ADP + phosphate + 2 H+ pmids: - '8626695' rhea: [] right: - ADP - H+ - L-glutamate - carbamoyl phosphate - phosphate yeastcyc_id: CARBPSYN-RXN - ec: - 2.6.1.11 genes: - *id052 left: - 2-oxoglutarate - N-acetyl-L-ornithine name: 2-oxoglutarate + N-acetyl-L-ornithine <- N-acetyl-L-glutamate 5-semialdehyde + L-glutamate pmids: [] rhea: [] right: - L-glutamate - N-acetyl-L-glutamate 5-semialdehyde yeastcyc_id: ACETYLORNTRANSAM-RXN - ec: - 4.3.2.1 genes: - *id053 left: - L-arginino-succinate name: L-arginino-succinate -> L-arginine + fumarate pmids: [] rhea: [] right: - L-arginine - fumarate yeastcyc_id: ARGSUCCINLYA-RXN - ec: - 6.3.4.5 genes: - *id054 left: - ATP - L-aspartate - L-citrulline name: L-aspartate + L-citrulline + ATP -> L-arginino-succinate + AMP + diphosphate + H+ pmids: [] rhea: [] right: - AMP - H+ - L-arginino-succinate - diphosphate yeastcyc_id: ARGSUCCINSYN-RXN - ec: - 2.3.1.35 genes: - *id055 left: - L-glutamate - N-acetyl-L-ornithine name: L-glutamate + N-acetyl-L-ornithine -> N-acetyl-L-glutamate + L-ornithine pmids: [] rhea: [] right: - L-ornithine - N-acetyl-L-glutamate yeastcyc_id: GLUTAMATE-N-ACETYLTRANSFERASE-RXN - ec: - 2.3.1.1 genes: - *id056 - *id055 left: - L-glutamate - acetyl-CoA name: L-glutamate + acetyl-CoA -> N-acetyl-L-glutamate + coenzyme A + H+ pmids: - '9428669' rhea: [] right: - H+ - N-acetyl-L-glutamate - coenzyme A yeastcyc_id: N-ACETYLTRANSFER-RXN - ec: - 2.1.3.3 genes: - *id057 left: - L-ornithine - carbamoyl phosphate name: L-ornithine + carbamoyl phosphate -> L-citrulline + phosphate + H+ pmids: [] rhea: [] right: - H+ - L-citrulline - phosphate yeastcyc_id: ORNCARBAMTRANSFER-RXN - ec: - 2.7.2.8 genes: - *id058 left: - ATP - N-acetyl-L-glutamate name: N-acetyl-L-glutamate + ATP -> N-acetylglutamyl-phosphate + ADP pmids: [] rhea: [] right: - ADP - N-acetylglutamyl-phosphate yeastcyc_id: ACETYLGLUTKIN-RXN - ec: - 1.2.1.38 genes: - *id058 left: - N-acetyl-L-glutamate 5-semialdehyde - NADP+ - phosphate name: N-acetyl-L-glutamate 5-semialdehyde + NADP+ + phosphate <- N-acetylglutamyl-phosphate + NADPH + H+ pmids: [] rhea: [] right: - H+ - N-acetylglutamyl-phosphate - NADPH yeastcyc_id: N-ACETYLGLUTPREDUCT-RXN yeastcyc_id: ARGSYNBSUB-PWY ARO-PWY-1: all_genes: - *id008 - *id011 - *id035 - *id036 comment: Chorismate, an intermediate in the synthesis of the aromatic amino acids and the vitamins, p-aminobenzoate and p-hydroxybenzoate, is synthesized by the shikimate pathway. The shikimate pathway has been found to be common to all eukaryotes and prokaryotes studied thus far (as reported in |CITS:[1943992]|). In Saccharomyces cerevisiae the initial step is catalyzed by two deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase isoenzymes, one of which (ARO3) is feedback inhibited by phenylalanine, and the other (ARO4) by tyrosine |CITS:[1943992]|. Both DAHP isoenzymes are derepressed by amino acid starvation (general control of amino acid biosynthesis) |CITS:[2906401]|. The 5 subsequent reactions are catalyzed by the pentafunctional arom enzyme, Aro1p |CITS:[1943992][2825635]|. Aro1p is a mosaic of five monofunctional domains, each of which corresponds to one of five separate monofunctional E. coli enzymes |CITS:[1943992][2825635]|. The last step of chorismate biosynthesis, before the pathway branches to synthesize different terminal products, is catalyzed by Aro2p |CITS:[Jones][1943992]|. name: chorismate biosynthesis pmids: - '1943992' reactions: - ec: - 4.2.1.10 genes: - *id008 left: - 3-dehydroquinate name: 3-dehydroquinate <-> 3-dehydroshikimate + H2O pmids: [] rhea: [] right: - 3-dehydroshikimate - H2O yeastcyc_id: 3-DEHYDROQUINATE-DEHYDRATASE-RXN - ec: - 4.2.3.4 genes: - *id008 left: - 3-deoxy-D-arabino-heptulosonate 7-phosphate name: 3-deoxy-D-arabino-heptulosonate 7-phosphate -> 3-dehydroquinate + phosphate pmids: [] rhea: [] right: - 3-dehydroquinate - phosphate yeastcyc_id: 3-DEHYDROQUINATE-SYNTHASE-RXN - ec: - 4.2.3.5 genes: - *id011 left: - 5-enolpyruvoyl-shikimate 3-phosphate name: 5-enolpyruvoyl-shikimate 3-phosphate -> chorismate + phosphate pmids: [] rhea: [] right: - chorismate - phosphate yeastcyc_id: CHORISMATE-SYNTHASE-RXN - ec: - 2.5.1.54 genes: - *id035 - *id036 left: - D-erythrose 4-phosphate - H2O - phosphoenolpyruvate name: phosphoenolpyruvate + D-erythrose 4-phosphate + H2O <-> 3-deoxy-D-arabino-heptulosonate 7-phosphate + phosphate pmids: [] rhea: [] right: - 3-deoxy-D-arabino-heptulosonate 7-phosphate - phosphate yeastcyc_id: DAHPSYN-RXN - ec: - 2.7.1.71 genes: - *id008 left: - ATP - shikimate name: shikimate + ATP <-> shikimate 3-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - shikimate 3-phosphate yeastcyc_id: SHIKIMATE-KINASE-RXN - ec: - 1.1.1.25 genes: - *id008 left: - NADP+ - shikimate name: shikimate + NADP+ <- 3-dehydroshikimate + NADPH + H+ pmids: [] rhea: [] right: - 3-dehydroshikimate - H+ - NADPH yeastcyc_id: SHIKIMATE-5-DEHYDROGENASE-RXN - ec: - 2.5.1.19 genes: - *id008 left: - phosphoenolpyruvate - shikimate 3-phosphate name: shikimate 3-phosphate + phosphoenolpyruvate <-> 5-enolpyruvoyl-shikimate 3-phosphate + phosphate pmids: [] rhea: [] right: - 5-enolpyruvoyl-shikimate 3-phosphate - phosphate yeastcyc_id: 2.5.1.19-RXN yeastcyc_id: ARO-PWY-1 ASPARAGINE-BIOSYNTHESIS-1: all_genes: - &id059 orf: YKL106W symbol: AAT1 uniprot: UniProtKB:Q01802 - &id060 orf: YLR027C symbol: AAT2 uniprot: UniProtKB:P23542 - &id061 orf: YPR145W symbol: ASN1 uniprot: UniProtKB:P49089 - &id062 orf: YGR124W symbol: ASN2 uniprot: UniProtKB:P49090 name: L-asparagine biosynthesis I pmids: [] reactions: - ec: - 2.6.1.1 genes: - *id059 - *id060 left: - 2-oxoglutarate - L-aspartate name: 2-oxoglutarate + L-aspartate <-> oxaloacetate + L-glutamate pmids: [] rhea: [] right: - L-glutamate - oxaloacetate yeastcyc_id: ASPAMINOTRANS-RXN - ec: - 6.3.5.4 genes: - *id061 - *id062 left: - ATP - H2O - L-aspartate - L-glutamine name: L-glutamine + L-aspartate + ATP + H2O -> L-glutamate + L-asparagine + AMP + diphosphate + H+ pmids: [] rhea: [] right: - AMP - H+ - L-asparagine - L-glutamate - diphosphate yeastcyc_id: ASNSYNB-RXN yeastcyc_id: ASPARAGINE-BIOSYNTHESIS-1 ASPARAGINE-DEG2-PWY: all_genes: - *id059 - *id060 - &id063 orf: YDR321W symbol: ASP1 uniprot: UniProtKB:P38986 - &id064 orf: YLR155C symbol: ASP3-1 uniprot: UniProtKB:P0CZ17 - &id065 orf: YLR157C symbol: ASP3-2 uniprot: UniProtKB:P0CX77 - &id066 orf: YLR158C symbol: ASP3-3 uniprot: UniProtKB:P0CX78 - &id067 orf: YLR160C symbol: ASP3-4 uniprot: UniProtKB:P0CX79 comment: 'Like many other amino acids, asparagine may be utilized by S. cerevisiae as a sole source of nitrogen. Catabolism of asparagine for nitrogen involves the action of asparaginases, which hydrolyze the amide group in the side chain of asparagine. This converts asparagine to aspartate and releases an assimilable molecule of ammonia. Further nitrogen can be derived from the newly generated aspartate molecule via its reversible conversion to glutamate by aspartate aminotransferases. Glutamate, whose amino group can be hydrolyzed to release ammonia, represents one of the major sources of nitrogen for biosynthetic reactions in S. cerevisiae. References: |CITS:[17308034]||CITS: [10640599]|' name: asparagine degradation pmids: - '10640599' - '17308034' reactions: - ec: - 2.6.1.1 genes: - *id059 - *id060 left: - 2-oxoglutarate - L-aspartate name: 2-oxoglutarate + L-aspartate <-> oxaloacetate + L-glutamate pmids: [] rhea: [] right: - L-glutamate - oxaloacetate yeastcyc_id: ASPAMINOTRANS-RXN - ec: - 3.5.1.1 - 3.5.1.38 genes: - *id063 - *id064 - *id065 - *id066 - *id067 left: - H2O - L-asparagine name: L-asparagine + H2O -> L-aspartate + ammonium pmids: [] rhea: [] right: - L-aspartate - ammonium yeastcyc_id: ASPARAGHYD-RXN yeastcyc_id: ASPARAGINE-DEG2-PWY ASPARTATESYN-PWY: all_genes: - *id059 - *id060 name: L-aspartate biosynthesis pmids: [] reactions: - ec: - 2.6.1.1 genes: - *id059 - *id060 left: - 2-oxoglutarate - L-aspartate name: 2-oxoglutarate + L-aspartate <-> oxaloacetate + L-glutamate pmids: [] rhea: [] right: - L-glutamate - oxaloacetate yeastcyc_id: ASPAMINOTRANS-RXN yeastcyc_id: ASPARTATESYN-PWY ASPBIO-PWY: all_genes: - *id059 - *id060 - &id068 orf: YGL062W symbol: PYC1 uniprot: UniProtKB:P11154 - &id069 orf: YBR218C symbol: PYC2 uniprot: UniProtKB:P32327 comment: 'The biosynthesis of aspartate is an interface between amino acid metabolism and carbohydrate metabolism. Aspartate is synthesized through a transamination reaction between oxaloacetate, an important Krebs cycle intermediate, and glutamate, an amino acid. Here, aspartate aminotransferase catalyzes the reversible transfer of an amino group from glutamate to oxaloacetate, forming -ketoglutarate and aspartate. Yeast aspartate aminotransferase is encoded by AAT1 and AAT2. Aat1p localizes to mitochondria and may be involved in a putative malate-aspartate shuttle, while Aat2p localizes to the cytosol and is required for growth on minimal media lacking aspartate. Aspartate, in addition to its role as a proteinogenic amino acid, is a substrate in the arginine biosynthesis pathway and a precursor to the aspartate family amino acids methionine, isoleucine, asparagine, and threonine in S. cerevisiae. References: |CITS: [354503]||CITS: [9655342]||CITS: [1482685]||CITS: [22010850]||CITS: [9288922]|' name: aspartate biosynthesis pmids: - '11082192' - '14745783' - '1482685' - '22010850' - '354503' - '9288922' - '9655342' reactions: - ec: - 2.6.1.1 genes: - *id059 - *id060 left: - 2-oxoglutarate - L-aspartate name: 2-oxoglutarate + L-aspartate <-> oxaloacetate + L-glutamate pmids: [] rhea: [] right: - L-glutamate - oxaloacetate yeastcyc_id: ASPAMINOTRANS-RXN - ec: - 6.4.1.1 genes: - *id068 - *id069 left: - ATP - hydrogencarbonate - pyruvate name: hydrogencarbonate + pyruvate + ATP -> oxaloacetate + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - oxaloacetate - phosphate yeastcyc_id: PYRUVATE-CARBOXYLASE-RXN yeastcyc_id: ASPBIO-PWY BIOTIN-SYNTHESIS-PWY: all_genes: - &id070 orf: YGR286C symbol: BIO2 uniprot: UniProtKB:P32451 - &id072 orf: YNR058W symbol: BIO3 uniprot: UniProtKB:P50277 - &id071 orf: YNR057C symbol: BIO4 uniprot: UniProtKB:P53630 comment: 'Biotin (vitamin H) is an essential vitamin for all organisms. It is a cofactor for many carboxylases, including those involved in fatty acid biosynthesis, gluconeogenesis, and amino acid metabolism. The ability to synthesize biotin varies among strains of S. cerevisiae; many isolates, including the reference genome strain S288c, do not encode a complete biotin biosynthesis pathway and are incapable of growth in medium lacking biotin. In biotin-producing strains such as A364a, the genes involved in the full pathway have been putatively identified as BIO1 through BIO6. Strain S288c retains only BIO2 through BIO4 and is a biotin auxotroph; if both BIO1 and BIO6 are expressed in this strain, it regains biotin prototrophy. The four steps of the biotin biosynthesis pathway have been elucidated in bacteria. First, KAPA synthase catalyzes the decarboxylative condensation of alanine and pimeloyl-CoA to form 7-keto-8-aminopelargonic acid (KAPA). Second, KAPA receives an amino group from S-adenosylmethionine via DAPA aminotransferase to form 7,8-diaminopelargonic acid (DAPA). Third, dethiobiotin synthetase catalyzes the ATP-dependent formation of dethiobiotin from DAPA and CO2. Lastly, biotin synthase inserts a sulfur atom between carbons C6 and C9 on dethiobiotin, forming biotin. The enzymes that catalyze these four reactions in S. cerevisiae are encoded by BIO6, BIO3, BIO4, and BIO2, respectively. Additionally, the KAPA precursor pimeloyl-CoA is presumed to be synthesized in yeast by the putative pimeloyl-CoA synthetase Bio1p. References: |CITS: [12658511]||CITS: [18073433]||CITS: [16269718]||CITS: [10333520]||CITS: [8117110]|' name: biotin biosynthesis pmids: - '10333520' - '12658511' - '16269718' - '18073433' - '8117110' reactions: - ec: - 2.8.1.6 genes: - *id070 left: - S-adenosyl-L-methionine - a reduced [2Fe-2S] ferredoxin - a sulfurated [sulfur carrier] - dethiobiotin name: 2 S-adenosyl-L-methionine + a sulfurated [sulfur carrier] + dethiobiotin + 2 a reduced [2Fe-2S] ferredoxin -> an unsulfurated [sulfur carrier] + biotin + 2 5'-deoxyadenosine + 2 L-methionine + 2 an oxidized [2Fe-2S] ferredoxin pmids: [] rhea: [] right: - 5'-deoxyadenosine - L-methionine - an oxidized [2Fe-2S] ferredoxin - an unsulfurated [sulfur carrier] - biotin yeastcyc_id: 2.8.1.6-RXN - ec: - 6.3.3.3 genes: - *id071 left: - 7,8-diaminopelargonate - ATP - CO2 name: CO2 + 7,8-diaminopelargonate + ATP -> dethiobiotin + ADP + phosphate + 3 H+ pmids: [] rhea: [] right: - ADP - H+ - dethiobiotin - phosphate yeastcyc_id: DETHIOBIOTIN-SYN-RXN - ec: - 2.6.1.62 genes: - *id072 left: - 8-amino-7-oxononanoate - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + 8-amino-7-oxononanoate <-> S-adenosyl-4-methylsulfanyl-2-oxobutanoate + 7,8-diaminopelargonate pmids: [] rhea: [] right: - 7,8-diaminopelargonate - S-adenosyl-4-methylsulfanyl-2-oxobutanoate yeastcyc_id: DAPASYN-RXN - ec: - 2.3.1.47 genes: [] left: - H+ - L-alanine - pimeloyl-CoA name: pimeloyl-CoA + L-alanine + H+ -> CO2 + 8-amino-7-oxononanoate + coenzyme A pmids: [] rhea: [] right: - 8-amino-7-oxononanoate - CO2 - coenzyme A yeastcyc_id: 7KAPSYN-RXN yeastcyc_id: BIOTIN-SYNTHESIS-PWY BRANCHED-CHAIN-AA-SYN-PWY-1: all_genes: - &id080 orf: YHR208W symbol: BAT1 uniprot: UniProtKB:P38891 - &id081 orf: YJR148W symbol: BAT2 uniprot: UniProtKB:P47176 - &id082 orf: YER086W symbol: ILV1 uniprot: UniProtKB:P00927 - &id076 orf: YMR108W symbol: ILV2 uniprot: UniProtKB:P07342 - &id073 orf: YJR016C symbol: ILV3 uniprot: UniProtKB:P39522 - &id074 orf: YLR355C symbol: ILV5 uniprot: UniProtKB:P06168 - &id077 orf: YCL009C symbol: ILV6 uniprot: UniProtKB:P25605 - &id075 orf: YGL009C symbol: LEU1 uniprot: UniProtKB:P07264 - &id078 orf: YNL104C symbol: LEU4 uniprot: UniProtKB:P06208 - &id079 orf: YOR108W symbol: LEU9 uniprot: UniProtKB:Q12166 comment: 'The biosynthesis of branched-chain amino acids (BCAA) in S. cerevisiae involves a common pathway that metabolizes pyruvate to valine or -ketobutyrate (derived from threonine) to isoleucine. This pathway occurs in the mitochondrion until the final step, where the immediate precursor to valine or isoleucine is converted to its respective amino acid either in the mitochondrion (via Bat1p) or the cytosol (via Bat2p). In a branch of the common pathway, valines immediate precursor can instead be converted to -isopropylmalate via -isopropylmalate synthase (Leu4p and Leu9p), which is subsequently exported to the cytosol and metabolized to leucine in three additional steps. Many genes in the common pathway of BCAA biosynthesis are induced by Gcn4 in response to starvation for any amino acid. Additionally, the flow of substrates into valine, isoleucine, or leucine biosynthesis is controlled depending on the concentration of each of the three amino acids. Threonine deaminase (Ilv1p), which converts threonine to -ketobutyrate for isoleucine biosynthesis, is inhibited by high concentrations of isoleucine. This inhibition is reversed by valine; however, high concentrations of both isoleucine and valine will also result in inhibition. Acetohydroxyacid synthase (AHAS; Ilv2p), which catalyzes the first step in the common pathway of BCAA biosynthesis, is subject to feedback inhibition by valine. Likewise, -isopropylmalate synthase (Leu4p and Leu9p) is also feedback inhibited by its end product, leucine. Although fungi, eubacteria, archaebacteria, and green plants possess pathways for BCAA biosynthesis, mammals do not. Because of this, identifying inhibitors that target BCAA biosynthesis has been a subject of interest in the development of antimicrobial agents. References: |CITS: [12626680]||CITS: [8798704]||CITS: [22419079]||CITS: [25408465]||CITS: [JONES]|' name: superpathway of branched chain amino acid biosynthesis pmids: - '12626680' - '22419079' - '25408465' - '8798704' reactions: - ec: - 4.2.1.9 genes: - *id073 left: - (2R)-2,3-dihydroxy-3-methylbutanoate name: (2R)-2,3-dihydroxy-3-methylbutanoate -> 3-methyl-2-oxobutanoate + H2O pmids: [] rhea: [] right: - 3-methyl-2-oxobutanoate - H2O yeastcyc_id: DIHYDROXYISOVALDEHYDRAT-RXN - ec: - 1.1.1.86 genes: - *id074 left: - (2R)-2,3-dihydroxy-3-methylbutanoate - NADP+ name: (2R)-2,3-dihydroxy-3-methylbutanoate + NADP+ <- (S)-2-acetolactate + NADPH + H+ pmids: [] rhea: [] right: - (S)-2-acetolactate - H+ - NADPH yeastcyc_id: ACETOLACTREDUCTOISOM-RXN - ec: - 4.2.1.33 genes: - *id075 left: - (2R,3S)-3-isopropylmalate name: (2R,3S)-3-isopropylmalate <-> (2S)-2-isopropylmalate pmids: [] rhea: [] right: - (2S)-2-isopropylmalate yeastcyc_id: RXN-13163 - ec: - 1.1.1.85 genes: [] left: - (2R,3S)-3-isopropylmalate - NAD+ name: (2R,3S)-3-isopropylmalate + NAD+ -> 4-methyl-2-oxopentanoate + CO2 + NADH pmids: [] rhea: [] right: - 4-methyl-2-oxopentanoate - CO2 - NADH yeastcyc_id: RXN-13158 - ec: - 4.2.1.9 genes: - *id073 left: - (R)-2,3-dihydroxy-3-methylpentanoate name: (R)-2,3-dihydroxy-3-methylpentanoate -> (S)-3-methyl-2-oxopentanoate + H2O pmids: [] rhea: [] right: - (S)-3-methyl-2-oxopentanoate - H2O yeastcyc_id: DIHYDROXYMETVALDEHYDRAT-RXN - ec: - 1.1.1.86 genes: - *id074 left: - (R)-2,3-dihydroxy-3-methylpentanoate - NADP+ name: (R)-2,3-dihydroxy-3-methylpentanoate + NADP+ <- (S)-2-aceto-2-hydroxybutanoate + NADPH + H+ pmids: [] rhea: [] right: - (S)-2-aceto-2-hydroxybutanoate - H+ - NADPH yeastcyc_id: ACETOOHBUTREDUCTOISOM-RXN - ec: - 2.2.1.6 genes: - *id076 - *id077 left: - H+ - pyruvate name: 2 pyruvate + H+ -> (S)-2-acetolactate + CO2 pmids: [] rhea: [] right: - (S)-2-acetolactate - CO2 yeastcyc_id: ACETOLACTSYN-RXN - ec: - 2.3.3.13 genes: - *id078 - *id079 left: - 3-methyl-2-oxobutanoate - H2O - acetyl-CoA name: 3-methyl-2-oxobutanoate + acetyl-CoA + H2O -> (2S)-2-isopropylmalate + coenzyme A + H+ pmids: [] rhea: [] right: - (2S)-2-isopropylmalate - H+ - coenzyme A yeastcyc_id: 2-ISOPROPYLMALATESYN-RXN - ec: - 2.6.1.42 genes: - *id080 - *id081 left: - 2-oxoglutarate - L-isoleucine name: L-isoleucine + 2-oxoglutarate <-> L-glutamate + (S)-3-methyl-2-oxopentanoate pmids: - '10989445' - '8702755' - '8798704' rhea: [] right: - (S)-3-methyl-2-oxopentanoate - L-glutamate yeastcyc_id: BRANCHED-CHAINAMINOTRANSFERILEU-RXN - ec: - 2.6.1.42 - 2.6.1.6 genes: - *id080 - *id081 left: - 2-oxoglutarate - L-leucine name: L-leucine + 2-oxoglutarate <-> L-glutamate + 4-methyl-2-oxopentanoate pmids: - '10989445' - '8702755' - '8798704' rhea: [] right: - 4-methyl-2-oxopentanoate - L-glutamate yeastcyc_id: BRANCHED-CHAINAMINOTRANSFERLEU-RXN - ec: - 4.3.1.19 genes: - *id082 left: - L-threonine name: L-threonine -> 2-oxobutanoate + ammonium pmids: [] rhea: [] right: - 2-oxobutanoate - ammonium yeastcyc_id: THREDEHYD-RXN - ec: - 2.6.1.42 genes: - *id080 - *id081 left: - 2-oxoglutarate - L-valine name: L-valine + 2-oxoglutarate <-> L-glutamate + 3-methyl-2-oxobutanoate pmids: - '10989445' - '8702755' - '8798704' rhea: [] right: - 3-methyl-2-oxobutanoate - L-glutamate yeastcyc_id: BRANCHED-CHAINAMINOTRANSFERVAL-RXN - ec: - 2.2.1.6 genes: - *id076 - *id077 left: - 2-oxobutanoate - H+ - pyruvate name: pyruvate + 2-oxobutanoate + H+ -> (S)-2-aceto-2-hydroxybutanoate + CO2 pmids: [] rhea: [] right: - (S)-2-aceto-2-hydroxybutanoate - CO2 yeastcyc_id: ACETOOHBUTSYN-RXN yeastcyc_id: BRANCHED-CHAIN-AA-SYN-PWY-1 BSUBPOLYAMSYN-PWY: all_genes: - *id047 - &id083 orf: YPR069C symbol: SPE3 uniprot: UniProtKB:Q12074 name: spermidine biosynthesis I pmids: [] reactions: - ec: - 4.1.1.50 genes: - *id047 left: - H+ - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + H+ -> CO2 + S-adenosyl 3-(methylsulfanyl)propylamine pmids: [] rhea: [] right: - CO2 - S-adenosyl 3-(methylsulfanyl)propylamine yeastcyc_id: SAMDECARB-RXN - ec: - 2.5.1.16 genes: - *id083 left: - S-adenosyl 3-(methylsulfanyl)propylamine - putrescine name: putrescine + S-adenosyl 3-(methylsulfanyl)propylamine -> spermidine + S-methyl-5'-thioadenosine + H+ pmids: [] rhea: [] right: - H+ - S-methyl-5'-thioadenosine - spermidine yeastcyc_id: SPERMIDINESYN-RXN yeastcyc_id: BSUBPOLYAMSYN-PWY CITRUL-BIO2-PWY: all_genes: - *id057 - *id049 - *id050 - *id051 comment: 'In S. cerevisiae, citrulline is a metabolic intermediate in the latter, cytosolic half of the arginine biosynthesis pathway. Citrulline production requires two intermediates: ornithine, the product of the first five steps of arginine biosynthesis in the mitochondrion, and carbamoyl phosphate, which is synthesized in the cytosol from ATP, CO2, and the amide group of glutamine via carbamoyl phosphate synthetase (Cpa1p/Cpa2p). After ornithine is transported from the mitochondrion to the cytosol by Ort1p, ornithine carbamoyltransferase (Arg3p) catalyzes the transfer of the carbamoyl group from carbamoyl phosphate to the -amino group of ornithine to form citrulline. References: |CITS: [22419079]||CITS: [205532]||CITS: [2945985]|' name: citrulline biosynthesis pmids: - '205532' - '22419079' - '2945985' - '8626695' reactions: - ec: - 6.3.5.5 genes: - *id049 - *id050 - *id051 left: - ATP - H2O - L-glutamine - hydrogencarbonate name: 2 ATP + L-glutamine + hydrogencarbonate + H2O -> L-glutamate + carbamoyl phosphate + 2 ADP + phosphate + 2 H+ pmids: - '8626695' rhea: [] right: - ADP - H+ - L-glutamate - carbamoyl phosphate - phosphate yeastcyc_id: CARBPSYN-RXN - ec: - 2.1.3.3 genes: - *id057 left: - L-ornithine - carbamoyl phosphate name: L-ornithine + carbamoyl phosphate -> L-citrulline + phosphate + H+ pmids: [] rhea: [] right: - H+ - L-citrulline - phosphate yeastcyc_id: ORNCARBAMTRANSFER-RXN yeastcyc_id: CITRUL-BIO2-PWY COMPLETE-ARO-PWY-1: all_genes: - *id008 - *id011 - *id035 - *id036 - *id029 - *id015 - *id017 - *id016 - *id037 - *id020 - *id030 - *id007 - *id028 - *id006 - *id038 comment: Biosynthesis of the aromatic amino acids tyrosine, phenylalanine, and tryptophan proceeds via a common pathway to chorismate, at which point the pathway branches. One branch proceeds to tryptophan and the other to phenylalanine and tyrosine |CITS:[Jones]|. Aromatic amino acid biosynthesis in S. cerevisiae is controlled by a combination of feedback inhibition, activation of enzyme activity, and regulation of enzyme synthesis |CITS:[Jones][1943992]|. The carbon flow through the pathways are regulated primarily at the initial step and the branching points by the terminal end-products. The initial step of chorismate biosynthesis can be catalyzed by either isoenzyme Aro3p or Aro4p; Aro3p is inhibited by phenylalanine, and Aro4p by tyrosine |CITS:[Jones][1943992]|. The first step in the phenylalanine-tyrosine branch is feedback inhibited by tyrosine and activated by tryptophan |CITS:[1943992]|, and the first step in the tryptophan branch is feedback inhibited by tryptophan. Most of the genes encoding for the aromatic amino acid biosynthetic enzymes are regulated by the transcriptional activator GCN4. name: superpathway of aromatic amino acid biosynthesis pmids: [] reactions: - ec: - 4.2.1.20 genes: - *id006 left: - (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate - L-serine name: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine -> L-tryptophan + D-glyceraldehyde 3-phosphate + H2O pmids: [] rhea: [] right: - D-glyceraldehyde 3-phosphate - H2O - L-tryptophan yeastcyc_id: TRYPSYN-RXN - ec: - 4.1.1.48 genes: - *id007 left: - 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate - H+ name: 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate + H+ -> (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O pmids: [] rhea: [] right: - (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate - CO2 - H2O yeastcyc_id: IGPSYN-RXN - ec: - 4.2.1.10 genes: - *id008 left: - 3-dehydroquinate name: 3-dehydroquinate <-> 3-dehydroshikimate + H2O pmids: [] rhea: [] right: - 3-dehydroshikimate - H2O yeastcyc_id: 3-DEHYDROQUINATE-DEHYDRATASE-RXN - ec: - 4.2.3.4 genes: - *id008 left: - 3-deoxy-D-arabino-heptulosonate 7-phosphate name: 3-deoxy-D-arabino-heptulosonate 7-phosphate -> 3-dehydroquinate + phosphate pmids: [] rhea: [] right: - 3-dehydroquinate - phosphate yeastcyc_id: 3-DEHYDROQUINATE-SYNTHASE-RXN - ec: - 4.2.3.5 genes: - *id011 left: - 5-enolpyruvoyl-shikimate 3-phosphate name: 5-enolpyruvoyl-shikimate 3-phosphate -> chorismate + phosphate pmids: [] rhea: [] right: - chorismate - phosphate yeastcyc_id: CHORISMATE-SYNTHASE-RXN - ec: - 2.6.1.1 - 2.6.1.27 - 2.6.1.57 - 2.6.1.9 genes: - *id015 - *id016 left: - 2-oxoglutarate - L-phenylalanine name: L-phenylalanine + 2-oxoglutarate <-> 3-phenyl-2-oxopropanoate + L-glutamate pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-phenyl-2-oxopropanoate - L-glutamate yeastcyc_id: RXN-10814 - ec: - 2.6.1.58 genes: - *id017 left: - L-phenylalanine - pyruvate name: L-phenylalanine + pyruvate <-> 3-phenyl-2-oxopropanoate + L-alanine pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-phenyl-2-oxopropanoate - L-alanine yeastcyc_id: 2.6.1.58-RXN - ec: - 2.6.1.27 - 2.6.1.5 - 2.6.1.57 genes: - *id015 left: - 2-oxoglutarate - L-tyrosine name: L-tyrosine + 2-oxoglutarate <-> 3-(4-hydroxyphenyl)pyruvate + L-glutamate pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - L-glutamate yeastcyc_id: TYROSINE-AMINOTRANSFERASE-RXN - ec: - 2.6.1.58 genes: - *id017 left: - L-tyrosine - pyruvate name: L-tyrosine + pyruvate <-> 3-(4-hydroxyphenyl)pyruvate + L-alanine pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - L-alanine yeastcyc_id: RXN3O-4157 - ec: - 5.3.1.24 genes: - *id020 left: - N-(5-phosphoribosyl)-anthranilate name: N-(5-phosphoribosyl)-anthranilate -> 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate pmids: [] rhea: [] right: - 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate yeastcyc_id: PRAISOM-RXN - ec: - 2.4.2.18 genes: - *id028 left: - 5-phospho-α-D-ribose 1-diphosphate - anthranilate name: anthranilate + 5-phospho-α-D-ribose 1-diphosphate -> N-(5-phosphoribosyl)-anthranilate + diphosphate pmids: [] rhea: [] right: - N-(5-phosphoribosyl)-anthranilate - diphosphate yeastcyc_id: PRTRANS-RXN - ec: - 5.4.99.5 genes: - *id029 left: - chorismate name: chorismate <-> prephenate pmids: [] rhea: [] right: - prephenate yeastcyc_id: CHORISMATEMUT-RXN - ec: - 4.1.3.27 genes: - *id030 - *id007 left: - L-glutamine - chorismate name: chorismate + L-glutamine -> anthranilate + L-glutamate + pyruvate + H+ pmids: [] rhea: [] right: - H+ - L-glutamate - anthranilate - pyruvate yeastcyc_id: ANTHRANSYN-RXN - ec: - 2.5.1.54 genes: - *id035 - *id036 left: - D-erythrose 4-phosphate - H2O - phosphoenolpyruvate name: phosphoenolpyruvate + D-erythrose 4-phosphate + H2O <-> 3-deoxy-D-arabino-heptulosonate 7-phosphate + phosphate pmids: [] rhea: [] right: - 3-deoxy-D-arabino-heptulosonate 7-phosphate - phosphate yeastcyc_id: DAHPSYN-RXN - ec: - 4.2.1.51 genes: - *id037 left: - H+ - prephenate name: prephenate + H+ <-> 3-phenyl-2-oxopropanoate + CO2 + H2O pmids: [] rhea: [] right: - 3-phenyl-2-oxopropanoate - CO2 - H2O yeastcyc_id: PREPHENATEDEHYDRAT-RXN - ec: - 1.3.1.13 genes: - *id038 left: - NADP+ - prephenate name: prephenate + NADP+ -> CO2 + 3-(4-hydroxyphenyl)pyruvate + NADPH pmids: [] rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - CO2 - NADPH yeastcyc_id: PREPHENATE-DEHYDROGENASE-NADP+-RXN - ec: - 2.7.1.71 genes: - *id008 left: - ATP - shikimate name: shikimate + ATP <-> shikimate 3-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - shikimate 3-phosphate yeastcyc_id: SHIKIMATE-KINASE-RXN - ec: - 1.1.1.25 genes: - *id008 left: - NADP+ - shikimate name: shikimate + NADP+ <- 3-dehydroshikimate + NADPH + H+ pmids: [] rhea: [] right: - 3-dehydroshikimate - H+ - NADPH yeastcyc_id: SHIKIMATE-5-DEHYDROGENASE-RXN - ec: - 2.5.1.19 genes: - *id008 left: - phosphoenolpyruvate - shikimate 3-phosphate name: shikimate 3-phosphate + phosphoenolpyruvate <-> 5-enolpyruvoyl-shikimate 3-phosphate + phosphate pmids: [] rhea: [] right: - 5-enolpyruvoyl-shikimate 3-phosphate - phosphate yeastcyc_id: 2.5.1.19-RXN yeastcyc_id: COMPLETE-ARO-PWY-1 CYSTEINE-SYN2-PWY: all_genes: - &id084 orf: YAL012W symbol: CYS3 uniprot: UniProtKB:P31373 - &id085 orf: YGR155W symbol: CYS4 uniprot: UniProtKB:P32582 comment: 'Cysteine is a proteinogenic amino acid and sulfur source in S. cerevisiae. As a thiol-containing amino acid, cysteine plays an important role in stabilizing protein structure via disulfide bridges and possesses numerous biochemical properties that can facilitate enzyme catalysis. It is also involved in the biosynthesis of glutathione, a tripeptide that acts as a cellular redox buffer. S. cerevisiae synthesizes cysteine through the reverse transsulfuration pathway, which converts homocysteine to cysteine via the formation of a cystathionine intermediate. This takes place over two steps: In the first, cystathionine -synthase (Cys4p) catalyzes a -displacement reaction where the thiol group of homocysteine displaces the hydroxyl group of serine to produce cystathionine. In the second, cystathionine -lyase (Cys3p) catalyzes an ,-elimination reaction where cystathionine is hydrolyzed to produce cysteine, -ketobutyrate, and ammonia. References: |CITS:[9409150]||CITS: [12480511]||CITS: [12702279]||CITS: [14967036]||CITS: [24291053]|' name: cysteine biosynthesis from homocysteine pmids: - '10509018' - '15042590' reactions: - ec: - 4.4.1.1 genes: - *id084 left: - H2O - L-cystathionine name: L-cystathionine + H2O <-> 2-oxobutanoate + L-cysteine + ammonia pmids: [] rhea: [] right: - 2-oxobutanoate - L-cysteine - ammonia yeastcyc_id: CYSTAGLY-RXN - ec: - 4.2.1.22 genes: - *id085 left: - L-homocysteine - L-serine name: L-homocysteine + L-serine <-> L-cystathionine + H2O pmids: [] rhea: [] right: - H2O - L-cystathionine yeastcyc_id: CYSTATHIONINE-BETA-SYNTHASE-RXN yeastcyc_id: CYSTEINE-SYN2-PWY DENOVOPURINE2-PWY: all_genes: - &id092 orf: YAR015W symbol: ADE1 uniprot: UniProtKB:P27616 - &id101 orf: YNL220W symbol: ADE12 uniprot: UniProtKB:P80210 - &id086 orf: YLR359W symbol: ADE13 uniprot: UniProtKB:Q05911 - &id096 orf: YLR028C symbol: ADE16 uniprot: UniProtKB:P54113 - &id097 orf: YMR120C symbol: ADE17 uniprot: UniProtKB:P38009 - &id087 orf: YOR128C symbol: ADE2 uniprot: UniProtKB:P21264 - &id088 orf: YMR300C symbol: ADE4 uniprot: UniProtKB:P04046 - &id091 orf: YGL234W symbol: ADE57 uniprot: UniProtKB:P07244 - &id093 orf: YGR061C symbol: ADE6 uniprot: UniProtKB:P38972 - &id103 orf: YDR408C symbol: ADE8 uniprot: UniProtKB:P04161 - &id089 orf: YDR226W symbol: ADK1 uniprot: UniProtKB:P07170 - &id090 orf: YER170W symbol: ADK2 uniprot: UniProtKB:P26364 - &id102 orf: YMR217W symbol: GUA1 uniprot: UniProtKB:P38625 - &id095 orf: YDR454C symbol: GUK1 uniprot: UniProtKB:P15454 - &id098 orf: YHR216W symbol: IMD2 uniprot: UniProtKB:P38697 - &id099 orf: YLR432W symbol: IMD3 uniprot: UniProtKB:P50095 - &id100 orf: YML056C symbol: IMD4 uniprot: UniProtKB:P50094 - &id104 orf: YER070W symbol: RNR1 uniprot: UniProtKB:P21524 - &id105 orf: YJL026W symbol: RNR2 uniprot: UniProtKB:P09938 - &id106 orf: YIL066C symbol: RNR3 uniprot: UniProtKB:P21672 - &id107 orf: YGR180C symbol: RNR4 uniprot: UniProtKB:P49723 - &id094 orf: YKL067W symbol: YNK1 uniprot: UniProtKB:P36010 name: superpathway of purine nucleotides de novo biosynthesis II pmids: [] reactions: - ec: - 4.3.2.2 genes: - *id086 left: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole name: 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <-> fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - fumarate yeastcyc_id: AICARSYN-RXN - ec: - 4.1.1.21 genes: - *id087 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - H+ name: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H+ <-> 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + CO2 pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - CO2 yeastcyc_id: AIRCARBOXY-RXN - ec: - 2.4.2.14 genes: - *id088 left: - 5-phospho-β-D-ribosylamine - L-glutamate - diphosphate name: 5-phospho-β-D-ribosylamine + L-glutamate + diphosphate <-> 5-phospho-α-D-ribose 1-diphosphate + L-glutamine + H2O pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - H2O - L-glutamine yeastcyc_id: PRPPAMIDOTRANS-RXN - ec: - 2.7.4.3 genes: - *id089 - *id090 left: - AMP - ATP name: AMP + ATP <-> 2 ADP pmids: [] rhea: [] right: - ADP yeastcyc_id: ADENYL-KIN-RXN - ec: - 6.3.3.1 genes: - *id091 left: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ATP name: ATP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine -> ADP + 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + phosphate + H+ pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - ADP - H+ - phosphate yeastcyc_id: AIRS-RXN - ec: - 6.3.2.6 genes: - *id092 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - ATP - L-aspartate name: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate -> ADP + 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole + phosphate + H+ pmids: [] rhea: [] right: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole - ADP - H+ - phosphate yeastcyc_id: SAICARSYN-RXN - ec: - 6.3.4.13 genes: - *id091 left: - 5-phospho-β-D-ribosylamine - ATP - glycine name: ATP + 5-phospho-β-D-ribosylamine + glycine -> ADP + N1-(5-phospho-β-D-ribosyl)glycinamide + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - N1-(5-phospho-β-D-ribosyl)glycinamide - phosphate yeastcyc_id: GLYRIBONUCSYN-RXN - ec: - 6.3.5.3 genes: - *id093 left: - ATP - H2O - L-glutamine - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide name: ATP + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + L-glutamine + H2O -> L-glutamate + ADP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine + phosphate + H+ pmids: [] rhea: [] right: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ADP - H+ - L-glutamate - phosphate yeastcyc_id: FGAMSYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - GDP name: GDP + ATP -> GTP + ADP pmids: [] rhea: [] right: - ADP - GTP yeastcyc_id: GDPKIN-RXN - ec: - 2.7.4.8 genes: - *id095 left: - ATP - GMP name: GMP + ATP <-> GDP + ADP pmids: [] rhea: [] right: - ADP - GDP yeastcyc_id: GUANYL-KIN-RXN - ec: - 3.5.4.10 genes: - *id096 - *id097 left: - H2O - IMP name: IMP + H2O <-> 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide yeastcyc_id: IMPCYCLOHYDROLASE-RXN - ec: - 1.1.1.205 genes: - *id098 - *id099 - *id100 left: - H2O - IMP - NAD+ name: IMP + NAD+ + H2O <-> XMP + NADH + H+ pmids: - '12746440' rhea: [] right: - H+ - NADH - XMP yeastcyc_id: IMP-DEHYDROG-RXN - ec: - 6.3.4.4 genes: - *id101 left: - GTP - IMP - L-aspartate name: L-aspartate + IMP + GTP -> adenylo-succinate + GDP + phosphate + 2 H+ pmids: [] rhea: [] right: - GDP - H+ - adenylo-succinate - phosphate yeastcyc_id: ADENYLOSUCCINATE-SYNTHASE-RXN - ec: - 6.3.5.2 genes: - *id102 left: - ATP - H2O - L-glutamine - XMP name: XMP + L-glutamine + ATP + H2O -> L-glutamate + GMP + AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - AMP - GMP - H+ - L-glutamate - diphosphate yeastcyc_id: GMP-SYN-GLUT-RXN - ec: - 2.1.2.3 genes: - *id096 - *id097 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide <-> a tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide - a tetrahydrofolate yeastcyc_id: AICARTRANSFORM-RXN - ec: - 2.1.2.2 genes: - *id103 left: - N1-(5-phospho-β-D-ribosyl)glycinamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + N1-(5-phospho-β-D-ribosyl)glycinamide <-> a tetrahydrofolate + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + H+ pmids: [] rhea: [] right: - H+ - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide - a tetrahydrofolate yeastcyc_id: GART-RXN - ec: - 4.3.2.2 genes: - *id086 left: - adenylo-succinate name: adenylo-succinate <-> fumarate + AMP pmids: [] rhea: [] right: - AMP - fumarate yeastcyc_id: AMPSYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dADP name: dADP + ATP -> dATP + ADP pmids: [] rhea: [] right: - ADP - dATP yeastcyc_id: DADPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dADP name: dADP + an oxidized thioredoxin + H2O <- ADP + a reduced thioredoxin pmids: [] rhea: [] right: - ADP - a reduced thioredoxin yeastcyc_id: ADPREDUCT-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dGDP name: dGDP + ATP -> dGTP + ADP pmids: [] rhea: [] right: - ADP - dGTP yeastcyc_id: DGDPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dGDP name: dGDP + an oxidized thioredoxin + H2O <- GDP + a reduced thioredoxin pmids: [] rhea: [] right: - GDP - a reduced thioredoxin yeastcyc_id: GDPREDUCT-RXN - ec: - 1.1.98.6 genes: [] left: - ATP - H+ - formate name: formate + ATP + H+ -> CO2 + dATP + H2O pmids: [] rhea: [] right: - CO2 - H2O - dATP yeastcyc_id: RXN0-745 - ec: - 1.1.98.6 genes: [] left: - GTP - H+ - formate name: formate + GTP + H+ -> dGTP + CO2 + H2O pmids: [] rhea: [] right: - CO2 - H2O - dGTP yeastcyc_id: RXN0-746 yeastcyc_id: DENOVOPURINE2-PWY DENOVOPURINE3-PWY: all_genes: - *id092 - *id101 - *id086 - *id096 - *id097 - *id087 - *id088 - *id091 - *id093 - *id103 - *id089 - *id090 - *id102 - *id095 - *id098 - *id099 - *id100 - *id104 - *id105 - *id106 - *id107 - *id094 comment: 'Purine and pyrimidine nucleotides serve many diverse and essential roles in the cell. They are precursors to DNA, RNA, and many important metabolites (e.g. CDP-diacylglycerol). In addition, nucleotides can be used as an energy source (primarily as ATP), signaling molecules, and cofactor components (e.g. coenzyme A). De novo purine nucleotide biosynthesis in yeast involves the 10-step production of the purine nucleotide inosine monophosphate (IMP), the common precursor to both adenosine monophosphate (AMP) and guanosine monophosphate (GMP). Synthesis of IMP begins with a reaction catalyzed by amidophosphoribosyltransferase (Ade4p) between PRPP (5-phosphoribosylpyrophosphate), glutamine, and water. Glutamine displaces the pyrophosphate group of PRPP, converting PRPP to phosphoribosylamine. The amino group of phosphoribosylamine subsequently reacts with a carboxyl group of glycine via Ade5,7p, forming the amide bond of phosphoribosylglycinamide. In the third reaction of the pathway, a tetrahydrofolate cofactor donates a one-carbon unit at the oxidation level of formate to the -amino group of phosphoribosylglycinamide. This forms phosphoribosyl-N-formylglycinamide, which reacts with an amino group from glutamine via Ade6p to form phosphoribosylformylglycinamidine. In three ATP-dependent steps, this product then undergoes closure of the imidazole ring by Ade5,7p, carboxylation by Ade2p, and condensation with aspartate by Ade1p. Adenylosuccinate lyase (Ade13p) subsequently catalyzes cleavage with release of fumarate to form aminoimidazole carboxamide ribonucleotide (AICAR). In the final two steps, Ade16p or Ade17p introduce a formyl group to the amino group on the imidazole ring, then condense the formyl carbon with the nitrogen from the amide group. This results in closure of the 6-membered ring and yields the purine nucleotide IMP. The incorporation of an aspartate group to IMP, followed by cleavage with the loss of fumarate, results in the conversion IMP to AMP. These reactions are catalyzed by adenylosuccinate synthetase (Ade12p) and adenylosuccinate lyase (Ade13p), respectively. Oxidation of IMP, on the other hand, converts it to xanthosine monophosphate (XMP). XMP can be amidated (using glutamine as the donor) to form GMP in a reaction catalyzed by GMP synthase (Gua1p). References: |CITS:[22419079]||CITS: [(JONES)]||CITS: [10877846]|' name: de novo biosynthesis of purine nucleotides pmids: - '11035032' - '11689683' - '15744050' reactions: - ec: - 4.3.2.2 genes: - *id086 left: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole name: 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <-> fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - fumarate yeastcyc_id: AICARSYN-RXN - ec: - 4.1.1.21 genes: - *id087 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - H+ name: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H+ <-> 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + CO2 pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - CO2 yeastcyc_id: AIRCARBOXY-RXN - ec: - 2.4.2.14 genes: - *id088 left: - 5-phospho-β-D-ribosylamine - L-glutamate - diphosphate name: 5-phospho-β-D-ribosylamine + L-glutamate + diphosphate <-> 5-phospho-α-D-ribose 1-diphosphate + L-glutamine + H2O pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - H2O - L-glutamine yeastcyc_id: PRPPAMIDOTRANS-RXN - ec: - 2.7.4.3 genes: - *id089 - *id090 left: - AMP - ATP name: AMP + ATP <-> 2 ADP pmids: [] rhea: [] right: - ADP yeastcyc_id: ADENYL-KIN-RXN - ec: - 6.3.3.1 genes: - *id091 left: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ATP name: ATP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine -> ADP + 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + phosphate + H+ pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - ADP - H+ - phosphate yeastcyc_id: AIRS-RXN - ec: - 6.3.2.6 genes: - *id092 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - ATP - L-aspartate name: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate -> ADP + 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole + phosphate + H+ pmids: [] rhea: [] right: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole - ADP - H+ - phosphate yeastcyc_id: SAICARSYN-RXN - ec: - 6.3.4.13 genes: - *id091 left: - 5-phospho-β-D-ribosylamine - ATP - glycine name: ATP + 5-phospho-β-D-ribosylamine + glycine -> ADP + N1-(5-phospho-β-D-ribosyl)glycinamide + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - N1-(5-phospho-β-D-ribosyl)glycinamide - phosphate yeastcyc_id: GLYRIBONUCSYN-RXN - ec: - 6.3.5.3 genes: - *id093 left: - ATP - H2O - L-glutamine - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide name: ATP + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + L-glutamine + H2O -> L-glutamate + ADP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine + phosphate + H+ pmids: [] rhea: [] right: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ADP - H+ - L-glutamate - phosphate yeastcyc_id: FGAMSYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - GDP name: GDP + ATP -> GTP + ADP pmids: [] rhea: [] right: - ADP - GTP yeastcyc_id: GDPKIN-RXN - ec: - 2.7.4.8 genes: - *id095 left: - ATP - GMP name: GMP + ATP <-> GDP + ADP pmids: [] rhea: [] right: - ADP - GDP yeastcyc_id: GUANYL-KIN-RXN - ec: - 3.5.4.10 genes: - *id096 - *id097 left: - H2O - IMP name: IMP + H2O <-> 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide yeastcyc_id: IMPCYCLOHYDROLASE-RXN - ec: - 1.1.1.205 genes: - *id098 - *id099 - *id100 left: - H2O - IMP - NAD+ name: IMP + NAD+ + H2O <-> XMP + NADH + H+ pmids: - '12746440' rhea: [] right: - H+ - NADH - XMP yeastcyc_id: IMP-DEHYDROG-RXN - ec: - 6.3.4.4 genes: - *id101 left: - GTP - IMP - L-aspartate name: L-aspartate + IMP + GTP -> adenylo-succinate + GDP + phosphate + 2 H+ pmids: [] rhea: [] right: - GDP - H+ - adenylo-succinate - phosphate yeastcyc_id: ADENYLOSUCCINATE-SYNTHASE-RXN - ec: - 6.3.5.2 genes: - *id102 left: - ATP - H2O - L-glutamine - XMP name: XMP + L-glutamine + ATP + H2O -> L-glutamate + GMP + AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - AMP - GMP - H+ - L-glutamate - diphosphate yeastcyc_id: GMP-SYN-GLUT-RXN - ec: [] genes: [] left: - ATP - XMP - ammonium name: XMP + ammonium + ATP -> GMP + AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - AMP - GMP - H+ - diphosphate yeastcyc_id: GMP-SYN-NH3-RXN - ec: - 2.1.2.3 genes: - *id096 - *id097 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide <-> a tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide - a tetrahydrofolate yeastcyc_id: AICARTRANSFORM-RXN - ec: - 2.1.2.2 genes: - *id103 left: - N1-(5-phospho-β-D-ribosyl)glycinamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + N1-(5-phospho-β-D-ribosyl)glycinamide <-> a tetrahydrofolate + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + H+ pmids: [] rhea: [] right: - H+ - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide - a tetrahydrofolate yeastcyc_id: GART-RXN - ec: - 4.3.2.2 genes: - *id086 left: - adenylo-succinate name: adenylo-succinate <-> fumarate + AMP pmids: [] rhea: [] right: - AMP - fumarate yeastcyc_id: AMPSYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dADP name: dADP + ATP -> dATP + ADP pmids: [] rhea: [] right: - ADP - dATP yeastcyc_id: DADPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dADP name: dADP + an oxidized thioredoxin + H2O <- ADP + a reduced thioredoxin pmids: [] rhea: [] right: - ADP - a reduced thioredoxin yeastcyc_id: ADPREDUCT-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dGDP name: dGDP + ATP -> dGTP + ADP pmids: [] rhea: [] right: - ADP - dGTP yeastcyc_id: DGDPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dGDP name: dGDP + an oxidized thioredoxin + H2O <- GDP + a reduced thioredoxin pmids: [] rhea: [] right: - GDP - a reduced thioredoxin yeastcyc_id: GDPREDUCT-RXN - ec: - 1.1.98.6 genes: [] left: - ATP - H+ - formate name: formate + ATP + H+ -> CO2 + dATP + H2O pmids: [] rhea: [] right: - CO2 - H2O - dATP yeastcyc_id: RXN0-745 - ec: - 1.1.98.6 genes: [] left: - GTP - H+ - formate name: formate + GTP + H+ -> dGTP + CO2 + H2O pmids: [] rhea: [] right: - CO2 - H2O - dGTP yeastcyc_id: RXN0-746 yeastcyc_id: DENOVOPURINE3-PWY DETOX1-PWY: all_genes: - &id108 orf: YDR256C symbol: CTA1 uniprot: UniProtKB:P15202 - &id109 orf: YGR088W symbol: CTT1 uniprot: UniProtKB:P06115 - &id110 orf: YJR104C symbol: SOD1 uniprot: UniProtKB:P00445 - &id111 orf: YHR008C symbol: SOD2 uniprot: UniProtKB:P00447 name: superoxide radicals degradation pmids: - '12054464' - '15851472' - '3290902' reactions: - ec: - 1.11.1.21 - 1.11.1.6 genes: - *id108 - *id109 left: - hydrogen peroxide name: 2 hydrogen peroxide -> 2 H2O + oxygen pmids: - '12054464' rhea: [] right: - H2O - oxygen yeastcyc_id: CATAL-RXN - ec: - 1.15.1.1 genes: - *id110 - *id111 left: - H+ - superoxide name: 2 superoxide + 2 H+ -> hydrogen peroxide + oxygen pmids: - '15851472' - '3290902' rhea: [] right: - hydrogen peroxide - oxygen yeastcyc_id: SUPEROX-DISMUT-RXN yeastcyc_id: DETOX1-PWY ERGOSTEROL-SYN-PWY-1: all_genes: - &id133 orf: YGR175C symbol: ERG1 uniprot: UniProtKB:P32476 - &id119 orf: YPL028W symbol: ERG10 uniprot: UniProtKB:P41338 - &id132 orf: YHR007C symbol: ERG11 uniprot: UniProtKB:P10614 - &id113 orf: YMR208W symbol: ERG12 uniprot: UniProtKB:P07277 - &id125 orf: YML126C symbol: ERG13 uniprot: UniProtKB:P54839 - &id130 orf: YMR202W symbol: ERG2 uniprot: UniProtKB:P32352 - &id126 orf: YJL167W symbol: ERG20 uniprot: UniProtKB:P08524 - &id121 orf: YNL280C symbol: ERG24 uniprot: UniProtKB:P32462 - &id120 orf: YGR060W symbol: ERG25 uniprot: UniProtKB:P53045 - &id122 orf: YGL001C symbol: ERG26 uniprot: UniProtKB:P53199 - &id123 orf: YLR100W symbol: ERG27 uniprot: UniProtKB:Q12452 - &id127 orf: YLR056W symbol: ERG3 uniprot: UniProtKB:P32353 - &id129 orf: YGL012W symbol: ERG4 uniprot: UniProtKB:P25340 - &id128 orf: YMR015C symbol: ERG5 uniprot: UniProtKB:P54781 - &id124 orf: YML008C symbol: ERG6 uniprot: UniProtKB:P25087 - &id112 orf: YHR072W symbol: ERG7 uniprot: UniProtKB:P38604 - &id116 orf: YMR220W symbol: ERG8 uniprot: UniProtKB:P24521 - &id118 orf: YHR190W symbol: ERG9 uniprot: UniProtKB:P29704 - &id114 orf: YML075C symbol: HMG1 uniprot: UniProtKB:P12683 - &id115 orf: YLR450W symbol: HMG2 uniprot: UniProtKB:P12684 - &id131 orf: YPL117C symbol: IDI1 uniprot: UniProtKB:P15496 - &id117 orf: YNR043W symbol: MVD1 uniprot: UniProtKB:P32377 comment: 'The ergosterol biosynthesis pathway is required for generation of a major constituent of the fungal plasma membrane, ergosterol |CITS: [Paltauf]||CITS: [8561481]|. This pathway is fungal-specific; plasma membranes of other organisms are composed predominantly of other types of sterol. However, the pathway is not universally present in fungi; for example, Pneumocystis carinii plasma membranes lack ergosterol |CITS: [12531182]|. In S. cerevisiae, some steps in the pathway are dispensible while others are essential for viability |CITS: [8277826]|. The ergosterol biosynthesis pathway has been the subject of intensive investigation as a target of antifungal drugs |CITS: [11815273]|. The major target of azole antifungal drugs is lanosterol 14-alpha demethylase, a member of the cytochrome P450 family known as Erg11 protein in many fungal species. Squalene epoxidase (Erg1p in S. cerevisiae) is the specific target of allylamine drugs such as terbinafine |CITS: [14638499]|. Mutations in the genes encoding these enzymes and others in the pathway, as well as alterations in the expression levels of the pathway constituents, can lead to antifungal drug resistance |CITS: [11815273]|.' name: superpathway of ergosterol biosynthesis I pmids: - '12119386' - '8552601' - '8561481' reactions: - ec: - 5.4.99.7 genes: - *id112 left: - (3S)-2,3-epoxy-2,3-dihydrosqualene name: (3S)-2,3-epoxy-2,3-dihydrosqualene -> lanosterol pmids: [] rhea: [] right: - lanosterol yeastcyc_id: LANOSTEROL-SYNTHASE-RXN - ec: - 2.7.1.36 genes: - *id113 left: - (R)-mevalonate - ATP name: (R)-mevalonate + ATP <-> (R)-mevalonate 5-phosphate + ADP + H+ pmids: [] rhea: [] right: - (R)-mevalonate 5-phosphate - ADP - H+ yeastcyc_id: MEVALONATE-KINASE-RXN - ec: - 1.1.1.34 genes: - *id114 - *id115 left: - (R)-mevalonate - NADP+ - coenzyme A name: (R)-mevalonate + coenzyme A + 2 NADP+ <-> (S)-3-hydroxy-3-methylglutaryl-CoA + 2 NADPH + 2 H+ pmids: [] rhea: [] right: - (S)-3-hydroxy-3-methylglutaryl-CoA - H+ - NADPH yeastcyc_id: 1.1.1.34-RXN - ec: - 2.7.4.2 genes: - *id116 left: - (R)-mevalonate 5-phosphate - ATP name: (R)-mevalonate 5-phosphate + ATP <-> (R)-mevalonate diphosphate + ADP pmids: [] rhea: [] right: - (R)-mevalonate diphosphate - ADP yeastcyc_id: PHOSPHOMEVALONATE-KINASE-RXN - ec: - 4.1.1.33 genes: - *id117 left: - (R)-mevalonate diphosphate - ATP name: (R)-mevalonate diphosphate + ATP -> CO2 + isopentenyl diphosphate + ADP + phosphate pmids: [] rhea: [] right: - ADP - CO2 - isopentenyl diphosphate - phosphate yeastcyc_id: DIPHOSPHOMEVALONTE-DECARBOXYLASE-RXN - ec: - 2.5.1.103 genes: - *id118 left: - (2E,6E)-farnesyl diphosphate name: 2 (2E,6E)-farnesyl diphosphate -> presqualene diphosphate + diphosphate pmids: - '2068081' - '3277535' rhea: [] right: - diphosphate - presqualene diphosphate yeastcyc_id: RXN-12263 - ec: - 2.3.1.9 genes: - *id119 left: - acetyl-CoA name: 2 acetyl-CoA <-> acetoacetyl-CoA + coenzyme A pmids: [] rhea: [] right: - acetoacetyl-CoA - coenzyme A yeastcyc_id: ACETYL-COA-ACETYLTRANSFER-RXN - ec: - 1.14.13.72 genes: - *id120 left: - 4,4-dimethylzymosterol - NAD(P)H - oxygen name: 4,4-dimethylzymosterol + NAD(P)H + oxygen -> 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + H2O pmids: [] rhea: [] right: - 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9821 - ec: - 1.3.1.70 genes: - *id121 left: - 4,4-dimethylzymosterol - NADP+ name: 4,4-dimethylzymosterol + NADP+ <- 4,4-dimethyl-cholesta-8,14,24-trienol + NADPH + H+ pmids: [] rhea: [] right: - 4,4-dimethyl-cholesta-8,14,24-trienol - H+ - NADPH yeastcyc_id: RXN66-306 - ec: - 1.1.1.170 genes: - *id122 left: - 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)+ name: 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ -> 3-dehydro-4-methylzymosterol + CO2 + NAD(P)H pmids: [] rhea: [] right: - 3-dehydro-4-methylzymosterol - CO2 - NAD(P)H yeastcyc_id: RXN66-313 - ec: - 1.1.1.170 genes: - *id122 left: - 4α-carboxy-5α-cholesta-8,24-dien-3β-ol - NAD(P)+ name: 4α-carboxy-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ -> zymosterone + CO2 + NAD(P)H pmids: [] rhea: [] right: - CO2 - NAD(P)H - zymosterone yeastcyc_id: RXN66-318 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)H - oxygen name: 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)H + oxygen -> 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + H2O pmids: [] rhea: [] right: - 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9823 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-formyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)H - oxygen name: 4α-formyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)H + oxygen -> 4α-carboxy-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + H2O pmids: [] rhea: [] right: - 4α-carboxy-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9826 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)H - oxygen name: 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)H + oxygen -> 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + 2 H2O pmids: [] rhea: [] right: - 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9822 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)H - oxygen name: 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)H + oxygen -> 4α-formyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + 2 H2O pmids: [] rhea: [] right: - 4α-formyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9825 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-methyl-zymosterol - NAD(P)H - oxygen name: 4α-methyl-zymosterol + NAD(P)H + oxygen -> 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + H2O pmids: [] rhea: [] right: - 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9824 - ec: - 1.1.1.270 genes: - *id123 left: - 4α-methyl-zymosterol - NADP+ name: 4α-methyl-zymosterol + NADP+ <- 3-dehydro-4-methylzymosterol + NADPH + H+ pmids: [] rhea: [] right: - 3-dehydro-4-methylzymosterol - H+ - NADPH yeastcyc_id: RXN66-314 - ec: - 2.1.1.41 genes: - *id124 left: - S-adenosyl-L-methionine - zymosterol name: S-adenosyl-L-methionine + zymosterol -> S-adenosyl-L-homocysteine + fecosterol + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - fecosterol yeastcyc_id: RXN3O-178 - ec: - 2.3.3.10 genes: - *id125 left: - H2O - acetoacetyl-CoA - acetyl-CoA name: acetoacetyl-CoA + acetyl-CoA + H2O <-> (S)-3-hydroxy-3-methylglutaryl-CoA + coenzyme A + H+ pmids: [] rhea: [] right: - (S)-3-hydroxy-3-methylglutaryl-CoA - H+ - coenzyme A yeastcyc_id: HYDROXYMETHYLGLUTARYL-COA-SYNTHASE-RXN - ec: - 2.5.1.1 genes: - *id126 left: - dimethylallyl diphosphate - isopentenyl diphosphate name: dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - geranyl diphosphate yeastcyc_id: GPPSYN-RXN - ec: [] genes: - *id127 left: - H+ - NADPH - episterol - oxygen name: episterol + NADPH + oxygen + H+ -> ergosta-5,7,24(28)-trien-3β-ol + NADP+ + 2 H2O pmids: [] rhea: [] right: - H2O - NADP+ - ergosta-5,7,24(28)-trien-3β-ol yeastcyc_id: RXN3O-9827 - ec: [] genes: - *id128 left: - H+ - NADPH - ergosta-5,7,24(28)-trien-3β-ol - oxygen name: ergosta-5,7,24(28)-trien-3β-ol + NADPH + oxygen + H+ -> ergosta-5,7,22,24(28)-tetraen-3-β-ol + NADP+ + 2 H2O pmids: [] rhea: [] right: - H2O - NADP+ - ergosta-5,7,22,24(28)-tetraen-3-β-ol yeastcyc_id: RXN3O-9828 - ec: - 1.3.1.71 genes: - *id129 left: - NADP+ - ergosterol name: ergosterol + NADP+ <- ergosta-5,7,22,24(28)-tetraen-3-β-ol + NADPH + H+ pmids: - '10722850' rhea: [] right: - H+ - NADPH - ergosta-5,7,22,24(28)-tetraen-3-β-ol yeastcyc_id: 1.3.1.71-RXN - ec: [] genes: - *id130 left: - fecosterol name: fecosterol -> episterol pmids: [] rhea: [] right: - episterol yeastcyc_id: RXN3O-203 - ec: - 2.5.1.10 genes: - *id126 left: - geranyl diphosphate - isopentenyl diphosphate name: geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate pmids: [] rhea: [] right: - (2E,6E)-farnesyl diphosphate - diphosphate yeastcyc_id: FPPSYN-RXN - ec: - 5.3.3.2 genes: - *id131 left: - isopentenyl diphosphate name: isopentenyl diphosphate <-> dimethylallyl diphosphate pmids: [] rhea: [] right: - dimethylallyl diphosphate yeastcyc_id: IPPISOM-RXN - ec: - 1.14.13.70 genes: - *id132 left: - H+ - NADPH - lanosterol - oxygen name: lanosterol + 3 NADPH + 3 oxygen + 3 H+ -> 4,4-dimethyl-cholesta-8,14,24-trienol + formate + 3 NADP+ + 4 H2O pmids: [] rhea: [] right: - 4,4-dimethyl-cholesta-8,14,24-trienol - H2O - NADP+ - formate yeastcyc_id: RXN3O-9820 - ec: [] genes: - *id118 left: - H+ - NAD(P)H - presqualene diphosphate name: presqualene diphosphate + NAD(P)H + H+ -> squalene + NAD(P)+ + diphosphate pmids: [] rhea: [] right: - NAD(P)+ - diphosphate - squalene yeastcyc_id: RXN66-281 - ec: - 1.14.14.17 genes: - *id133 left: - a reduced electron acceptor - oxygen - squalene name: squalene + a reduced electron acceptor + oxygen -> (3S)-2,3-epoxy-2,3-dihydrosqualene + an oxidized electron acceptor + H2O pmids: [] rhea: [] right: - (3S)-2,3-epoxy-2,3-dihydrosqualene - H2O - an oxidized electron acceptor yeastcyc_id: RXN3O-9816 - ec: - 1.1.1.270 genes: - *id123 left: - NADP+ - zymosterol name: zymosterol + NADP+ <- zymosterone + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - zymosterone yeastcyc_id: RXN66-319 yeastcyc_id: ERGOSTEROL-SYN-PWY-1 FASYN-ELONG2-PWY: all_genes: - &id137 orf: YER061C symbol: CEM1 uniprot: UniProtKB:P39525 - &id134 orf: YKL182W symbol: FAS1 uniprot: UniProtKB:P07149 - &id135 orf: YPL231W symbol: FAS2 uniprot: UniProtKB:P19097 - &id136 orf: YKL055C symbol: OAR1 uniprot: UniProtKB:P35731 comment: 'Fatty acids are essential to all organisms except for archaea; they are major constituents of cellular membranes, and are used for energy storage and for posttranslational protein modifications. Most organisms are capable of synthesizing long chain (C12:0-C16:0) saturated fatty acids de novo. Although the initiation and termination reactions may vary, the cyclic series of chain-lengthening reactions are essentially the same across all organisms. The fatty acid chain, which starts as a 2-carbon chain from acetyl-CoA, is extended two carbons at a time by the addition of an acetyl group from malonyl-CoA. When the final length of the fatty acid is achieved, fatty acid synthesis is terminated. Each cycle of chain elongation involves 5 reactions with the following enzymatic activities: malonyl transferase (EC: 2.3.1.39), ketoacyl synthase (EC: 2.3.1.41), ketoacyl reductase (EC: 1.1.1.100), 3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61), and enoyl-acyl reductase (EC: 1.3.1.10). In yeast, fatty acid biosynthesis is terminated with the release of fatty acyl-CoAs from fatty acid synthase (FAS), the enzyme complex that carries out de novo fatty acid biosynthesis. Palmitoyl- (C16) and stearoyl-CoA (C18) are the main products in yeast, while myristoyl-CoA (C14) is only produced in small amounts |CITS: [Lynen69]|. To synthesize palmitoyl-CoA (C16) one acetyl-CoA and 7 malonyl-CoA molecules are required. The elongation substrate, malonyl-CoA is synthesized from the carboxylation of acetyl-CoA (EC 6.4.1.2) by the biotin-containing enzyme, acetyl-CoA carboxylase (Acc1p) |CITS: [1350093]|). Acetyl-CoA carboxylase is activated by the biotin:apoprotein ligase (Bpl1p) |CITS: [7649444]|). There are two types of FAS systems based on the organization of the catalytic sites. Fungi, animals, and some bacteria have type I FASs, which are large multi-functional proteins that contain all of the requisite catalytic active sites for fatty acid biosynthesis within domains on a single polypeptide (alpha) or on two polypeptides (alpha and beta). Fungal FASs are alpha6beta6 heterododecamers, animal FASs are alpha2 homodimers, and some type I bacterial FASs are alpha6 |CITS: [17448991]|. Bacteria, plants and mitochondria, on the other hand, have type II FAS systems, which are comprised of independent proteins, whereby each protein catalyzes a single step in the cyclic series of reactions |CITS: [15952903]|. The yeast FAS complex catalyzes a total of 8 reactions. The alpha subunit(Fas2p) catalyzes 3 reactions, ketoacyl synthase (EC: 2.3.1.41),ketoacyl reductase (EC: 1.1.1.100) and self pantetheinylation and the yeast beta subunit (Fas1p) catalyzes 5 reactions, acetyltransferase (EC 2.3.1.38), malonyl transferase (EC: 2.3.1.39),3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61),enoyl-acyl reductase (EC: 1.3.1.10), and palmitoyl transferase (EC:2.3.1.-) |CITS: [365179], [1100391], [10785388], [3528750], [374077]|. FASs are regulated at the transcriptional and translational level as well as posttranslationally. In yeast, FAS is a housekeeping enzyme that is expressed constitutively at a low level, but its expression is also activated by the general yeast transcription factors Rap1, Abf1 and Reb1 |CITS: [7925441]| and theinositol/choline-responsive transcription factor heterodimer, Ino2p-Ino4p |CITS: [1461729][7862526]|. The coordinate expression of the two subunits also appears to be regulated by Fas1p controlling the expression of FAS2 |CITS: [11713312]|. The FAS subunits are further regulated by proteolytic degradation of excess subunits. While the intact FAS multimeric complex (alpha6beta6 ) is stable, its individual subunits are rapidly degraded |CITS: [1735446][8262967]|.' name: fatty acid elongation pmids: [] reactions: - ec: - 4.2.1.- genes: - *id134 left: - a (3R)-3-hydroxyacyl-[acyl-carrier protein] name: a (3R)-3-hydroxyacyl-[acyl-carrier protein] -> a trans-2-enoyl-[acyl-carrier protein] + H2O pmids: [] rhea: [] right: - H2O - a trans-2-enoyl-[acyl-carrier protein] yeastcyc_id: 3-HYDROXYDECANOYL-ACP-DEHYDR-RXN - ec: - 2.3.1.86 genes: - *id135 - *id136 left: - NADP+ - a (3R)-3-hydroxyacyl-[acyl-carrier protein] name: a (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ <- a 3-oxoacyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxoacyl-[acp] yeastcyc_id: 3-OXOACYL-ACP-REDUCT-RXN - ec: - 1.3.1.104 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - NADP+ - a 2,3,4-saturated fatty acyl-[acp] name: a 2,3,4-saturated fatty acyl-[acp] + NADP+ <- a trans-2-enoyl-[acyl-carrier protein] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a trans-2-enoyl-[acyl-carrier protein] yeastcyc_id: ENOYL-ACP-REDUCT-NADPH-RXN - ec: - 2.3.1.179 genes: - *id137 - *id135 left: - H+ - a 2,3,4-saturated fatty acyl-[acp] - a malonyl-[acp] name: a 2,3,4-saturated fatty acyl-[acp] + a malonyl-[acp] + H+ -> acyl-carrier protein + a 3-oxoacyl-[acp] + CO2 pmids: [] rhea: [] right: - CO2 - a 3-oxoacyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: 3-OXOACYL-ACP-SYNTH-RXN - ec: - 2.3.1.- genes: - *id134 left: - a palmitoyl-[acp] - coenzyme A name: a palmitoyl-[acp] + coenzyme A -> palmitoyl-CoA + acyl-carrier protein pmids: - '365179' rhea: [] right: - a soluble [acyl-carrier protein] - palmitoyl-CoA yeastcyc_id: RXN3O-9780 - ec: - 3.1.2.2 genes: [] left: - H2O - palmitoyl-CoA name: palmitoyl-CoA + H2O -> palmitate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - palmitate yeastcyc_id: PALMITOYL-COA-HYDROLASE-RXN yeastcyc_id: FASYN-ELONG2-PWY FOLSYN-PWY-1: all_genes: - *id014 - *id009 - *id021 - *id026 - *id027 - *id010 - *id012 - *id013 - *id031 - *id032 - *id033 - *id034 - *id023 - *id024 - *id022 - *id025 - *id018 - *id019 comment: 'Folates are heterocyclic compounds based on a pteroic acid skeleton conjugated to one or more glutamate molecules. The biologically active form of folate is tetrahydrofolate (THF), whose metabolic derivatives serve as cofactors that carry and chemically activate one-carbon (1C) units at different levels of oxidation (methyl-THF, methylene-THF, etc.) The 1C units carried by these folate cofactors are utilized in one-carbon metabolism for the biosynthesis of various compounds including methionine, thymidylate, and purines. S. cerevisiae and many other microorganisms are able to synthesize tetrahydrofolate de novo, unlike humans who must acquire it from the environment. In the folate biosynthesis pathway, chorismate is converted to p-aminobenzoic acid (PABA) and coupled to a GTP-derived pteridine moiety to form 7,8-dihydropteroate. Dihydrofolate synthetase (encoded by FOL3 in S. cerevisiae) subsequently adds a glutamate molecule to form 7,8-dihydrofolate, which is reduced by dihydrofolate reductase (Dfr1p) to tetrahydrofolate. Tetrahydrofolate can then be converted to one of the various 1C unit-carrying folate cofactors. Many of these cofactor forms, which differ in the position and the oxidation state of the 1C unit, mediate one-carbon transfer reactions in a specific biosynthetic pathway and can be enzymatically interconverted to one another. Furthermore, the folates produced in this pathway are subject to further glutamylation by folylpolyglutamate synthetase (Met7p), which catalyzes ATP-dependent extension of the glutamate side chain to yield folate polyglutamates. Polyglutamylation is thought to increase the affinity of intracellular folates for folate-dependent enzymes and prevent their efflux out of cells and organelles. References: |CITS:[3665922]||CITS: [18804690]||CITS: [16700064]||CITS: [10799479]||CITS: [(SCOTT)]|' name: superpathway of tetrahydrofolate biosynthesis and salvage pmids: - '10871621' - '1916088' - '2836393' - '8852837' reactions: - ec: - 4.1.3.38 genes: - *id009 left: - 4-amino-4-deoxychorismate name: 4-amino-4-deoxychorismate -> 4-aminobenzoate + pyruvate + H+ pmids: [] rhea: [] right: - 4-aminobenzoate - H+ - pyruvate yeastcyc_id: ADCLY-RXN - ec: - 2.5.1.15 genes: - *id010 left: - (7,8-dihydropterin-6-yl)methyl diphosphate - 4-aminobenzoate name: 4-aminobenzoate + (7,8-dihydropterin-6-yl)methyl diphosphate -> 7,8-dihydropteroate + diphosphate pmids: [] rhea: [] right: - 7,8-dihydropteroate - diphosphate yeastcyc_id: H2PTEROATESYNTH-RXN - ec: - 2.7.6.3 genes: - *id010 left: - 6-(hydroxymethyl)-7,8-dihydropterin - ATP name: 6-(hydroxymethyl)-7,8-dihydropterin + ATP -> (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H+ pmids: [] rhea: [] right: - (7,8-dihydropterin-6-yl)methyl diphosphate - AMP - H+ yeastcyc_id: H2PTERIDINEPYROPHOSPHOKIN-RXN - ec: - 4.1.2.25 genes: - *id010 left: - 7,8-dihydroneopterin name: 7,8-dihydroneopterin -> glycolaldehyde + 6-(hydroxymethyl)-7,8-dihydropterin pmids: [] rhea: [] right: - 6-(hydroxymethyl)-7,8-dihydropterin - glycolaldehyde yeastcyc_id: H2NEOPTERINALDOL-RXN - ec: - 3.6.1.- genes: [] left: - 7,8-dihydroneopterin 3'-phosphate - H2O name: 7,8-dihydroneopterin 3'-phosphate + H2O -> 7,8-dihydroneopterin + phosphate pmids: [] rhea: [] right: - 7,8-dihydroneopterin - phosphate yeastcyc_id: DIHYDRONEOPTERIN-MONO-P-DEPHOS-RXN - ec: - 3.6.1.67 genes: [] left: - 7,8-dihydroneopterin 3'-triphosphate - H2O name: 7,8-dihydroneopterin 3'-triphosphate + H2O -> 7,8-dihydroneopterin 3'-phosphate + diphosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydroneopterin 3'-phosphate - H+ - diphosphate yeastcyc_id: H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN - ec: - 3.5.4.16 genes: - *id012 left: - GTP - H2O name: GTP + H2O -> formate + 7,8-dihydroneopterin 3'-triphosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydroneopterin 3'-triphosphate - H+ - formate yeastcyc_id: GTP-CYCLOHYDRO-I-RXN - ec: - 6.3.2.12 genes: - *id013 left: - 7,8-dihydropteroate - ATP - L-glutamate name: L-glutamate + 7,8-dihydropteroate + ATP -> ADP + 7,8-dihydrofolate monoglutamate + phosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydrofolate monoglutamate - ADP - H+ - phosphate yeastcyc_id: DIHYDROFOLATESYNTH-RXN - ec: - 2.6.1.85 genes: - *id014 left: - L-glutamine - chorismate name: L-glutamine + chorismate <-> 4-amino-4-deoxychorismate + L-glutamate pmids: [] rhea: [] right: - 4-amino-4-deoxychorismate - L-glutamate yeastcyc_id: PABASYN-RXN - ec: - 2.1.2.1 genes: - *id018 - *id019 left: - L-serine - a tetrahydrofolate name: L-serine + a tetrahydrofolate <-> glycine + a 5,10-methylenetetrahydrofolate + H2O pmids: [] rhea: [] right: - H2O - a 5,10-methylenetetrahydrofolate - glycine yeastcyc_id: GLYOHMETRANS-RXN - ec: - 3.5.4.9 genes: - *id021 - *id022 left: - H2O - a 5,10-methenyltetrahydrofolate name: a 5,10-methenyltetrahydrofolate + H2O <-> a 10-formyltetrahydrofolate + H+ pmids: [] rhea: [] right: - H+ - a 10-formyltetrahydrofolate yeastcyc_id: METHENYLTHFCYCLOHYDRO-RXN - ec: - 1.5.1.20 genes: - *id023 - *id024 left: - H+ - NAD(P)H - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NAD(P)H + H+ -> a 5-methyltetrahydrofolate + NAD(P)+ pmids: [] rhea: [] right: - NAD(P)+ - a 5-methyltetrahydrofolate yeastcyc_id: RXN3O-9789 - ec: - 1.5.1.15 genes: - *id025 left: - NAD+ - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NAD+ -> a 5,10-methenyltetrahydrofolate + NADH pmids: - '8608153' rhea: [] right: - NADH - a 5,10-methenyltetrahydrofolate yeastcyc_id: 1.5.1.15-RXN - ec: - 1.5.1.5 genes: - *id021 - *id022 left: - NADP+ - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NADP+ <-> a 5,10-methenyltetrahydrofolate + NADPH pmids: [] rhea: [] right: - NADPH - a 5,10-methenyltetrahydrofolate yeastcyc_id: METHYLENETHFDEHYDROG-NADP-RXN - ec: - 2.1.1.45 genes: - *id026 left: - a 5,10-methylenetetrahydrofolate - dUMP name: a 5,10-methylenetetrahydrofolate + dUMP -> dTMP + a 7,8-dihydrofolate pmids: [] rhea: [] right: - a 7,8-dihydrofolate - dTMP yeastcyc_id: THYMIDYLATESYN-RXN - ec: - 6.3.4.3 genes: - *id021 - *id022 left: - ATP - a tetrahydrofolate - formate name: a tetrahydrofolate + ATP + formate <-> a 10-formyltetrahydrofolate + ADP + phosphate pmids: - '1916088' rhea: [] right: - ADP - a 10-formyltetrahydrofolate - phosphate yeastcyc_id: FORMATETHFLIG-RXN - ec: - 1.5.1.3 genes: - *id027 left: - NADP+ - a tetrahydrofolate name: a tetrahydrofolate + NADP+ <- a 7,8-dihydrofolate + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 7,8-dihydrofolate yeastcyc_id: DIHYDROFOLATEREDUCT-RXN - ec: [] genes: - *id031 - *id032 - *id033 - *id034 left: - NAD+ - a tetrahydrofolate - glycine name: glycine + a tetrahydrofolate + NAD+ -> a 5,10-methylenetetrahydrofolate + ammonium + CO2 + NADH pmids: - '1916088' rhea: [] right: - CO2 - NADH - a 5,10-methylenetetrahydrofolate - ammonium yeastcyc_id: GCVMULTI-RXN yeastcyc_id: FOLSYN-PWY-1 GLNSYN-PWY: all_genes: - &id138 orf: YPR035W symbol: GLN1 uniprot: UniProtKB:P32288 name: L-glutamine biosynthesis I pmids: [] reactions: - ec: - 6.3.1.2 genes: - *id138 left: - ATP - L-glutamate - ammonium name: ammonium + L-glutamate + ATP -> L-glutamine + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - L-glutamine - phosphate yeastcyc_id: GLUTAMINESYN-RXN yeastcyc_id: GLNSYN-PWY GLUCFERMEN-PWY: all_genes: - &id157 orf: YOL086C symbol: ADH1 uniprot: UniProtKB:P00330 - &id158 orf: YMR303C symbol: ADH2 uniprot: UniProtKB:P00331 - &id159 orf: YMR083W symbol: ADH3 uniprot: UniProtKB:P07246 - &id160 orf: YGL256W symbol: ADH4 uniprot: UniProtKB:P10127 - &id161 orf: YBR145W symbol: ADH5 uniprot: UniProtKB:P38113 - &id155 orf: YMR170C symbol: ALD2 uniprot: UniProtKB:P47771 - &id153 orf: YOR374W symbol: ALD4 uniprot: UniProtKB:P46367 - &id154 orf: YER073W symbol: ALD5 uniprot: UniProtKB:P40047 - &id156 orf: YPL061W symbol: ALD6 uniprot: UniProtKB:P54115 - &id162 orf: YAL038W symbol: CDC19 uniprot: UniProtKB:P00549 - &id140 orf: YGR254W symbol: ENO1 uniprot: UniProtKB:P00924 - &id141 orf: YHR174W symbol: ENO2 uniprot: UniProtKB:P00925 - &id167 orf: YKL060C symbol: FBA1 uniprot: UniProtKB:P14540 - &id168 orf: YLR377C symbol: FBP1 uniprot: UniProtKB:P09201 - &id145 orf: YCL040W symbol: GLK1 uniprot: UniProtKB:P17709 - &id139 orf: YKL152C symbol: GPM1 uniprot: UniProtKB:P00950 - &id146 orf: YFR053C symbol: HXK1 uniprot: UniProtKB:P04806 - &id147 orf: YGL253W symbol: HXK2 uniprot: UniProtKB:P04807 - &id164 orf: YLR044C symbol: PDC1 uniprot: UniProtKB:P06169 - &id165 orf: YLR134W symbol: PDC5 uniprot: UniProtKB:P16467 - &id166 orf: YGR087C symbol: PDC6 uniprot: UniProtKB:P26263 - &id143 orf: YGR240C symbol: PFK1 uniprot: UniProtKB:P16861 - &id144 orf: YMR205C symbol: PFK2 uniprot: UniProtKB:P16862 - &id148 orf: YBR196C symbol: PGI1 uniprot: UniProtKB:P12709 - &id142 orf: YCR012W symbol: PGK1 uniprot: UniProtKB:P00560 - &id163 orf: YOR347C symbol: PYK2 uniprot: UniProtKB:P52489 - &id150 orf: YJL052W symbol: TDH1 uniprot: UniProtKB:P00360 - &id151 orf: YJR009C symbol: TDH2 uniprot: UniProtKB:P00358 - &id152 orf: YGR192C symbol: TDH3 uniprot: UniProtKB:P00359 - &id149 orf: YDR050C symbol: TPI1 uniprot: UniProtKB:P00942 comment: 'Glycolysis consists of ten reactions that can be conceptually split into an energy investment and phase and an energy-producing phase. In the initial energy investment phase, 2 molecules of ATP are consumed to convert glucose into fructose-1,6-bisphosphate. In the downstream energy producing phase, fructose-1,6-bisphosphate is then broken down into two 3-carbon sugars that are each converted into a molecule of pyruvate. 2 ATP and 1 NADH are produced for each 3-carbon sugar converted to pyruvate, therefore glycolysis nets 2 ATP, 2 NADH, and 2 pyruvate molecules for each glucose fed through the pathway. In S. cerevisiae, further degradation of pyruvate can occur via respiration or fermentation. The respiration pathway involves the complete oxidation of pyruvate to CO2 via pyruvate dehydrogenase and the TCA cycle, yielding ATP and reduced cofactors (e.g. NADH) that can be oxidized in the mitochondria to produce more ATP. In the fermentation pathway, pyruvate is decarboxylated by pyruvate decarboxylase to acetaldehyde, which is then reduced to ethanol by alcohol dehydrogenase. The respiratory pathway in S. cerevisiae yields approximately 16 ATP per glucose, whereas the fermentation pathway results in a net gain of only two ATP per glucose. Despite the greater ATP-to-glucose ratio afforded by the respiration pathway, S. cerevisiae nevertheless ferments glucose in the presence of oxygen when this sugar is abundant in the growth medium. This phenomenon- the fermentation of sugar under aerobic conditions- is referred to as the Crabtree effect. In the respiratory pathway, pyruvate dehydrogenase (PDH) converts pyruvate to acetyl-CoA in the mitochondrion. However, because S. cerevisiae is unable to transport acetyl-CoA from the mitochondrion to the cytoplasm, this organism utilizes an alternative, cytosolic pathway known as the PDH bypass to generate cytosolic acetyl-CoA from pyruvate by using acetate as an intermediate. The PDH bypass involves the concerted action of pyruvate decarboxylase, which converts pyruvate to acetaldehyde; acetaldehyde dehydrogenase, which oxidizes acetaldehyde to acetate; and acetyl-CoA synthetase, which ligates acetate with coenzyme A to form acetyl-CoA. The PDH bypass is the source of the acetate that accumulates in S. cerevisiae cultures when shifted from glucose limitation to glucose excess. References: |CITS:[11152939]||CITS: [25988158]||CITS: [9123965]||CITS: [10919763]||CITS: [10234824]|' name: superpathway of glucose fermentation pmids: - '6985717' reactions: - ec: - 5.4.2.12 genes: - *id139 left: - 2-phospho-D-glycerate name: 2-phospho-D-glycerate <-> 3-phospho-D-glycerate pmids: [] rhea: [] right: - 3-phospho-D-glycerate yeastcyc_id: 3PGAREARR-RXN - ec: - 5.4.2.11 genes: - *id139 left: - 2-phospho-D-glycerate name: 2-phospho-D-glycerate <-> 3-phospho-D-glycerate pmids: [] rhea: [] right: - 3-phospho-D-glycerate yeastcyc_id: RXN-15513 - ec: - 4.2.1.11 genes: - *id140 - *id141 left: - 2-phospho-D-glycerate name: 2-phospho-D-glycerate <-> phosphoenolpyruvate + H2O pmids: [] rhea: [] right: - H2O - phosphoenolpyruvate yeastcyc_id: 2PGADEHYDRAT-RXN - ec: - 2.7.2.3 genes: - *id142 left: - 3-phospho-D-glycerate - ATP name: 3-phospho-D-glycerate + ATP <-> 3-phospho-D-glyceroyl-phosphate + ADP pmids: [] rhea: [] right: - 3-phospho-D-glyceroyl-phosphate - ADP yeastcyc_id: PHOSGLYPHOS-RXN - ec: - 2.7.1.11 genes: - *id143 - *id144 left: - ATP - β-D-fructofuranose 6-phosphate name: ATP + β-D-fructofuranose 6-phosphate -> β-D-fructose 1,6-bisphosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - β-D-fructose 1,6-bisphosphate yeastcyc_id: 6PFRUCTPHOS-RXN - ec: - 2.7.1.1 - 2.7.1.2 genes: - *id145 - *id146 - *id147 left: - ATP - D-glucopyranose name: D-glucopyranose + ATP -> D-glucopyranose 6-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - D-glucopyranose 6-phosphate - H+ yeastcyc_id: GLUCOKIN-RXN - ec: - 5.3.1.9 genes: - *id148 left: - D-glucopyranose 6-phosphate name: D-glucopyranose 6-phosphate <-> β-D-fructofuranose 6-phosphate pmids: [] rhea: [] right: - β-D-fructofuranose 6-phosphate yeastcyc_id: PGLUCISOM-RXN - ec: - 5.3.1.1 genes: - *id149 left: - D-glyceraldehyde 3-phosphate name: D-glyceraldehyde 3-phosphate <-> glycerone phosphate pmids: [] rhea: [] right: - glycerone phosphate yeastcyc_id: TRIOSEPISOMERIZATION-RXN - ec: - 1.2.1.12 genes: - *id150 - *id151 - *id152 left: - D-glyceraldehyde 3-phosphate - NAD+ - phosphate name: D-glyceraldehyde 3-phosphate + NAD+ + phosphate <-> 3-phospho-D-glyceroyl-phosphate + NADH + H+ pmids: [] rhea: [] right: - 3-phospho-D-glyceroyl-phosphate - H+ - NADH yeastcyc_id: GAPOXNPHOSPHN-RXN - ec: - 1.2.1.5 genes: - *id153 - *id154 left: - H2O - NAD(P)+ - acetaldehyde name: acetaldehyde + NAD(P)+ + H2O -> acetate + NAD(P)H pmids: [] rhea: [] right: - NAD(P)H - acetate yeastcyc_id: RXN3O-274 - ec: - 1.2.1.3 genes: - *id155 - *id153 - *id154 left: - H2O - NAD+ - an aldehyde name: an aldehyde + NAD+ + H2O -> a carboxylate + NADH + 2 H+ pmids: [] rhea: [] right: - H+ - NADH - a carboxylate yeastcyc_id: ALDHDEHYDROG-RXN - ec: - 1.2.1.4 genes: - *id153 - *id154 - *id156 left: - H2O - NADP+ - an aldehyde name: an aldehyde + NADP+ + H2O -> a carboxylate + NADPH + 2 H+ pmids: [] rhea: [] right: - H+ - NADPH - a carboxylate yeastcyc_id: ALDEHYDE-DEHYDROGENASE-NADP+-RXN - ec: - 1.1.1.1 genes: - *id157 - *id158 - *id159 - *id160 - *id161 left: - NAD+ - ethanol name: ethanol + NAD+ <-> acetaldehyde + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - acetaldehyde yeastcyc_id: ALCOHOL-DEHYDROG-RXN - ec: - 2.7.1.40 genes: - *id162 - *id163 left: - ATP - pyruvate name: pyruvate + ATP <- phosphoenolpyruvate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - phosphoenolpyruvate yeastcyc_id: PEPDEPHOS-RXN - ec: - 4.1.1.1 genes: - *id164 - *id165 - *id166 left: - H+ - pyruvate name: pyruvate + H+ -> acetaldehyde + CO2 pmids: - '9123965' rhea: [] right: - CO2 - acetaldehyde yeastcyc_id: RXN-6161 - ec: - 4.1.2.13 genes: - *id167 left: - β-D-fructose 1,6-bisphosphate name: β-D-fructose 1,6-bisphosphate <-> glycerone phosphate + D-glyceraldehyde 3-phosphate pmids: [] rhea: [] right: - D-glyceraldehyde 3-phosphate - glycerone phosphate yeastcyc_id: F16ALDOLASE-RXN - ec: - 3.1.3.11 genes: - *id168 left: - H2O - β-D-fructose 1,6-bisphosphate name: β-D-fructose 1,6-bisphosphate + H2O -> β-D-fructofuranose 6-phosphate + phosphate pmids: [] rhea: [] right: - phosphate - β-D-fructofuranose 6-phosphate yeastcyc_id: F16BDEPHOS-RXN yeastcyc_id: GLUCFERMEN-PWY GLUCONEO-PWY-1: all_genes: - *id140 - *id141 - *id167 - *id168 - *id139 - &id169 orf: YKL029C symbol: MAE1 uniprot: UniProtKB:P36013 - &id170 orf: YKL085W symbol: MDH1 uniprot: UniProtKB:P17505 - &id171 orf: YOL126C symbol: MDH2 uniprot: UniProtKB:P22133 - &id172 orf: YDL078C symbol: MDH3 uniprot: UniProtKB:P32419 - &id173 orf: YKR097W symbol: PCK1 uniprot: UniProtKB:P10963 - *id148 - *id142 - *id068 - *id069 - *id150 - *id151 - *id152 name: gluconeogenesis I pmids: - '9467897' reactions: - ec: - 1.1.1.38 genes: - *id169 left: - (S)-malate - NAD+ name: (S)-malate + NAD+ -> CO2 + pyruvate + NADH pmids: [] rhea: [] right: - CO2 - NADH - pyruvate yeastcyc_id: 1.1.1.39-RXN - ec: - 1.1.1.37 genes: - *id170 - *id171 - *id172 left: - (S)-malate - NAD+ name: (S)-malate + NAD+ <-> oxaloacetate + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - oxaloacetate yeastcyc_id: MALATE-DEH-RXN - ec: - 5.4.2.11 genes: - *id139 left: - 2-phospho-D-glycerate name: 2-phospho-D-glycerate <-> 3-phospho-D-glycerate pmids: [] rhea: [] right: - 3-phospho-D-glycerate yeastcyc_id: RXN-15513 - ec: - 4.2.1.11 genes: - *id140 - *id141 left: - 2-phospho-D-glycerate name: 2-phospho-D-glycerate <-> phosphoenolpyruvate + H2O pmids: [] rhea: [] right: - H2O - phosphoenolpyruvate yeastcyc_id: 2PGADEHYDRAT-RXN - ec: - 2.7.2.3 genes: - *id142 left: - 3-phospho-D-glycerate - ATP name: 3-phospho-D-glycerate + ATP <-> 3-phospho-D-glyceroyl-phosphate + ADP pmids: [] rhea: [] right: - 3-phospho-D-glyceroyl-phosphate - ADP yeastcyc_id: PHOSGLYPHOS-RXN - ec: - 5.3.1.9 genes: - *id148 left: - D-glucopyranose 6-phosphate name: D-glucopyranose 6-phosphate <-> β-D-fructofuranose 6-phosphate pmids: [] rhea: [] right: - β-D-fructofuranose 6-phosphate yeastcyc_id: PGLUCISOM-RXN - ec: - 1.2.1.12 genes: - *id150 - *id151 - *id152 left: - D-glyceraldehyde 3-phosphate - NAD+ - phosphate name: D-glyceraldehyde 3-phosphate + NAD+ + phosphate <-> 3-phospho-D-glyceroyl-phosphate + NADH + H+ pmids: [] rhea: [] right: - 3-phospho-D-glyceroyl-phosphate - H+ - NADH yeastcyc_id: GAPOXNPHOSPHN-RXN - ec: - 6.4.1.1 genes: - *id068 - *id069 left: - ATP - hydrogencarbonate - pyruvate name: hydrogencarbonate + pyruvate + ATP -> oxaloacetate + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - oxaloacetate - phosphate yeastcyc_id: PYRUVATE-CARBOXYLASE-RXN - ec: - 4.1.1.49 genes: - *id173 left: - ATP - oxaloacetate name: oxaloacetate + ATP -> CO2 + phosphoenolpyruvate + ADP pmids: [] rhea: [] right: - ADP - CO2 - phosphoenolpyruvate yeastcyc_id: PEPCARBOXYKIN-RXN - ec: - 4.1.2.13 genes: - *id167 left: - β-D-fructose 1,6-bisphosphate name: β-D-fructose 1,6-bisphosphate <-> glycerone phosphate + D-glyceraldehyde 3-phosphate pmids: [] rhea: [] right: - D-glyceraldehyde 3-phosphate - glycerone phosphate yeastcyc_id: F16ALDOLASE-RXN - ec: - 3.1.3.11 genes: - *id168 left: - H2O - β-D-fructose 1,6-bisphosphate name: β-D-fructose 1,6-bisphosphate + H2O -> β-D-fructofuranose 6-phosphate + phosphate pmids: [] rhea: [] right: - phosphate - β-D-fructofuranose 6-phosphate yeastcyc_id: F16BDEPHOS-RXN yeastcyc_id: GLUCONEO-PWY-1 GLUCOSE-MANNOSYL-CHITO-DOLICHOL: all_genes: - &id178 orf: YBR110W symbol: ALG1 uniprot: UniProtKB:P16661 - &id175 orf: YNL048W symbol: ALG11 uniprot: UniProtKB:P53954 - &id185 orf: YNR030W symbol: ALG12 uniprot: UniProtKB:P53730 - &id176 orf: YGL047W symbol: ALG13 uniprot: UniProtKB:P53178 - &id177 orf: YBR070C symbol: ALG14 uniprot: UniProtKB:P38242 - &id174 orf: YGL065C symbol: ALG2 uniprot: UniProtKB:P43636 - &id183 orf: YBL082C symbol: ALG3 uniprot: UniProtKB:P38179 - &id182 orf: YOR002W symbol: ALG6 uniprot: UniProtKB:Q12001 - &id179 orf: YBR243C symbol: ALG7 uniprot: UniProtKB:P07286 - &id180 orf: YOR067C symbol: ALG8 uniprot: UniProtKB:P40351 - &id184 orf: YNL219C symbol: ALG9 uniprot: UniProtKB:P53868 - &id181 orf: YGR227W symbol: DIE2 uniprot: UniProtKB:P50076 comment: 'In eukaryotes, N-linked (asparagine-linked) glycosylation is the most common form of protein modification of secretory and membrane proteins, and is involved in a variety of cellular processes, such as protein folding, sorting and stability (reviewed in |CITS: [15189166][8472892][3896128]|). The initial steps of N-linked glycosylation, which are also known as the dolichol pathway of N-linked glycosylation, and lipid- and dolichol-linked oligosaccharide biosynthesis, involve the synthesis of a core oligosaccharide (glucosyl)3(mannosyl)9(N-acetylglucosamine)2, abbreviated, Glc3Man9GlcNAc2, on the lipid carrier, dolichol-pyrophosphate (Dol-PP) (reviewed in |CITS: [9878760][8472892][3896128]|). The ordered assembly of the core oligosaccharide is highly conserved throughout eukaryotic evolution. The assembly starts on the cytoplasmic side of the endoplasmic reticulum (ER), where N-acetylglucosamine-1-phosphate (GlcNAc-1-phosphate) is transferred from uridine 5''-diphospho-N-acetylglucosamine (UDP-GlcNAc) to dolichol-phosphate (Dol-P) followed by the addition of one N-acetylglucosamine (GlcNAc) and five mannose residues from UDP-GlcNAc and guanosine 5''-diphosphomannose (GDP-Man), respectively. The resulting lipid-linked precursor (Man5GlcNAc2-PP-Dol) is translocated "flipped" into the lumen of the ER by a flippase, which which is endoded by RFT1 in S. cerevisiae. Once in the lumen, the oligosaccharide is extended by four mannose and three glucose residues derived from dolichyl-phosphate-mannose (Dol-P-Man) and dolichyl-phosphate-glucose (Dol-P-Glc), respectively. The enzyme complex oligosaccharyltransferase (OST) transfers the preassembled oligosaccharide, Glc3Man9GlcNAc2, from the lipid carrier Dol-PP to selected asparagine residues of nascent polypeptides as the polypeptides pass into the lumen of the ER |CITS: [11580295]||CITS: [9405463]|. Once attached to the protein, the N-linked oligosaccharide is further modified by a series of trimming and elongation reactions beginning in the ER and ending in the late Golgi compartment |CITS: [8054711]|. In the ER, the oligosaccharide is trimmed of its 3 glucose residues and a specific mannose residue to form Man8GlcNAc2. The glucose residues are removed by glucosidases I and II, and in S. cerevisiae the mannose is removed by the alpha-1,2-mannosidase Mns1p, which is part of the editing mechanism that promotes the exit of correctly folded glycoproteins from the ER |CITS: [9732283]|. Once the four monosaccharides are removed, the glycoproteins are transported from the ER to the Golgi, where the yeast and mammalian pathways diverge |CITS: [3304149]|. The lipid-linked oligosaccharide biosynthetic pathway is of particular interest in humans, because defects in the glycosyltransferases involved lead to congenital disorders of glycosylation |CITS: [11306275][17024709]|. ' name: lipid-linked oligosaccharide biosynthesis pmids: - '10336995' - '11278778' - '9878760' reactions: - ec: - 2.4.1.132 genes: - *id174 left: - GDP-α-D-mannose - Man(1)GlcNAc(2)-PP-Dol name: GDP-α-D-mannose + Man(1)GlcNAc(2)-PP-Dol -> a lipid-linked α(1->3)-D-mannosyl-D-mannose-oligosaccharide + Man(2)GlcNAc(2)-PP-Dol + GDP pmids: [] rhea: [] right: - GDP - Man(2)GlcNAc(2)-PP-Dol - a lipid-linked α(1->3)-D-mannosyl-D-mannose-oligosaccharide yeastcyc_id: 2.4.1.132-RXN - ec: - 2.4.1.- genes: - *id174 left: - GDP-α-D-mannose - Man(2)GlcNAc(2)-PP-Dol name: GDP-α-D-mannose + Man(2)GlcNAc(2)-PP-Dol -> GDP + Man(3)GlcNAc(2)-PP-Dol pmids: [] rhea: [] right: - GDP - Man(3)GlcNAc(2)-PP-Dol yeastcyc_id: RXN3O-378 - ec: - 2.4.1.- genes: - *id175 left: - GDP-α-D-mannose - Man(3)GlcNAc(2)-PP-Dol name: GDP-α-D-mannose + Man(3)GlcNAc(2)-PP-Dol -> GDP + Man(4)GlcNAc(2)-PP-Dol pmids: [] rhea: [] right: - GDP - Man(4)GlcNAc(2)-PP-Dol yeastcyc_id: RXN3O-379 - ec: - 2.4.1.- genes: - *id175 left: - GDP-α-D-mannose - Man(4)GlcNAc(2)-PP-Dol name: GDP-α-D-mannose + Man(4)GlcNAc(2)-PP-Dol -> GDP + Man(5)GlcNAc(2)-PP-Dol pmids: [] rhea: [] right: - GDP - Man(5)GlcNAc(2)-PP-Dol yeastcyc_id: 2.4.1.131-RXN - ec: - 2.4.1.141 genes: - *id176 - *id177 left: - N-acetyl-α-D-glucosaminyl-diphosphodolichol - UDP-N-acetyl-α-D-glucosamine name: N-acetyl-α-D-glucosaminyl-diphosphodolichol + UDP-N-acetyl-α-D-glucosamine -> N-acetyl-β-D-glucosaminyl-(1->4)-N-acetyl-α-D-glucosaminyl-diphosphodolichol + UDP + H+ pmids: - '15615718' - '16100110' - '16100113' rhea: [] right: - H+ - N-acetyl-β-D-glucosaminyl-(1->4)-N-acetyl-α-D-glucosaminyl-diphosphodolichol - UDP yeastcyc_id: 2.4.1.141-RXN - ec: - 2.4.1.142 genes: - *id178 left: - GDP-α-D-mannose - N-acetyl-β-D-glucosaminyl-(1->4)-N-acetyl-α-D-glucosaminyl-diphosphodolichol name: N-acetyl-β-D-glucosaminyl-(1->4)-N-acetyl-α-D-glucosaminyl-diphosphodolichol + GDP-α-D-mannose -> Man(1)GlcNAc(2)-PP-Dol + GDP pmids: [] rhea: [] right: - GDP - Man(1)GlcNAc(2)-PP-Dol yeastcyc_id: RXN3O-9818 - ec: - 2.7.8.15 genes: - *id179 left: - UDP-N-acetyl-α-D-glucosamine - a dolichyl phosphate name: a dolichyl phosphate + UDP-N-acetyl-α-D-glucosamine -> N-acetyl-α-D-glucosaminyl-diphosphodolichol + UMP pmids: [] rhea: [] right: - N-acetyl-α-D-glucosaminyl-diphosphodolichol - UMP yeastcyc_id: 2.7.8.15-RXN - ec: - 2.4.1.- genes: - *id180 left: - Glc(1)Man(9)GlcNAc(2)-PP-Dol - a dolichyl β-D-glucosyl phosphate name: a dolichyl β-D-glucosyl phosphate + Glc(1)Man(9)GlcNAc(2)-PP-Dol -> a dolichyl phosphate + Glc(2)Man(9)GlcNac(2)-PP-Dol pmids: [] rhea: [] right: - Glc(2)Man(9)GlcNac(2)-PP-Dol - a dolichyl phosphate yeastcyc_id: RXN3O-412 - ec: - 2.4.1.- genes: - *id181 left: - Glc(2)Man(9)GlcNac(2)-PP-Dol - a dolichyl β-D-glucosyl phosphate name: a dolichyl β-D-glucosyl phosphate + Glc(2)Man(9)GlcNac(2)-PP-Dol -> a dolichyl phosphate + Glc(3)Man(9)GlcNAc(2)-PP-Dol pmids: [] rhea: [] right: - Glc(3)Man(9)GlcNAc(2)-PP-Dol - a dolichyl phosphate yeastcyc_id: RXN3O-413 - ec: - 2.4.1.- genes: - *id182 left: - Man(9)GlcNAc(2)-PP-Dol - a dolichyl β-D-glucosyl phosphate name: a dolichyl β-D-glucosyl phosphate + Man(9)GlcNAc(2)-PP-Dol -> a dolichyl phosphate + Glc(1)Man(9)GlcNAc(2)-PP-Dol pmids: [] rhea: [] right: - Glc(1)Man(9)GlcNAc(2)-PP-Dol - a dolichyl phosphate yeastcyc_id: RXN3O-411 - ec: - 2.4.1.130 genes: - *id183 left: - Man(5)GlcNAc(2)-PP-Dol - a dolichyl β-D-mannosyl phosphate name: a dolichyl β-D-mannosyl phosphate + Man(5)GlcNAc(2)-PP-Dol -> a dolichyl phosphate + Man(6)GlcNAc(2)-PP-Dol pmids: [] rhea: [] right: - Man(6)GlcNAc(2)-PP-Dol - a dolichyl phosphate yeastcyc_id: RXN3O-291 - ec: - 2.4.1.130 genes: - *id184 left: - Man(6)GlcNAc(2)-PP-Dol - a dolichyl β-D-mannosyl phosphate name: a dolichyl β-D-mannosyl phosphate + Man(6)GlcNAc(2)-PP-Dol -> a dolichyl phosphate + Man(7)GlcNAc(2)-PP-Dol pmids: [] rhea: [] right: - Man(7)GlcNAc(2)-PP-Dol - a dolichyl phosphate yeastcyc_id: RXN3O-3 - ec: - 2.4.1.130 genes: - *id185 left: - Man(7)GlcNAc(2)-PP-Dol - a dolichyl β-D-mannosyl phosphate name: a dolichyl β-D-mannosyl phosphate + Man(7)GlcNAc(2)-PP-Dol -> a dolichyl phosphate + Man(8)GlcNAc(2)-PP-Dol pmids: [] rhea: [] right: - Man(8)GlcNAc(2)-PP-Dol - a dolichyl phosphate yeastcyc_id: RXN3O-11 - ec: - 2.4.1.130 genes: - *id184 left: - Man(8)GlcNAc(2)-PP-Dol - a dolichyl β-D-mannosyl phosphate name: a dolichyl β-D-mannosyl phosphate + Man(8)GlcNAc(2)-PP-Dol -> a dolichyl phosphate + Man(9)GlcNAc(2)-PP-Dol pmids: [] rhea: [] right: - Man(9)GlcNAc(2)-PP-Dol - a dolichyl phosphate yeastcyc_id: RXN3O-259 yeastcyc_id: GLUCOSE-MANNOSYL-CHITO-DOLICHOL GLUDEG-I-PWY-1: all_genes: - &id187 orf: YMR250W symbol: GAD1 uniprot: UniProtKB:Q04792 - &id186 orf: YGR019W symbol: UGA1 uniprot: UniProtKB:P17649 - &id188 orf: YBR006W symbol: UGA2 uniprot: UniProtKB:P38067 comment: 'In S. cerevisiae, the main pathway for glutamate degradation is catalyzed by the glutamate dehydrogenase encoded by GDH2 |CITS: [1975578]|. However, glutamate can also by degraded into gamma-aminobutyrate (GABA) by the glutamate decarboxylase Gad1p and then converted into succinate by the enzymes encoded by UGA1 and UGA2 |CITS: [11031268]|. Glutamate degradation by this pathway and expression of its genes have been shown to be important for oxidative stress tolerance. Conditions of oxidative stress elevate the transcript levels of GAD1 and UGA2 |CITS: [11031268]|. UGA1 and UGA2 expression is also upregulated in the presence of GABA which is mediated by the transcriptional activators Uga3p and Uga35p/Dal81p |CITS: [3888627]|, |CITS:[2653828]|. These transcription factors bind to upstream activation sites in the promoters of GABA-regulated genes known as the UAS-GABA |CITS: [12235130]|, |CITS:[2653838]|. Regulation of Gad1p is suggested to be linked to calcium levels as the protein is able to bind calmodulin |CITS:[11031268]|. S. cerevisiae cells in which this pathway is blocked are more sensitive to oxidative stress and can no longer grow on GABA as their sole nitrogen source |CITS: [11031268]|, |CITS: [3888627]|].' name: glutamate degradation I pmids: - '11031268' reactions: - ec: - 2.6.1.19 genes: - *id186 left: - 2-oxoglutarate - 4-aminobutanoate name: 2-oxoglutarate + 4-aminobutanoate <-> L-glutamate + succinate semialdehyde pmids: - '3888627' rhea: [] right: - L-glutamate - succinate semialdehyde yeastcyc_id: GABATRANSAM-RXN - ec: - 4.1.1.15 genes: - *id187 left: - H+ - L-glutamate name: L-glutamate + H+ -> CO2 + 4-aminobutanoate pmids: [] rhea: [] right: - 4-aminobutanoate - CO2 yeastcyc_id: GLUTDECARBOX-RXN - ec: - 1.2.1.16 genes: - *id188 left: - H2O - NAD(P)+ - succinate semialdehyde name: succinate semialdehyde + NAD(P)+ + H2O -> succinate + NAD(P)H + 2 H+ pmids: [] rhea: [] right: - H+ - NAD(P)H - succinate yeastcyc_id: RXN0-5293 yeastcyc_id: GLUDEG-I-PWY-1 GLUGLNSYN-PWY: all_genes: - &id189 orf: YDL171C symbol: GLT1 uniprot: UniProtKB:Q12680 comment: 'Yeast cells contain 3 pathways for the synthesis of glutamate. Two pathways are mediated by two isoforms of glutamate dehydrogenase, encoded by GDH1 and GDH3 |CITS: [2989290]||CITS: [9287019]|. The third pathway is driven by the combined activities of glutamine synthetase and glutamate synthase, encoded by GLN1 and GLT1, respectively |CITS: [2570348]||CITS: [8923741]|. Gln1p catalyzes amination of glutamate to form glutamine; Glt1p then transfers the amide group of glutamine to 2-oxoglutarate, generating two molecules of glutamate. Glutamate synthase, also referred to as GOGAT, is a trimer of three Glt1p subunits. Expression of the GLT1 gene is modulated by glutamate-mediated repression and by Gln3p/Gcn4p-mediated activation, depending upon the availability of nitrogen and glutamate in the medium. In amino acid starvation conditions, GLT1 expression is activated to a moderate degree by Gcn4p |CITS: [9657994]|.' name: L-glutamate biosynthesis IV pmids: [] reactions: - ec: - 1.4.1.14 genes: - *id189 left: - L-glutamate - NAD+ name: 2 L-glutamate + NAD+ <- L-glutamine + 2-oxoglutarate + NADH + H+ pmids: [] rhea: [] right: - 2-oxoglutarate - H+ - L-glutamine - NADH yeastcyc_id: GLUTAMATE-SYNTHASE-NADH-RXN yeastcyc_id: GLUGLNSYN-PWY GLUNH3-PWY: all_genes: - &id190 orf: YOR375C symbol: GDH1 uniprot: UniProtKB:P07262 - &id191 orf: YAL062W symbol: GDH3 uniprot: UniProtKB:P39708 comment: 'Yeast cells contain 3 pathways for the synthesis of glutamate. Two pathways are mediated by two isoforms of glutamate dehydrogenase, encoded by GDH1 and GDH3 |CITS: [2989290]||CITS: [9287019]|. The third pathway is driven by the combined activities of glutamine synthetase and glutamate synthase, encoded by GLN1 and GLT1, respectively |CITS: [2570348]||CITS: [8923741]|. Studies of GDH1 and GDH3 regulation indicate that the cell uses these isoforms under different growth conditions |CITS: [11562373]|. Expression of GDH3 is induced by ethanol and repressed by glucose, whereas GDH1 expression is high in either carbon source. Gdh1p uses alpha-ketoglutarate at a higher rate than Gdh3p. Thus, under fermentative growth conditions, Gdh1p drives glutamate biosynthesis, whereas in nonfermentable or limiting carbon sources, Gdh3p is the key isoform involved in balancing distribution of alpha-ketoglutarate to glutamate biosynthesis and energy metabolism.' name: glutamate biosynthesis from ammonia pmids: - '11562373' - '9287019' reactions: - ec: - 1.4.1.4 genes: - *id190 - *id191 left: - H2O - L-glutamate - NADP+ name: L-glutamate + NADP+ + H2O <-> ammonium + 2-oxoglutarate + NADPH + H+ pmids: [] rhea: [] right: - 2-oxoglutarate - H+ - NADPH - ammonium yeastcyc_id: GLUTDEHYD-RXN yeastcyc_id: GLUNH3-PWY GLUT-REDOX2-PWY: all_genes: - &id192 orf: YPL091W symbol: GLR1 uniprot: UniProtKB:P41921 - &id195 orf: YKL026C symbol: GPX1 uniprot: UniProtKB:P36014 - &id196 orf: YBR244W symbol: GPX2 uniprot: UniProtKB:P38143 - &id193 orf: YIR038C symbol: GTT1 uniprot: UniProtKB:P40582 - &id194 orf: YLL060C symbol: GTT2 uniprot: UniProtKB:Q12390 - &id197 orf: YIR037W symbol: HYR1 uniprot: UniProtKB:P40581 comment: 'The tripeptide glutathione (GSH: L-γ-glutamyl-L-cysteinylglycine) is a prevalent intracellular thiol that is able to act as a cellular redox buffer due to its low redox potential (as reviewed in |CITS: [12702279]|). GSH is involved in many biological processes including: protein and DNA synthesis; amino acid transport; enzyme regulation; protection of cells against reactive oxygen compounds and free radicals, xenobiotics and heavy metals (as reviewed in |CITS: [12702279]|). GSH can also be used as a source of sulfur and cysteine in |CITS: [1674526], [10514563]|. Reactive oxygen species (ROS) such as hydrogen peroxide and alkylperoxides produced by various metabolic processes can cause irreversible oxidative damage to the cell if they are not rapidly detoxified by antioxidant defenses. The redox-active sulphydryl group of GSH can protect cells from ROS by directly scavenging free radicals and acting as a cofactor for antioxidant enzymes such as glutathione peroxidases (Gpx1p, Gpx2p and Gpx3p) |CITS: [10480913], [11445588], [15337745]|. Glutathione oxidized in this manner forms glutathione disulphide (GSSG), which is recycled back to GSH by the enzyme glutathione reductase (Glr1p) |CITS: [8843443]|. Some glutathione peroxidases such as Gpx2p, however, may be re-reduced by the thioredoxin system rather than the glutathione-glutaredoxin system |CITS: [16251189]|. GSH also protects the cell from xenobiotics and heavy metals through the formation of GSH S-conjugates and their subsequent export in the vacuole or directly out of the cell |CITS: [8990158], [8626454]|. Some xenobiotics can react spontaneously with the thiol moiety of GSH to form GSH S-conjugates, while others react through GSH S-transferases (GST). Two GSTs (Gtt1p and Gtt2p) were identified in yeast and shown to have GST activity with 1-chloro-2,4-dintrobenzene |CITS: [9792709]|. In yeast the GSH conjugates are transported to the vacuole by the GS-X pump Ycf1p |CITS: [8990158], [8626454], [10220408], [8626454], [12755704]| or directly out of the cell by other GS-X pumps |CITS: [10220408]|.' name: glutathione-glutaredoxin redox reactions pmids: - '11169096' reactions: - ec: - 1.8.1.7 genes: - *id192 left: - NADP+ - glutathione name: 2 glutathione + NADP+ <- glutathione disulfide + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - glutathione disulfide yeastcyc_id: GLUTATHIONE-REDUCT-NADPH-RXN - ec: [] genes: [] left: - an oxidized glutaredoxin - glutathione name: 2 glutathione + an oxidized glutaredoxin -> glutathione disulfide + a reduced glutaredoxin pmids: [] rhea: [] right: - a reduced glutaredoxin - glutathione disulfide yeastcyc_id: PRODISULFREDUCT-A-RXN - ec: - 2.5.1.18 genes: - *id193 - *id194 left: - RX - glutathione name: glutathione + RX -> a glutathione-S-conjugate + HX pmids: [] rhea: [] right: - HX - a glutathione-S-conjugate yeastcyc_id: GSHTRAN-RXN - ec: - 1.11.1.9 genes: - *id195 - *id196 - *id197 left: - glutathione - hydrogen peroxide name: hydrogen peroxide + 2 glutathione -> glutathione disulfide + 2 H2O pmids: [] rhea: [] right: - H2O - glutathione disulfide yeastcyc_id: GLUTATHIONE-PEROXIDASE-RXN yeastcyc_id: GLUT-REDOX2-PWY GLUTATHIONESYN-PWY: all_genes: - &id198 orf: YJL101C symbol: GSH1 uniprot: UniProtKB:P32477 - &id199 orf: YOL049W symbol: GSH2 uniprot: UniProtKB:Q08220 comment: 'The tripeptide glutathione (GSH: L-γ-glutamyl-L-cysteinylglycine) is a prevalent intracellular thiol that is able to act as a cellular redox buffer due to its low redox potential (as reviewed in |CITS: [12702279]|). GSH is involved in many biological processes including: protein and DNA synthesis; amino acid transport; enzyme regulation; protection of cells against reactive oxygen compounds and free radicals, xenobiotics and heavy metals (as reviewed in |CITS: [12702279]|). GSH can also be used as a source of sulfur and cysteine in |CITS: [1674526], [10514563]|. GSH is synthesized from its constituent amino acids by two ATP-dependent steps (as reviewed in |CITS: [12702279]|). In the first step γ-glutamylcysteine synthetase (Gsh1p) catalyzes the formation of the dipeptide γ-glutamylcysteine from glutamate and cysteine. In the second step, GSH synthetase (Gsh2p) catalyzes the ligation of glycine with γ-glutamylcysteine to form GSH. GSH is an essential reductant in yeast during normal metabolic processes |CITS: [8662189]|, but the dipeptide γ-glutamylcysteine is able to substitute for GSH as an antioxidant |CITS: [9307967]|. GSH biosynthesis is co-regulated by Met4p, a transcription factor that induces expression of genes involved in sulfur assimilation, by Yap1p, a stress-responsive transcription factor, and by GSH feedback inhibition, which inhibits both GSH1 expression and Gsh1p enzyme activity |CITS: [12406228], [14514673]|. Expression of GSH1 and GSH2 is induced by oxidative stress in a Yap1p-dependent manner with subsequent increases in intracellular GSH content |CITS: [7915005], [10809786]|. GSH1 is also transcriptionally up-regulated by the heavy metal cadmium in the presence of Met4p and the DNA-binding proteins Met31p and Met32p |CITS: [9044254], [10921921]|.' name: glutathione biosynthesis pmids: - '11169096' reactions: - ec: - 6.3.2.2 genes: - *id198 left: - ATP - L-cysteine - L-glutamate name: L-cysteine + L-glutamate + ATP -> γ-L-glutamyl-L-cysteine + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - phosphate - γ-L-glutamyl-L-cysteine yeastcyc_id: GLUTCYSLIG-RXN - ec: - 6.3.2.3 genes: - *id199 left: - ATP - glycine - γ-L-glutamyl-L-cysteine name: glycine + γ-L-glutamyl-L-cysteine + ATP -> glutathione + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - glutathione - phosphate yeastcyc_id: GLUTATHIONE-SYN-RXN yeastcyc_id: GLUTATHIONESYN-PWY GLYCLEAV-PWY: all_genes: - *id031 - *id032 - *id034 name: glycine cleavage pmids: [] reactions: - ec: - 2.1.2.10 genes: - *id031 left: - a [glycine-cleavage complex H protein] N6-aminomethyldihydrolipoyl-L-lysine - a tetrahydrofolate name: a [glycine-cleavage complex H protein] N6-aminomethyldihydrolipoyl-L-lysine + a tetrahydrofolate <-> a [glycine-cleavage complex H protein] N6-dihydrolipoyl-L-lysine + a 5,10-methylenetetrahydrofolate + ammonium pmids: [] rhea: [] right: - a 5,10-methylenetetrahydrofolate - a [glycine-cleavage complex H protein] N6-dihydrolipoyl-L-lysine - ammonium yeastcyc_id: GCVT-RXN - ec: - 1.8.1.4 genes: - *id034 left: - NAD+ - a [glycine-cleavage complex H protein] N6-dihydrolipoyl-L-lysine name: a [glycine-cleavage complex H protein] N6-dihydrolipoyl-L-lysine + NAD+ <-> a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine + NADH + H+ pmids: - '2821168' rhea: [] right: - H+ - NADH - a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine yeastcyc_id: RXN-8629 - ec: - 1.4.4.2 genes: - *id032 left: - H+ - a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine - glycine name: glycine + a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine + H+ <-> CO2 + a [glycine-cleavage complex H protein] N6-aminomethyldihydrolipoyl-L-lysine pmids: [] rhea: [] right: - CO2 - a [glycine-cleavage complex H protein] N6-aminomethyldihydrolipoyl-L-lysine yeastcyc_id: GCVP-RXN yeastcyc_id: GLYCLEAV-PWY GLYCOCAT-YEAST-PWY: all_genes: - &id202 orf: YPR184W symbol: GDB1 uniprot: UniProtKB:Q06625 - &id201 orf: YPR160W symbol: GPH1 uniprot: UniProtKB:P06738 - &id203 orf: YKL127W symbol: PGM1 uniprot: UniProtKB:P33401 - &id204 orf: YMR105C symbol: PGM2 uniprot: UniProtKB:P37012 - &id200 orf: YIL099W symbol: SGA1 uniprot: UniProtKB:P08019 comment: 'Glycogen, a branched polymer of glucose, is a storage molecule whose accumulation is under rigorous control in many cells |CITS: 11152943|. Glycogen metabolism increases in response to a wide variety of environmental stresses, including heat stress or exposure to sodium chloride, hydrogen peroxide, copper sulfate, high levels of ethanol, or weak organic acids, such as sorbate or benzoate |CITS: 11152943|. Glycogen metabolism also increases in response to conditions of nutrient starvation, such as limited nitrogen, carbon, phosphorous, or sulfur, and during diauxic growth on glucose |CITS: 11152943|. Under all of the above conditions, glycogen is degraded by Gph1p and Gdb1p enzymes, which are phosphorylase and debranching enzymes respectively |CITS: 11152943|. GPH1 progressively releases glucose-1-phosphate from linear alpha (1,4)-glucosidic bonds in glycogen |CITS: 2657401||CITS: 1092346| but is not able to break alpha (1,4)-glucosidic bonds that are close to alpha (1,6)-branch linkages |CITS: 11152943|. The branches are resolved by Gdb1p, which eliminates branch points in a two-step process. The first step of the process is the transfer of a maltotriosyl (or maltosyl) unit from the branch to an adjacent alpha-1,4-glucosyl chain by the oligo-1,4 to 1,4-glucanotransferase activity (EC 2.4.1.25) of Gdb1p |CITS: 11094287|. The second step is the subsequent hydrolysis of the residual alpha-1,6-linked glucose residue by the alpha-1,6-glucosidase activity (EC 3.2.1.33) of Gdb1p |CITS: 11094287|. Once the branch is resolved, Gph1p can continue glycogen degradation |CITS: 11152943|. In sporulating cells, glycogen can also be degraded by Sga1p, which is a glucoamylase enzyme only expressed during late sporulation |CITS: 11152943|. SGA1 encodes an amylo (1,4-1,6)-glucosidase |CITS: 11152943| capable of degrading glycogen, starch, maltotriose, and maltose into glucose, with maximum activity against glycogen at pH 5.5 |CITS: 2493265|. The role of glycogen degradation during sporulation is not fully understood, since glycogen is rapidly degraded during sporulation in wild-type cells, but approximately 90% of all sga1 homozygous null mutants are able to produce viable spores |CITS: 11152943|. Thus far, none of the phenotypes seen in S. cerevisiae glycogen catabolism mutants correspond to the mammalian glycogen storage diseases associated with mutations in human genes involved in glycogen catabolism |CITS: 11152943|. ' name: glycogen catabolism pmids: - '11152943' reactions: - ec: - 3.2.1.3 genes: - *id200 left: - H2O - a debranched α-limit dextrin name: a debranched α-limit dextrin + n H2O -> n D-glucopyranose pmids: [] rhea: [] right: - D-glucopyranose yeastcyc_id: RXN-9024 - ec: - 2.4.1.1 genes: - *id201 left: - a debranched α-limit dextrin - phosphate name: a debranched α-limit dextrin + n phosphate -> n α-D-glucopyranose 1-phosphate pmids: [] rhea: [] right: - α-D-glucopyranose 1-phosphate yeastcyc_id: RXN-9025 - ec: - 3.2.1.33 genes: - *id202 left: - a glycogen name: a glycogen -> maltotetraose pmids: [] rhea: [] right: - maltotetraose yeastcyc_id: RXN3O-4038 - ec: - 2.4.1.1 genes: - *id201 left: - a glycogen - phosphate name: a glycogen + phosphate -> an α-limit dextrin + α-D-glucopyranose 1-phosphate pmids: [] rhea: [] right: - an α-limit dextrin - α-D-glucopyranose 1-phosphate yeastcyc_id: GLYCOPHOSPHORYL-RXN - ec: - 3.2.1.33 genes: - *id202 left: - H2O - a α-limit dextrin with short branches name: a α-limit dextrin with short branches + n H2O -> a debranched α-limit dextrin + n D-glucopyranose pmids: [] rhea: [] right: - D-glucopyranose - a debranched α-limit dextrin yeastcyc_id: 3.2.1.33-RXN - ec: - 2.4.1.25 genes: - *id202 left: - an α-limit dextrin name: an α-limit dextrin <-> a α-limit dextrin with short branches pmids: [] rhea: [] right: - a α-limit dextrin with short branches yeastcyc_id: RXN-9023 - ec: - 2.4.1.25 genes: - *id202 left: - D-glucopyranose - maltotetraose name: maltotetraose + D-glucopyranose <-> maltotriose + maltose pmids: [] rhea: [] right: - maltose - maltotriose yeastcyc_id: AMYLOMALT-RXN - ec: - 3.2.1.3 genes: - *id200 left: - H2O - a glycogen name: '{6-α-D-(1,4-α-D-glucano)-glucan}n + H2O -> {6-α-D-(1,4-α-D-glucano)-glucan}n-1 + D-glucopyranose' pmids: [] rhea: [] right: - D-glucopyranose - a glycogen yeastcyc_id: 3.2.1.3-RXN - ec: - 5.4.2.2 genes: - *id203 - *id204 left: - α-D-glucopyranose 1-phosphate name: α-D-glucopyranose 1-phosphate <-> D-glucopyranose 6-phosphate pmids: [] rhea: [] right: - D-glucopyranose 6-phosphate yeastcyc_id: PHOSPHOGLUCMUT-RXN yeastcyc_id: GLYCOCAT-YEAST-PWY GLYCOLYSIS: all_genes: - *id162 - *id140 - *id141 - *id167 - *id168 - *id139 - *id143 - *id144 - *id148 - *id142 - *id163 - *id150 - *id151 - *id152 - *id149 name: glycolysis I (from glucose 6-phosphate) pmids: [] reactions: - ec: - 5.4.2.12 genes: - *id139 left: - 2-phospho-D-glycerate name: 2-phospho-D-glycerate <-> 3-phospho-D-glycerate pmids: [] rhea: [] right: - 3-phospho-D-glycerate yeastcyc_id: 3PGAREARR-RXN - ec: - 5.4.2.11 genes: - *id139 left: - 2-phospho-D-glycerate name: 2-phospho-D-glycerate <-> 3-phospho-D-glycerate pmids: [] rhea: [] right: - 3-phospho-D-glycerate yeastcyc_id: RXN-15513 - ec: - 4.2.1.11 genes: - *id140 - *id141 left: - 2-phospho-D-glycerate name: 2-phospho-D-glycerate <-> phosphoenolpyruvate + H2O pmids: [] rhea: [] right: - H2O - phosphoenolpyruvate yeastcyc_id: 2PGADEHYDRAT-RXN - ec: - 2.7.2.3 genes: - *id142 left: - 3-phospho-D-glycerate - ATP name: 3-phospho-D-glycerate + ATP <-> 3-phospho-D-glyceroyl-phosphate + ADP pmids: [] rhea: [] right: - 3-phospho-D-glyceroyl-phosphate - ADP yeastcyc_id: PHOSGLYPHOS-RXN - ec: - 2.7.1.11 genes: - *id143 - *id144 left: - ATP - β-D-fructofuranose 6-phosphate name: ATP + β-D-fructofuranose 6-phosphate -> β-D-fructose 1,6-bisphosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - β-D-fructose 1,6-bisphosphate yeastcyc_id: 6PFRUCTPHOS-RXN - ec: - 5.3.1.9 genes: - *id148 left: - D-glucopyranose 6-phosphate name: D-glucopyranose 6-phosphate <-> β-D-fructofuranose 6-phosphate pmids: [] rhea: [] right: - β-D-fructofuranose 6-phosphate yeastcyc_id: PGLUCISOM-RXN - ec: - 5.3.1.1 genes: - *id149 left: - D-glyceraldehyde 3-phosphate name: D-glyceraldehyde 3-phosphate <-> glycerone phosphate pmids: [] rhea: [] right: - glycerone phosphate yeastcyc_id: TRIOSEPISOMERIZATION-RXN - ec: - 1.2.1.12 genes: - *id150 - *id151 - *id152 left: - D-glyceraldehyde 3-phosphate - NAD+ - phosphate name: D-glyceraldehyde 3-phosphate + NAD+ + phosphate <-> 3-phospho-D-glyceroyl-phosphate + NADH + H+ pmids: [] rhea: [] right: - 3-phospho-D-glyceroyl-phosphate - H+ - NADH yeastcyc_id: GAPOXNPHOSPHN-RXN - ec: - 2.7.1.40 genes: - *id162 - *id163 left: - ATP - pyruvate name: pyruvate + ATP <- phosphoenolpyruvate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - phosphoenolpyruvate yeastcyc_id: PEPDEPHOS-RXN - ec: - 4.1.2.13 genes: - *id167 left: - β-D-fructose 1,6-bisphosphate name: β-D-fructose 1,6-bisphosphate <-> glycerone phosphate + D-glyceraldehyde 3-phosphate pmids: [] rhea: [] right: - D-glyceraldehyde 3-phosphate - glycerone phosphate yeastcyc_id: F16ALDOLASE-RXN - ec: - 3.1.3.11 genes: - *id168 left: - H2O - β-D-fructose 1,6-bisphosphate name: β-D-fructose 1,6-bisphosphate + H2O -> β-D-fructofuranose 6-phosphate + phosphate pmids: [] rhea: [] right: - phosphate - β-D-fructofuranose 6-phosphate yeastcyc_id: F16BDEPHOS-RXN yeastcyc_id: GLYCOLYSIS GLYOXYLATE-BYPASS: all_genes: - &id208 orf: YLR304C symbol: ACO1 uniprot: UniProtKB:P19414 - &id209 orf: YJL200C symbol: ACO2 uniprot: UniProtKB:P39533 - &id210 orf: YNR001C symbol: CIT1 uniprot: UniProtKB:P00890 - &id211 orf: YCR005C symbol: CIT2 uniprot: UniProtKB:P08679 - &id212 orf: YPR001W symbol: CIT3 uniprot: UniProtKB:P43635 - &id206 orf: YIR031C symbol: DAL7 uniprot: UniProtKB:P21826 - &id205 orf: YER065C symbol: ICL1 uniprot: UniProtKB:P28240 - *id170 - *id171 - *id172 - &id207 orf: YNL117W symbol: MLS1 uniprot: UniProtKB:P30952 comment: The glyoxylate cycle, also called the glyoxylate shunt, is present in fungi, plants, and bacteria, but not in mammals. The cycle is essential for growth on two-carbon compounds such as ethanol and acetate, and plays an anaplerotic role in the provision of precursors for biosynthesis. The glyoxylate cycle is comprised of many of the same reactions as the TCA cycle, but it does not include the two decarboxylation reactions. As a result, two-carbon substrates, which enter the cycle as acetyl-CoA, can be converted to four-carbon compounds, which in turn can be further metabolized to create sugars and other essential organic compounds. Although several of the reactions of the glyoxylate and TCA cycle are identical, many of them are catalyzed by different isozymes in different cellular compartments. The glyoxylate cycle occurs in the peroxisome and cytoplasm, while the TCA cycle occurs in the mitochondria. Utilization of two-carbon compounds by yeast also requires the TCA cycle and gluconeogenesis, which are coordinately regulated with the glyoxylate cycle. The succinate provided by the glyoxylate cycle enters the TCA cycle where it is converted to malate; malate then reenters the cytoplasm where it is converted to oxaloacetate and eventually to glucose via gluconeogenesis. The key enzymes of the glyoxylate cycle, isocitrate lyase and malate synthase, as well as malate dehydrogenase, are regulated in yeast in response to the carbon source of the growth medium. Synthesis of these enzymes is repressed in cells grown on glucose and derepressed in media lacking glucose (as reported in |CITS:[5345986]|. Although S. cerevisiae is rarely found in human hosts, phagocytosis of S. cerevisiae by mammalian macrophages results in the induction of genes encoding glyoxylate cycle enzymes; this is thought to be a response to the nutrient-poor environment of the phagolysosome |CITS:[12455685][11452311]|. name: glyoxylate cycle pmids: - '12455685' - '15975908' reactions: - ec: - 1.1.1.37 genes: - *id170 - *id171 - *id172 left: - (S)-malate - NAD+ name: (S)-malate + NAD+ <-> oxaloacetate + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - oxaloacetate yeastcyc_id: MALATE-DEH-RXN - ec: - 4.1.3.1 genes: - *id205 left: - D-threo-isocitrate name: D-threo-isocitrate -> glyoxylate + succinate pmids: [] rhea: [] right: - glyoxylate - succinate yeastcyc_id: ISOCIT-CLEAV-RXN - ec: - 2.3.3.9 genes: - *id206 - *id207 left: - H2O - acetyl-CoA - glyoxylate name: acetyl-CoA + glyoxylate + H2O -> (S)-malate + coenzyme A + H+ pmids: [] rhea: [] right: - (S)-malate - H+ - coenzyme A yeastcyc_id: MALSYN-RXN - ec: [] genes: - *id208 left: - H2O - cis-aconitate name: cis-aconitate + H2O <-> D-threo-isocitrate pmids: [] rhea: [] right: - D-threo-isocitrate yeastcyc_id: ACONITATEHYDR-RXN - ec: [] genes: - *id208 - *id209 left: - citrate name: citrate <-> cis-aconitate + H2O pmids: [] rhea: [] right: - H2O - cis-aconitate yeastcyc_id: ACONITATEDEHYDR-RXN - ec: - 2.3.3.1 - 2.3.3.16 genes: - *id210 - *id211 - *id212 left: - H2O - acetyl-CoA - oxaloacetate name: oxaloacetate + acetyl-CoA + H2O -> citrate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - citrate - coenzyme A yeastcyc_id: CITSYN-RXN yeastcyc_id: GLYOXYLATE-BYPASS GLYSYN-ALA-PWY: all_genes: - &id213 orf: YFL030W symbol: AGX1 uniprot: UniProtKB:P43567 name: glycine biosynthesis III pmids: - '14745783' reactions: - ec: - 2.6.1.44 genes: - *id213 left: - L-alanine - glyoxylate name: glyoxylate + L-alanine -> glycine + pyruvate pmids: [] rhea: [] right: - glycine - pyruvate yeastcyc_id: ALANINE--GLYOXYLATE-AMINOTRANSFERASE-RXN yeastcyc_id: GLYSYN-ALA-PWY GLYSYN-PWY: all_genes: - *id018 - *id019 name: glycine biosynthesis I pmids: - '7498764' reactions: - ec: - 2.1.2.1 genes: - *id018 - *id019 left: - L-serine - a tetrahydrofolate name: L-serine + a tetrahydrofolate <-> glycine + a 5,10-methylenetetrahydrofolate + H2O pmids: [] rhea: [] right: - H2O - a 5,10-methylenetetrahydrofolate - glycine yeastcyc_id: GLYOHMETRANS-RXN yeastcyc_id: GLYSYN-PWY GLYSYN-THR-PWY: all_genes: - &id214 orf: YEL046C symbol: GLY1 uniprot: UniProtKB:P37303 name: glycine biosynthesis IV pmids: - '9163906' reactions: - ec: - 4.1.2.48 - 4.1.2.5 genes: - *id214 left: - L-threonine name: L-threonine -> acetaldehyde + glycine pmids: [] rhea: [] right: - acetaldehyde - glycine yeastcyc_id: THREONINE-ALDOLASE-RXN yeastcyc_id: GLYSYN-THR-PWY HEME-BIOSYNTHESIS-II: all_genes: - &id218 orf: YDR047W symbol: HEM12 uniprot: UniProtKB:P32347 - &id215 orf: YDR044W symbol: HEM13 uniprot: UniProtKB:P11353 - &id217 orf: YER014W symbol: HEM14 uniprot: UniProtKB:P40012 - &id216 orf: YOR176W symbol: HEM15 uniprot: UniProtKB:P16622 comment: 'Tetrapyrroles are a group of molecules that contain of four pyrrole rings linked together by single-atom bridges in a cyclic or linear arrangement. Biologically important cyclic tetrapyrroles, such as chlorophyll, cobalamin, heme, and siroheme, coordinate a metal ion in their central cavity and function as cofactors in numerous biological processes. Heme, which coordinates an iron atom, functions in oxygen sensing and utilization. To synthesize heme and other tetrapyrrole-derived compounds, S. cerevisiae utilizes a common biosynthetic pathway that leads up to the formation of the first macrocyclic intermediate, uroporphyrinogen-III, upon which the pathways diverge. In the heme biosynthetic route, four carboxyl groups are removed sequentially from the acetate side chains of uroporphyrinogen-III by uroporphyrinogen decarboxylase (Hem12p) to form coproporphyrinogen III. Decarboxylation of two of the carboxyethyl side chains of coproporphyrinogen III by coproporphyrinogen III oxidase (Hem13p) then forms protoporphyrinogen IX, which is subsequently oxidized by protoporphyrinogen oxidase (Hem14p) to yield protoporphyrin IX. In the final step, a ferrous ion is inserted into protoporphyrin IX by ferrochelatase (Hem15p), forming the end-product heme. References: |CITS:[11212295]||CITS: [2180703]||CITS: [2838478]||CITS: [7798202]||CITS: [2185242]|' name: heme b biosynthesis I (aerobic) pmids: - '11212295' - '2180703' - '2185242' - '2838478' - '7798202' - '8473299' - '8621563' reactions: - ec: - 1.3.3.3 genes: - *id215 left: - H+ - coproporphyrinogen III - oxygen name: coproporphyrinogen III + oxygen + 2 H+ -> protoporphyrinogen IX + 2 CO2 + 2 H2O pmids: - '2838478' rhea: [] right: - CO2 - H2O - protoporphyrinogen IX yeastcyc_id: RXN0-1461 - ec: - 4.99.1.1 genes: - *id216 left: - H+ - ferroheme b name: ferroheme b + 2 H+ <- protoporphyrin IX + Fe2+ pmids: - '8473299' rhea: [] right: - Fe2+ - protoporphyrin IX yeastcyc_id: PROTOHEMEFERROCHELAT-RXN - ec: - 1.3.3.4 genes: - *id217 left: - oxygen - protoporphyrinogen IX name: protoporphyrinogen IX + 3 oxygen -> protoporphyrin IX + 3 hydrogen peroxide pmids: - '8621563' rhea: [] right: - hydrogen peroxide - protoporphyrin IX yeastcyc_id: PROTOPORGENOXI-RXN - ec: - 4.1.1.37 genes: - *id218 left: - H+ - uroporphyrinogen-III name: uroporphyrinogen-III + 4 H+ -> 4 CO2 + coproporphyrinogen III pmids: - '2180703' rhea: [] right: - CO2 - coproporphyrinogen III yeastcyc_id: UROGENDECARBOX-RXN yeastcyc_id: HEME-BIOSYNTHESIS-II HEXPPSYN-PWY-2: all_genes: - &id220 orf: YPL069C symbol: BTS1 uniprot: UniProtKB:Q12051 - &id219 orf: YBR003W symbol: COQ1 uniprot: UniProtKB:P18900 - *id126 name: hexaprenyl diphosphate biosynthesis pmids: - '11583838' - '2681213' reactions: - ec: - 2.5.1.1 genes: - *id126 left: - dimethylallyl diphosphate - isopentenyl diphosphate name: dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - geranyl diphosphate yeastcyc_id: GPPSYN-RXN - ec: - 2.5.1.10 genes: - *id126 left: - geranyl diphosphate - isopentenyl diphosphate name: geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate pmids: [] rhea: [] right: - (2E,6E)-farnesyl diphosphate - diphosphate yeastcyc_id: FPPSYN-RXN - ec: - 2.5.1.- genes: - *id219 left: - geranylfarnesyl diphosphate - isopentenyl diphosphate name: geranylfarnesyl diphosphate + isopentenyl diphosphate -> all-trans-hexaprenyl diphosphate + diphosphate pmids: [] rhea: [] right: - all-trans-hexaprenyl diphosphate - diphosphate yeastcyc_id: RXN3O-9805 - ec: - 2.5.1.81 genes: [] left: - geranylgeranyl diphosphate - isopentenyl diphosphate name: geranylgeranyl diphosphate + isopentenyl diphosphate -> geranylfarnesyl diphosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - geranylfarnesyl diphosphate yeastcyc_id: RXN-8813 - ec: - 2.5.1.29 genes: - *id220 left: - (2E,6E)-farnesyl diphosphate - isopentenyl diphosphate name: isopentenyl diphosphate + (2E,6E)-farnesyl diphosphate -> geranylgeranyl diphosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - geranylgeranyl diphosphate yeastcyc_id: FARNESYLTRANSTRANSFERASE-RXN yeastcyc_id: HEXPPSYN-PWY-2 HISTSYN-PWY: all_genes: - &id223 orf: YER055C symbol: HIS1 uniprot: UniProtKB:P00498 - &id225 orf: YFR025C symbol: HIS2 uniprot: UniProtKB:P38635 - &id224 orf: YOR202W symbol: HIS3 uniprot: UniProtKB:P06633 - &id222 orf: YCL030C symbol: HIS4 uniprot: UniProtKB:P00815 - *id016 - &id221 orf: YIL020C symbol: HIS6 uniprot: UniProtKB:P40545 - &id226 orf: YBR248C symbol: HIS7 uniprot: UniProtKB:P33734 name: L-histidine biosynthesis pmids: - '15744050' - '8852895' - '9822821' reactions: - ec: - 5.3.1.16 genes: - *id221 left: - 1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide name: 1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide -> phosphoribulosylformimino-AICAR-phosphate pmids: [] rhea: [] right: - phosphoribulosylformimino-AICAR-phosphate yeastcyc_id: PRIBFAICARPISOM-RXN - ec: - 3.5.4.19 genes: - *id222 left: - 1-(5-phospho-β-D-ribosyl)-AMP - H2O name: 1-(5-phospho-β-D-ribosyl)-AMP + H2O -> 1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide pmids: [] rhea: [] right: - 1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide yeastcyc_id: HISTCYCLOHYD-RXN - ec: - 3.6.1.31 genes: - *id222 left: - 1-(5-phospho-β-D-ribosyl)-ATP - H2O name: 1-(5-phospho-β-D-ribosyl)-ATP + H2O -> 1-(5-phospho-β-D-ribosyl)-AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - 1-(5-phospho-β-D-ribosyl)-AMP - H+ - diphosphate yeastcyc_id: HISTPRATPHYD-RXN - ec: - 2.4.2.17 genes: - *id223 left: - 1-(5-phospho-β-D-ribosyl)-ATP - diphosphate name: 1-(5-phospho-β-D-ribosyl)-ATP + diphosphate <- ATP + 5-phospho-α-D-ribose 1-diphosphate + H+ pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - ATP - H+ yeastcyc_id: ATPPHOSPHORIBOSYLTRANS-RXN - ec: - 4.2.1.19 genes: - *id224 left: - D-erythro-imidazole-glycerol-phosphate name: D-erythro-imidazole-glycerol-phosphate -> imidazole acetol-phosphate + H2O pmids: [] rhea: [] right: - H2O - imidazole acetol-phosphate yeastcyc_id: IMIDPHOSDEHYD-RXN - ec: - 2.6.1.9 genes: - *id016 left: - 2-oxoglutarate - L-histidinol phosphate name: L-histidinol phosphate + 2-oxoglutarate <- imidazole acetol-phosphate + L-glutamate pmids: [] rhea: [] right: - L-glutamate - imidazole acetol-phosphate yeastcyc_id: HISTAMINOTRANS-RXN - ec: - 3.1.3.15 genes: - *id225 left: - H2O - L-histidinol phosphate name: L-histidinol phosphate + H2O -> histidinol + phosphate pmids: [] rhea: [] right: - histidinol - phosphate yeastcyc_id: HISTIDPHOS-RXN - ec: [] genes: - *id222 left: - H2O - NAD+ - histidinal name: histidinal + NAD+ + H2O -> L-histidine + NADH + 2 H+ pmids: [] rhea: [] right: - H+ - L-histidine - NADH yeastcyc_id: HISTALDEHYD-RXN - ec: [] genes: - *id222 left: - NAD+ - histidinol name: histidinol + NAD+ -> histidinal + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - histidinal yeastcyc_id: HISTOLDEHYD-RXN - ec: - 4.3.2.10 genes: - *id226 left: - L-glutamine - phosphoribulosylformimino-AICAR-phosphate name: phosphoribulosylformimino-AICAR-phosphate + L-glutamine -> L-glutamate + D-erythro-imidazole-glycerol-phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + H+ pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - D-erythro-imidazole-glycerol-phosphate - H+ - L-glutamate yeastcyc_id: GLUTAMIDOTRANS-RXN yeastcyc_id: HISTSYN-PWY HOMOCYS-CYS-CONVERT: all_genes: - *id084 - *id085 - &id228 orf: YJR130C symbol: STR2 uniprot: UniProtKB:P47164 - &id227 orf: YGL184C symbol: STR3 uniprot: UniProtKB:P53101 comment: 'The metabolic interconversion of cysteine and homocysteine via formation of a cystathionine intermediate is known as the transsulfuration pathway. While the transsulfuration pathway proceeds in only one direction in many bacteria and fungi, S. cerevisiae encodes for both a forward and reverse version of the pathway and is able to convert cysteine and homocysteine to one or the other reversibly. In the forward pathway, cysteine reacts with O-acetylhomoserine in a reaction catalyzed by cystathionine -synthase to form cystathionine. Cystathionine is then cleaved by cystathionine -lyase, yielding pyruvate, ammonia, and homocysteine. In S. cerevisiae, cystathionine -synthase and -lyase are thought to be encoded by STR2 and STR3 respectively, due to their similarity to the aforementioned enzymes in other organisms and the inability of str2 or str3 null mutants to utilize cysteine as a sole sulfur source. In the reverse pathway, cystathionine -synthase (Cys4p) catalyzes the condensation of homocysteine and serine to form cystathionine. Cystathionine -lyase (Cys3p) then catalyzes hydrolysis of cystathionine to produce cysteine, -ketobutyrate, and ammonia. The presence of two transsulfuration pathways in S. cerevisiae enables the cell to acquire methionine from cysteine and vice-versa by using homocysteine as an intermediate. Homocysteine derived from cysteine in the forward transsulfuration pathway can be converted to methionine, while homocysteine derived from methionine can be converted to cysteine via the reverse transsulfuration pathway. This enables S. cerevisiae to utilize methionine or cysteine as a sole source of sulfur. References: |CITS:[9409150]||CITS: [10821189]||CITS: [14967036]||CITS: [24291053]|' name: homocysteine and cysteine interconversion pmids: - '9409150' reactions: - ec: - 4.4.1.13 genes: - *id227 left: - H2O - L-cystathionine name: L-cystathionine + H2O -> L-homocysteine + pyruvate + ammonium pmids: [] rhea: [] right: - L-homocysteine - ammonium - pyruvate yeastcyc_id: CYSTATHIONINE-BETA-LYASE-RXN - ec: - 4.4.1.1 genes: - *id084 left: - H2O - L-cystathionine name: L-cystathionine + H2O <-> 2-oxobutanoate + L-cysteine + ammonia pmids: [] rhea: [] right: - 2-oxobutanoate - L-cysteine - ammonia yeastcyc_id: CYSTAGLY-RXN - ec: [] genes: - *id228 left: - L-cysteine - O-acetyl-L-homoserine name: L-cysteine + O-acetyl-L-homoserine -> L-cystathionine + acetate pmids: [] rhea: [] right: - L-cystathionine - acetate yeastcyc_id: RXN-721 - ec: - 4.2.1.22 genes: - *id085 left: - L-homocysteine - L-serine name: L-homocysteine + L-serine <-> L-cystathionine + H2O pmids: [] rhea: [] right: - H2O - L-cystathionine yeastcyc_id: CYSTATHIONINE-BETA-SYNTHASE-RXN yeastcyc_id: HOMOCYS-CYS-CONVERT HOMOCYSDEGR-PWY-1: all_genes: - *id084 - *id085 comment: The amino acid cysteine has important roles in protein structure and function, including the catalytic activity of some enzymes. It is also a component of glutathione and thioredoxin, which maintain a reducing environment inside the cell. In eukaryotes, cysteine derives its carbon and nitrogen from serine and its sulfur from methionine. name: L-cysteine biosynthesis III (from L-homocysteine) pmids: - '10509018' - '15042590' reactions: - ec: - 4.4.1.1 genes: - *id084 left: - H2O - L-cystathionine name: L-cystathionine + H2O <-> 2-oxobutanoate + L-cysteine + ammonia pmids: [] rhea: [] right: - 2-oxobutanoate - L-cysteine - ammonia yeastcyc_id: CYSTAGLY-RXN - ec: - 4.2.1.22 genes: - *id085 left: - L-homocysteine - L-serine name: L-homocysteine + L-serine <-> L-cystathionine + H2O pmids: [] rhea: [] right: - H2O - L-cystathionine yeastcyc_id: CYSTATHIONINE-BETA-SYNTHASE-RXN yeastcyc_id: HOMOCYSDEGR-PWY-1 HOMOSER-THRESYN-PWY: all_genes: - &id229 orf: YHR025W symbol: THR1 uniprot: UniProtKB:P17423 - &id230 orf: YCR053W symbol: THR4 uniprot: UniProtKB:P16120 name: L-threonine biosynthesis pmids: [] reactions: - ec: - 2.7.1.39 genes: - *id229 left: - ATP - L-homoserine name: L-homoserine + ATP -> O-phospho-L-homoserine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - O-phospho-L-homoserine yeastcyc_id: HOMOSERKIN-RXN - ec: - 4.2.3.1 genes: - *id230 left: - H2O - O-phospho-L-homoserine name: O-phospho-L-homoserine + H2O -> L-threonine + phosphate pmids: [] rhea: [] right: - L-threonine - phosphate yeastcyc_id: THRESYN-RXN yeastcyc_id: HOMOSER-THRESYN-PWY HOMOSERSYN-PWY: all_genes: - &id232 orf: YDR158W symbol: HOM2 uniprot: UniProtKB:P13663 - &id231 orf: YER052C symbol: HOM3 uniprot: UniProtKB:P10869 - &id233 orf: YJR139C symbol: HOM6 uniprot: UniProtKB:P31116 name: L-homoserine biosynthesis pmids: - '14745783' - '1789001' reactions: - ec: - 2.7.2.4 genes: - *id231 left: - ATP - L-aspartate name: L-aspartate + ATP -> L-aspartyl-4-phosphate + ADP pmids: [] rhea: [] right: - ADP - L-aspartyl-4-phosphate yeastcyc_id: ASPARTATEKIN-RXN - ec: - 1.2.1.11 genes: - *id232 left: - L-aspartate 4-semialdehyde - NADP+ - phosphate name: L-aspartate 4-semialdehyde + NADP+ + phosphate <- L-aspartyl-4-phosphate + NADPH + H+ pmids: [] rhea: [] right: - H+ - L-aspartyl-4-phosphate - NADPH yeastcyc_id: ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN - ec: - 1.1.1.3 genes: - *id233 left: - L-homoserine - NAD(P)+ name: L-homoserine + NAD(P)+ <- L-aspartate 4-semialdehyde + NAD(P)H + H+ pmids: [] rhea: [] right: - H+ - L-aspartate 4-semialdehyde - NAD(P)H yeastcyc_id: HOMOSERDEHYDROG-RXN yeastcyc_id: HOMOSERSYN-PWY ILEUSYN-PWY-1: all_genes: - *id080 - *id081 - *id082 - *id076 - *id073 - *id074 - *id077 name: L-isoleucine biosynthesis I (from threonine) pmids: - '3289762' reactions: - ec: - 4.2.1.9 genes: - *id073 left: - (R)-2,3-dihydroxy-3-methylpentanoate name: (R)-2,3-dihydroxy-3-methylpentanoate -> (S)-3-methyl-2-oxopentanoate + H2O pmids: [] rhea: [] right: - (S)-3-methyl-2-oxopentanoate - H2O yeastcyc_id: DIHYDROXYMETVALDEHYDRAT-RXN - ec: - 1.1.1.86 genes: - *id074 left: - (R)-2,3-dihydroxy-3-methylpentanoate - NADP+ name: (R)-2,3-dihydroxy-3-methylpentanoate + NADP+ <- (S)-2-aceto-2-hydroxybutanoate + NADPH + H+ pmids: [] rhea: [] right: - (S)-2-aceto-2-hydroxybutanoate - H+ - NADPH yeastcyc_id: ACETOOHBUTREDUCTOISOM-RXN - ec: - 2.6.1.42 genes: - *id080 - *id081 left: - 2-oxoglutarate - L-isoleucine name: L-isoleucine + 2-oxoglutarate <-> L-glutamate + (S)-3-methyl-2-oxopentanoate pmids: - '10989445' - '8702755' - '8798704' rhea: [] right: - (S)-3-methyl-2-oxopentanoate - L-glutamate yeastcyc_id: BRANCHED-CHAINAMINOTRANSFERILEU-RXN - ec: - 4.3.1.19 genes: - *id082 left: - L-threonine name: L-threonine -> 2-oxobutanoate + ammonium pmids: [] rhea: [] right: - 2-oxobutanoate - ammonium yeastcyc_id: THREDEHYD-RXN - ec: - 2.2.1.6 genes: - *id076 - *id077 left: - 2-oxobutanoate - H+ - pyruvate name: pyruvate + 2-oxobutanoate + H+ -> (S)-2-aceto-2-hydroxybutanoate + CO2 pmids: [] rhea: [] right: - (S)-2-aceto-2-hydroxybutanoate - CO2 yeastcyc_id: ACETOOHBUTSYN-RXN yeastcyc_id: ILEUSYN-PWY-1 IPPSYN-PWY: all_genes: - *id119 - *id113 - *id125 - *id116 - *id114 - *id115 - *id131 - *id117 comment: 'The mevalonate (MVA) pathway synthesizes the two common precursors to all isoprenoids: isopentenyl pyrophosphate (IPP) and its isomer, dimethylallyl pyrophosphate (DMAPP). The MVA pathway exists largely in eukaryotes and archaebacteria and is one of two pathways for IPP and DMAPP biosynthesis found in nature. The other pathway, the methylerythritol phosphate (MEP) pathway, exists mainly in eubacteria and higher plants. Yeasts and other fungi employ the MVA pathway for isoprenoid production. In S. cerevisiae, the MVA pathway begins with the condensation of two molecules of acetyl-CoA by acetoacetyl-CoA thiolase (Erg10p). This reaction forms acetoacetyl-CoA, which reacts with a third molecule of acetyl-CoA via 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase (Erg13p) to form HMG-CoA. In turn, HMG-CoA is converted to mevalonate by HMG-CoA reductase in two NADPH-dependent reduction steps. This reaction is catalyzed by two isozymes in S. cerevisiae: Hmg1p and Hmg2p. Depending on culture conditions, Hmg1p accounts for around 83% of HMG-CoA reductase activity in wild type cells. After sequential phosphorylation of MVA to MVA-5-diphosphate via MVA kinase (Erg12p) and phospho-MVA kinase (Erg8), MVA-5-diphosphate is decarboxylated in an ATP-dependent manner by MVA pyrophosphate decarboxylase (Mvd1p) to yield IPP. IPP can then go to be isomerized to DMAPP via isopentenyl diphosphate:dimethylallyl diphosphate isomerase (Idi1p). The addition of IPP units to DMAPP produces short-chain prenyl diphosphates that serve as precursors to many essential metabolites. For example, DMAPP can be sequentially condensed with two molecules of IPP to form farnesyl pyrophosphate (FPP). FPP can undergo a long series of conversion steps in the sterol biosynthesis pathway to produce ergosterol, an important contributor to membrane integrity and the major sterol in S. cerevisiae. In addition to sterols, FPP is a precursor to many other primary metabolites including dolichols, ubiquinones, carotenoids, and polyprenols for protein prenylation. References: |CITS:[23451776]||CITS: [24520995]||CITS: [3526336]||CITS: [19744247]||CITS: [24227704]|' name: mevalonate pathway pmids: [] reactions: - ec: - 2.7.1.36 genes: - *id113 left: - (R)-mevalonate - ATP name: (R)-mevalonate + ATP <-> (R)-mevalonate 5-phosphate + ADP + H+ pmids: [] rhea: [] right: - (R)-mevalonate 5-phosphate - ADP - H+ yeastcyc_id: MEVALONATE-KINASE-RXN - ec: - 1.1.1.34 genes: - *id114 - *id115 left: - (R)-mevalonate - NADP+ - coenzyme A name: (R)-mevalonate + coenzyme A + 2 NADP+ <-> (S)-3-hydroxy-3-methylglutaryl-CoA + 2 NADPH + 2 H+ pmids: [] rhea: [] right: - (S)-3-hydroxy-3-methylglutaryl-CoA - H+ - NADPH yeastcyc_id: 1.1.1.34-RXN - ec: - 2.7.4.2 genes: - *id116 left: - (R)-mevalonate 5-phosphate - ATP name: (R)-mevalonate 5-phosphate + ATP <-> (R)-mevalonate diphosphate + ADP pmids: [] rhea: [] right: - (R)-mevalonate diphosphate - ADP yeastcyc_id: PHOSPHOMEVALONATE-KINASE-RXN - ec: - 4.1.1.33 genes: - *id117 left: - (R)-mevalonate diphosphate - ATP name: (R)-mevalonate diphosphate + ATP -> CO2 + isopentenyl diphosphate + ADP + phosphate pmids: [] rhea: [] right: - ADP - CO2 - isopentenyl diphosphate - phosphate yeastcyc_id: DIPHOSPHOMEVALONTE-DECARBOXYLASE-RXN - ec: - 2.3.1.9 genes: - *id119 left: - acetyl-CoA name: 2 acetyl-CoA <-> acetoacetyl-CoA + coenzyme A pmids: [] rhea: [] right: - acetoacetyl-CoA - coenzyme A yeastcyc_id: ACETYL-COA-ACETYLTRANSFER-RXN - ec: - 2.3.3.10 genes: - *id125 left: - H2O - acetoacetyl-CoA - acetyl-CoA name: acetoacetyl-CoA + acetyl-CoA + H2O <-> (S)-3-hydroxy-3-methylglutaryl-CoA + coenzyme A + H+ pmids: [] rhea: [] right: - (S)-3-hydroxy-3-methylglutaryl-CoA - H+ - coenzyme A yeastcyc_id: HYDROXYMETHYLGLUTARYL-COA-SYNTHASE-RXN - ec: - 5.3.3.2 genes: - *id131 left: - isopentenyl diphosphate name: isopentenyl diphosphate <-> dimethylallyl diphosphate pmids: [] rhea: [] right: - dimethylallyl diphosphate yeastcyc_id: IPPISOM-RXN yeastcyc_id: IPPSYN-PWY LEUSYN-PWY-1: all_genes: - *id080 - *id081 - *id075 - *id078 - *id079 name: L-leucine biosynthesis pmids: - '12626680' reactions: - ec: - 4.2.1.33 genes: - *id075 left: - (2R,3S)-3-isopropylmalate name: (2R,3S)-3-isopropylmalate <-> (2S)-2-isopropylmalate pmids: [] rhea: [] right: - (2S)-2-isopropylmalate yeastcyc_id: RXN-13163 - ec: - 1.1.1.85 genes: [] left: - (2R,3S)-3-isopropylmalate - NAD+ name: (2R,3S)-3-isopropylmalate + NAD+ -> 4-methyl-2-oxopentanoate + CO2 + NADH pmids: [] rhea: [] right: - 4-methyl-2-oxopentanoate - CO2 - NADH yeastcyc_id: RXN-13158 - ec: - 2.3.3.13 genes: - *id078 - *id079 left: - 3-methyl-2-oxobutanoate - H2O - acetyl-CoA name: 3-methyl-2-oxobutanoate + acetyl-CoA + H2O -> (2S)-2-isopropylmalate + coenzyme A + H+ pmids: [] rhea: [] right: - (2S)-2-isopropylmalate - H+ - coenzyme A yeastcyc_id: 2-ISOPROPYLMALATESYN-RXN - ec: - 2.6.1.42 - 2.6.1.6 genes: - *id080 - *id081 left: - 2-oxoglutarate - L-leucine name: L-leucine + 2-oxoglutarate <-> L-glutamate + 4-methyl-2-oxopentanoate pmids: - '10989445' - '8702755' - '8798704' rhea: [] right: - 4-methyl-2-oxopentanoate - L-glutamate yeastcyc_id: BRANCHED-CHAINAMINOTRANSFERLEU-RXN yeastcyc_id: LEUSYN-PWY-1 LIPASYN-PWY-1: all_genes: - &id235 orf: YER019W symbol: ISC1 uniprot: UniProtKB:P40015 - &id234 orf: YPL268W symbol: PLC1 uniprot: UniProtKB:P32383 - &id236 orf: YKR031C symbol: SPO14 uniprot: UniProtKB:P36126 comment: 'In addition to being a primary structural components of cell membranes, phospholipids may also be thought of as a reservoir of signaling molecules. Hydrolysis of phosphatidylinositol 4,5-biphosphate (PIP2) by phospholipase C, for instance, generates the signaling molecules inositol triphosphate (IP3) and diacylglycerol (DAG). S. cerevisiae catalyzes this reaction via Plc1p, a phosphatidylinositol-specific phospholipase C involved in a variety of biological processes including nutrient sensing and filamentous growth. On the other hand, degradation of phosphatidylcholine (PC) by phospholipase D (Spo14p) yields phosphatidic acid and choline; this activity generates PA required for sporulation in S. cerevisiae. A phospholipase C specific for PC has yet to be identified in S. cerevisiae, however PC may also serve as substrate for phospholipases B (Plb1-3p and Nte1p), which hydrolyze PC to yield glycerophosphocholine (GPC) and two fatty acids. Both phospholipases B and D are thought to mediate PC turnover in yeast, and phospholipase B (as Plb1p) has also been implicated in acyl chain remodeling. References: |CITS:[11015615]||CITS: [23631861]||CITS: [22345606]||CITS: [14528019]||CITS: [11006294]|' name: phospholipids degradation pmids: [] reactions: - ec: - 3.1.4.11 genes: - *id234 left: - H2O - a 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate name: a 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O -> a 1,2-diacyl-sn-glycerol + D-myo-inositol (1,4,5)-trisphosphate + H+ pmids: - '8395015' rhea: [] right: - D-myo-inositol (1,4,5)-trisphosphate - H+ - a 1,2-diacyl-sn-glycerol yeastcyc_id: 3.1.4.11-RXN - ec: - 3.1.4.3 genes: - *id235 left: - H2O - a phosphatidylcholine name: a phosphatidylcholine + H2O -> a 1,2-diacyl-sn-glycerol + phosphocholine + H+ pmids: [] rhea: [] right: - H+ - a 1,2-diacyl-sn-glycerol - phosphocholine yeastcyc_id: PHOSPHOLIPASE-C-RXN - ec: - 3.1.4.4 genes: - *id236 left: - H2O - a phosphatidylcholine name: a phosphatidylcholine + H2O -> a 1,2-diacyl-sn-glycerol 3-phosphate + choline + H+ pmids: [] rhea: [] right: - H+ - a 1,2-diacyl-sn-glycerol 3-phosphate - choline yeastcyc_id: PHOSCHOL-RXN yeastcyc_id: LIPASYN-PWY-1 LYSDEGII-PWY: all_genes: [] name: L-lysine degradation III pmids: - '131119' - '8257283' reactions: - ec: - 1.1.1.- genes: [] left: - 2-keto-6-acetamidocaproate - H2O - NAD+ name: 2-keto-6-acetamidocaproate + NAD+ + H2O -> 5-acetamidovalerate + CO2 + NADH + H+ pmids: [] rhea: [] right: - 5-acetamidovalerate - CO2 - H+ - NADH yeastcyc_id: KETAMID-RXN - ec: - 3.5.1.- genes: [] left: - 5-acetamidovalerate - H2O name: 5-acetamidovalerate + H2O -> acetate + 5-aminopentanoate pmids: [] rhea: [] right: - 5-aminopentanoate - acetate yeastcyc_id: AMVAL-RXN - ec: - 2.6.1.48 genes: [] left: - 2-oxoglutarate - 5-aminopentanoate name: 5-aminopentanoate + 2-oxoglutarate <-> glutarate semialdehyde + L-glutamate pmids: [] rhea: [] right: - L-glutamate - glutarate semialdehyde yeastcyc_id: VAGL-RXN - ec: - 2.3.1.- genes: [] left: - L-lysine - acetyl-CoA name: L-lysine + acetyl-CoA -> N6-acetyl-L-lysine + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - N6-acetyl-L-lysine - coenzyme A yeastcyc_id: LYSACET-RXN - ec: - 2.6.1.- genes: [] left: - 2-oxoglutarate - N6-acetyl-L-lysine name: N6-acetyl-L-lysine + 2-oxoglutarate <-> 2-keto-6-acetamidocaproate + L-glutamate pmids: [] rhea: [] right: - 2-keto-6-acetamidocaproate - L-glutamate yeastcyc_id: ACETCAPR-RXN - ec: - 1.2.1.20 genes: [] left: - H2O - NAD+ - glutarate semialdehyde name: glutarate semialdehyde + NAD+ + H2O -> glutarate + NADH + 2 H+ pmids: [] rhea: [] right: - H+ - NADH - glutarate yeastcyc_id: GLUTARATE-SEMIALDEHYDE-DEHYDROGENASE-RXN yeastcyc_id: LYSDEGII-PWY LYSINE-AMINOAD-PWY-2: all_genes: - &id242 orf: YIR034C symbol: LYS1 uniprot: UniProtKB:P38998 - &id238 orf: YIL094C symbol: LYS12 uniprot: UniProtKB:P40495 - &id241 orf: YBR115C symbol: LYS2 uniprot: UniProtKB:P07702 - &id239 orf: YDL182W symbol: LYS20 uniprot: UniProtKB:P48570 - &id240 orf: YDL131W symbol: LYS21 uniprot: UniProtKB:Q12122 - &id237 orf: YDR234W symbol: LYS4 uniprot: UniProtKB:P49367 - &id243 orf: YNR050C symbol: LYS9 uniprot: UniProtKB:P38999 comment: 'S. cerevisiae synthesizes the essential amino acid L-lysine via the L-alpha-aminoadipic acid pathway instead of the diaminopmelate pathway |CITS: [10714900]|. Originally proposed to be characteristic of fungi, recent studies suggest prokaryotes also synthesize lysine via the alpha-aminoadipic acid pathway |CITS: [11029074]|. Intermediates in this pathway are often incorporated into secondary metabolites. For example, it has been well- studied that alpha-aminoadipate is required for penicillin production |CITS: [10714900]|. Regulation of the lysine biosynthetic pathway in S. cerevisiae is an interaction between general amino acid control (via Gcn4p) |CITS: [Hinnebusch]|, feedback inhibition of homocitrate synthase activity by lysine |CITS: [10103047]|, and induction of Lys14p by alpha-aminoadipate semialdehyde |CITS: [10975256]|.' name: L-lysine biosynthesis IV pmids: - '10714900' reactions: - ec: - 4.2.1.36 genes: - *id237 left: - (1R,2S)-homoisocitrate name: (1R,2S)-homoisocitrate <-> cis-homoaconitate + H2O pmids: [] rhea: [] right: - H2O - cis-homoaconitate yeastcyc_id: HOMOACONITATE-HYDRATASE-RXN - ec: - 1.1.1.286 - 1.1.1.87 genes: - *id238 left: - (1R,2S)-homoisocitrate - NAD+ name: (1R,2S)-homoisocitrate + NAD+ -> CO2 + 2-oxoadipate + NADH pmids: [] rhea: [] right: - 2-oxoadipate - CO2 - NADH yeastcyc_id: RXN-7970 - ec: [] genes: - *id237 left: - (2R)-homocitrate name: (2R)-homocitrate -> cis-homoaconitate + H2O pmids: [] rhea: [] right: - H2O - cis-homoaconitate yeastcyc_id: RXN3O-1983 - ec: - 2.6.1.39 genes: [] left: - 2-oxoglutarate - L-2-aminoadipate name: 2-oxoglutarate + L-2-aminoadipate <- 2-oxoadipate + L-glutamate pmids: [] rhea: [] right: - 2-oxoadipate - L-glutamate yeastcyc_id: 2-AMINOADIPATE-AMINOTRANSFERASE-RXN - ec: - 2.3.3.14 genes: - *id239 - *id240 left: - 2-oxoglutarate - H2O - acetyl-CoA name: 2-oxoglutarate + acetyl-CoA + H2O -> (2R)-homocitrate + coenzyme A + H+ pmids: [] rhea: [] right: - (2R)-homocitrate - H+ - coenzyme A yeastcyc_id: HOMOCITRATE-SYNTHASE-RXN - ec: - 1.2.1.31 genes: - *id241 left: - H+ - L-2-aminoadipate - NADPH name: L-2-aminoadipate + NADPH + 2 H+ -> (S)-2-amino-6-oxohexanoate + NADP+ + H2O pmids: [] rhea: [] right: - (S)-2-amino-6-oxohexanoate - H2O - NADP+ yeastcyc_id: RXN3O-9808 - ec: - 1.5.1.7 genes: - *id242 left: - H2O - L-saccharopine - NAD+ name: L-saccharopine + NAD+ + H2O -> 2-oxoglutarate + L-lysine + NADH + H+ pmids: [] rhea: [] right: - 2-oxoglutarate - H+ - L-lysine - NADH yeastcyc_id: 1.5.1.7-RXN - ec: - 1.5.1.10 genes: - *id243 left: - H2O - L-saccharopine - NADP+ name: L-saccharopine + NADP+ + H2O <- L-glutamate + (S)-2-amino-6-oxohexanoate + NADPH + H+ pmids: [] rhea: [] right: - (S)-2-amino-6-oxohexanoate - H+ - L-glutamate - NADPH yeastcyc_id: RXN3O-127 yeastcyc_id: LYSINE-AMINOAD-PWY-2 NADSYN-PWY: all_genes: - &id245 orf: YJR025C symbol: BNA1 uniprot: UniProtKB:P47096 - &id249 orf: YJR078W symbol: BNA2 uniprot: UniProtKB:P47125 - &id250 orf: YJL060W symbol: BNA3 uniprot: UniProtKB:P47039 - &id248 orf: YBL098W symbol: BNA4 uniprot: UniProtKB:P38169 - &id244 orf: YLR231C symbol: BNA5 uniprot: UniProtKB:Q05979 - &id247 orf: YFR047C symbol: BNA6 uniprot: UniProtKB:P43619 - &id251 orf: YDR428C symbol: BNA7 uniprot: UniProtKB:Q04066 - &id252 orf: YLR328W symbol: NMA1 uniprot: UniProtKB:Q06178 - &id253 orf: YGR010W symbol: NMA2 uniprot: UniProtKB:P53204 - &id246 orf: YHR074W symbol: QNS1 uniprot: UniProtKB:P38795 comment: 'Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and energy metabolism. NAD also has been shown to be an important substrate in a variety of biological processes, including transcriptional regulation, DNA repair, calcium-dependent signaling pathways, calorie-restriction-mediated life-span extension and age-associated diseases |CITS: [12736687],[12648681]|. NAD appears to affect these processes by regulating the Sir2p family of NAD-dependent deacetylases (Sirtuins) |CITS: [12648681]|. There are a number of pathways for NAD biosynthesis. In yeast and most other organisms, the two major pathways are de novo synthesis of NAD (the de novo pathway) and regeneration of NAD from its nicotinamide degradation products (the NAD salvage pathway) |CITS: [12972620], [12648681]|. NAD is synthesized de novo from tryptophan via kynurenine |CITS: [12972620]|. In this pathway tryptophan is converted to nicotinic acid mononucleotide (NAMN) in 6 enzymatic steps (catalyzed by Bna1-2p, and Bna4-7p) and one non-enzymatic step |CITS: [12972620]|. At NAMN the de novo pathway converges with the NAD salvage pathway and the last two steps to NAD are shared |CITS: [12972620], [12648681]|. In the yeast NAD salvage pathway, the vitamin precursors nicotinamide and nicotinic acid are converted to NAMN, the point of convergence with the de novo pathway |CITS: [12648681]|. The steps from nicotinic acid to NAD were elucidated by Preiss and Handler and are sometimes referred to as the Preiss-Handler pathway |CITS: [13416279], [13563526]|. Yeast can also import extracellular nicotinic acid into the cell by the permease Tna1p and then convert it into NAD via the Preiss-Handler pathway |CITS: [12648681]|. There are four additional pathways for synthesizing NAD in yeast: two salvage pathways from the vitamin precursor nicotinamide riboside (NR) and two salvage pathways from nicotinic acid riboside (NaR) |CITS: [15137942], [17482543], [17914902]|. Three of these salvage pathways converge first with the NAD salvage pathway and then with the de novo pathway, while the fourth, the NR salvage pathway I, is independent of both of these pathways. In the NR salvage pathway I, NR is phosphorylated to nicotinamide mononucleotide by the kinase Nrk1p, and then adenylated to NAD by Nma1p or Nma2p |CITS: [15137942]|. Bacteria such as Haemophilus influenza that lack the enzymes of the de novo and Preiss-Handler pathway can synthesize NAD from NR and nicotinamide mononucleotide as well |CITS: [15137942]|. Humans also appear to have this NR salvage pathway |CITS: [15137942]|. Yeast have a second NR salvage pathway (NR salvage pathway II) that is independent of Nrk1p; in NR salvage pathway II NR is split into a ribosyl product and nicotinamide, which is subsequently converted to NAD via enzymes of the NAD salvage pathway and de novo pathway |CITS: [17482543]|. The initial steps in the two NaR salvage pathways are similar to those of the NR salvage pathways and are catalyzed by the same enzymes; Nrk1p catalyzes the first step in the NR and NaR salvage pathways I and Urh1p and Pnp1p catalyze the first steps of the NR and NaR salvage pathways II |CITS: [17914902]|.' name: NAD de novo biosynthesis II (from tryptophan) pmids: - '12062417' reactions: - ec: [] genes: [] left: - 2-amino-3-carboxymuconate-6-semialdehyde name: 2-amino-3-carboxymuconate-6-semialdehyde -> quinolinate + H2O pmids: [] rhea: [] right: - H2O - quinolinate yeastcyc_id: RXN-5721 - ec: - 3.7.1.3 genes: - *id244 left: - 3-hydroxy-L-kynurenine - H2O name: 3-hydroxy-L-kynurenine + H2O -> 3-hydroxyanthranilate + L-alanine + H+ pmids: [] rhea: [] right: - 3-hydroxyanthranilate - H+ - L-alanine yeastcyc_id: 3-HYDROXY-KYNURENINASE-RXN - ec: - 1.13.11.6 genes: - *id245 left: - 3-hydroxyanthranilate - oxygen name: 3-hydroxyanthranilate + oxygen -> 2-amino-3-carboxymuconate-6-semialdehyde + H+ pmids: [] rhea: [] right: - 2-amino-3-carboxymuconate-6-semialdehyde - H+ yeastcyc_id: 1.13.11.6-RXN - ec: - 6.3.5.1 genes: - *id246 left: - ATP - H2O - L-glutamine - nicotinate adenine dinucleotide name: ATP + nicotinate adenine dinucleotide + L-glutamine + H2O -> L-glutamate + AMP + NAD+ + diphosphate + H+ pmids: [] rhea: [] right: - AMP - H+ - L-glutamate - NAD+ - diphosphate yeastcyc_id: NAD-SYNTH-GLN-RXN - ec: - 2.4.2.19 genes: - *id247 left: - CO2 - diphosphate - β-nicotinate D-ribonucleotide name: CO2 + β-nicotinate D-ribonucleotide + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + quinolinate + 2 H+ pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - H+ - quinolinate yeastcyc_id: QUINOPRIBOTRANS-RXN - ec: - 1.14.13.9 genes: - *id248 left: - H+ - L-kynurenine - NADPH - oxygen name: L-kynurenine + NADPH + oxygen + H+ -> 3-hydroxy-L-kynurenine + NADP+ + H2O pmids: [] rhea: [] right: - 3-hydroxy-L-kynurenine - H2O - NADP+ yeastcyc_id: KYNURENINE-3-MONOOXYGENASE-RXN - ec: - 1.13.11.11 - 1.13.11.52 genes: - *id249 left: - L-tryptophan - oxygen name: L-tryptophan + oxygen -> N-Formyl-L-kynurenine pmids: [] rhea: [] right: - N-Formyl-L-kynurenine yeastcyc_id: RXN-8665 - ec: - 3.5.1.9 genes: - *id250 - *id251 left: - H2O - N-Formyl-L-kynurenine name: N-Formyl-L-kynurenine + H2O -> L-kynurenine + formate + H+ pmids: [] rhea: [] right: - H+ - L-kynurenine - formate yeastcyc_id: ARYLFORMAMIDASE-RXN - ec: - 2.7.7.18 genes: - *id252 - *id253 left: - ATP - H+ - β-nicotinate D-ribonucleotide name: β-nicotinate D-ribonucleotide + ATP + H+ -> nicotinate adenine dinucleotide + diphosphate pmids: [] rhea: [] right: - diphosphate - nicotinate adenine dinucleotide yeastcyc_id: NICONUCADENYLYLTRAN-RXN yeastcyc_id: NADSYN-PWY NONOXIPENT-PWY: all_genes: - &id255 orf: YOR095C symbol: RKI1 uniprot: UniProtKB:Q12189 - &id256 orf: YJL121C symbol: RPE1 uniprot: UniProtKB:P46969 - &id258 orf: YLR354C symbol: TAL1 uniprot: UniProtKB:P15019 - &id254 orf: YPR074C symbol: TKL1 uniprot: UniProtKB:P23254 - &id257 orf: YBR117C symbol: TKL2 uniprot: UniProtKB:P33315 comment: 'The reactions of the non-oxidative branch of the pentose phosphate pathway are reversible and are important for generating ribose-5-phosphate, which is required for the biosynthesis of several biomolecules, including RNA and DNA. These reactions also catalyze the interconversion of a variety of 3, 5 and 6 carbon sugars, which is important for several biosynthetic pathways, including the biosynthesis of pyrimidines, purines, tryptophan, histidine, and aromatic amino acids |CITS:[8929392]||CITS:[15960801]||CITS:[7916691]||CITS:[14690456]|. The flow of glucose 6-phosphate through glycolysis and the pentose phosphate pathway is linked through two enzymes of the non-oxidative branch of the pentose phosphate pathway, transketolase (Tkl1p and Tkl2p) and transaldolase (Tal1p). The ability of these enzymes to convert one type of sugar into another allows them to convert the byproduct of one pathway into the substrate of another pathway in order to meet the metabolic needs of the cell. For example, if the cell needs ribose 5-phosphate, glyceraldehyde 3-phosphate and fructose 6-phosphate will be converted to ribose 5-phosphate. If the cell needs NADPH or ATP more than ribose 5-phosphate, ribose 5-phosphate will be converted to glyceraldehyde 3-phosphate and fructose 6-phosphate for use by the oxidative branch of the pentose phosphate pathway or glycolysis, respectively |CITS:[11298766]||CITS:[15960801]||CITS:[1628611]|. ' name: pentose phosphate pathway (non-oxidative branch) pmids: - '14690456' - '1737042' - '2185015' - '7916691' - '8534086' - '8929392' reactions: - ec: - 2.2.1.1 genes: - *id254 left: - D-erythrose 4-phosphate - D-xylulose 5-phosphate name: D-erythrose 4-phosphate + D-xylulose 5-phosphate <-> β-D-fructofuranose 6-phosphate + D-glyceraldehyde 3-phosphate pmids: [] rhea: [] right: - D-glyceraldehyde 3-phosphate - β-D-fructofuranose 6-phosphate yeastcyc_id: 2TRANSKETO-RXN - ec: - 5.3.1.6 genes: - *id255 left: - D-ribose 5-phosphate name: D-ribose 5-phosphate <-> D-ribulose 5-phosphate pmids: [] rhea: [] right: - D-ribulose 5-phosphate yeastcyc_id: RIB5PISOM-RXN - ec: - 5.1.3.1 genes: - *id256 left: - D-ribulose 5-phosphate name: D-ribulose 5-phosphate <-> D-xylulose 5-phosphate pmids: [] rhea: [] right: - D-xylulose 5-phosphate yeastcyc_id: RIBULP3EPIM-RXN - ec: - 2.2.1.1 genes: - *id254 - *id257 left: - D-glyceraldehyde 3-phosphate - D-sedoheptulose 7-phosphate name: D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate <-> D-ribose 5-phosphate + D-xylulose 5-phosphate pmids: [] rhea: [] right: - D-ribose 5-phosphate - D-xylulose 5-phosphate yeastcyc_id: 1TRANSKETO-RXN - ec: - 2.2.1.2 genes: - *id258 left: - D-glyceraldehyde 3-phosphate - D-sedoheptulose 7-phosphate name: D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate <-> β-D-fructofuranose 6-phosphate + D-erythrose 4-phosphate pmids: [] rhea: [] right: - D-erythrose 4-phosphate - β-D-fructofuranose 6-phosphate yeastcyc_id: TRANSALDOL-RXN yeastcyc_id: NONOXIPENT-PWY OXIDATIVEPENT-PWY: all_genes: - &id259 orf: YHR163W symbol: SOL3 uniprot: UniProtKB:P38858 - &id260 orf: YGR248W symbol: SOL4 uniprot: UniProtKB:P53315 - &id261 orf: YNL241C symbol: ZWF1 uniprot: UniProtKB:P11412 comment: 'The reactions of the oxidative branch of the pentose phosphate pathway occur in the cytosol and are important for generating NADPH through the oxidative reduction of NADP+. NADPH is an important source of the reducing energy required by many enzymes in central biosynthetic pathways |CITS:[8929392]| |CITS:[8910528]| |CITS:[9813062]| |CITS:[11298766]| |CITS:[1628611]|. Although there are other biochemical pathways that generate NADPH in yeast, the pentose phosphate pathway is considered the major source of NADPH, and insufficient NADPH probably contributes to the fitness defects seen in mutants of the oxidative branch of the pentose phosphate pathway |CITS:[12047390]| |CITS:[15960801]|. Because NADPH is an essential cofactor for glutathione- and thioredoxin-dependent enzymes that defend cells against oxidative damage, the oxidative branch of the pentose phosphate pathway is also important for protecting yeast from oxidative stress |CITS:[8929392]||CITS:[8910528]||CITS:[11557322]||CITS:[16179340]|. Metabolism through the pentose phosphate pathway varies according to the metabolic needs of the cell |CITS:[10803891]| |CITS:[15066826]|. The first reaction of the oxidative branch of the pentose phosphate pathway is irreversible, and is the rate limiting reaction for the entire pentose phosphate pathway |CITS:[12047390]|. Although Zwf1p expression in yeast is essentially constitutive |CITS:[16179340]|, Zwf1p activity is inhibited by NADPH and stimulated by processes that decrease the cytosolic levels of NADPH |CITS:[ 3277619]|. ' name: pentose phosphate pathway (oxidative branch) I pmids: - '1328471' - '15454531' - '2269430' reactions: - ec: - 3.1.1.31 genes: - *id259 - *id260 left: - 6-phospho D-glucono-1,5-lactone - H2O name: 6-phospho D-glucono-1,5-lactone + H2O -> D-gluconate 6-phosphate + H+ pmids: [] rhea: [] right: - D-gluconate 6-phosphate - H+ yeastcyc_id: 6PGLUCONOLACT-RXN - ec: - 1.1.1.44 genes: [] left: - D-gluconate 6-phosphate - NADP+ name: D-gluconate 6-phosphate + NADP+ -> D-ribulose 5-phosphate + CO2 + NADPH pmids: [] rhea: [] right: - CO2 - D-ribulose 5-phosphate - NADPH yeastcyc_id: RXN-9952 - ec: - 1.1.1.49 genes: - *id261 left: - D-glucopyranose 6-phosphate - NADP+ name: D-glucopyranose 6-phosphate + NADP+ -> 6-phospho D-glucono-1,5-lactone + NADPH + H+ pmids: [] rhea: [] right: - 6-phospho D-glucono-1,5-lactone - H+ - NADPH yeastcyc_id: GLU6PDEHYDROG-RXN yeastcyc_id: OXIDATIVEPENT-PWY P4-PWY-1: all_genes: - *id059 - *id060 - *id232 - *id231 - *id233 - &id264 orf: YLR303W symbol: MET17 uniprot: UniProtKB:P06106 - &id263 orf: YNL277W symbol: MET2 uniprot: UniProtKB:P08465 - &id262 orf: YER091C symbol: MET6 uniprot: UniProtKB:P05694 - &id265 orf: YOR241W symbol: MET7 uniprot: UniProtKB:Q08645 - *id229 - *id230 comment: 'The biosynthesis of threonine and methionine in S. cerevisiae begins in a common three-step pathway that converts aspartate to homoserine. HOM3 and HOM2, which encode the enzymes responsible for the first and second steps of this pathway respectively, are regulated by Gcn4p under the general control of amino acid biosynthesis. Additionally, threonine represses HOM3 and competitively inhibits homoserine dehydrogenase (encoded by HOM6), lending that the flow of carbon into the common pathway is primarily regulated by threonine. The Hom3p, Hom2p, and Hom6p-catalyzed reactions yield homoserine, at which point the threonine and methionine pathways diverge. Phosphorylation of homoserine by homoserine kinase (encoded by THR1) directs homoserine towards the biosynthesis of threonine, whereas acetylation by homoserine O-transacetylase (encoded by MET2) commits homoserine to the biosynthesis of sulfur amino acids. If homoserine is phosphorylated by homoserine kinase (Thr1p), threonine synthase (Thr4p) can subsequently catalyze its conversion to threonine. THR1 and THR4 are both transcriptionally regulated by general control of amino acid biosynthesis. Like Hom3p and Hom6p, homoserine kinase is also subject to feedback inhibition by threonine. If homoserine is acetylated by homoserine O-transacetylase (Met2p), it can enter one of two routes to be converted to homocysteine, the immediate precursor to methionine. In the first route, homocysteine is synthesized from the direct incorporation of sufide into O-acetylhomoserine via Met17p. In the second route, O-acetylhomoserine is condensed with cysteine via the transsulfuration pathway and subsequently cleaved, yielding homocysteine and pyruvate. Homocysteine can then accept a methyl group from a 1C unit-carrying derivative of tetrahydrofolate via Met6p to form methionine. When yeast cells are grown in methionine, synthesis of enzymes required for sulfate assimilation (which provides sulfide for homocysteine production) as well as methionine biosynthesis is repressed. Activation of most genes involved in the sulfur metabolic network (MET genes) requires the transcriptional activator Met4p. The activity of Met4p is regulated in response to the sulfur status of the cell, with cysteine levels serving as the major regulatory signal. References: |CITS:[(JONES)]||CITS: [(HINNEBUSCH)]||CITS: [22419079]||CITS: [9409150]||CITS: [5764336]|' name: superpathway of threonine and methionine biosynthesis pmids: [] reactions: - ec: - 2.6.1.1 genes: - *id059 - *id060 left: - 2-oxoglutarate - L-aspartate name: 2-oxoglutarate + L-aspartate <-> oxaloacetate + L-glutamate pmids: [] rhea: [] right: - L-glutamate - oxaloacetate yeastcyc_id: ASPAMINOTRANS-RXN - ec: - 2.7.2.4 genes: - *id231 left: - ATP - L-aspartate name: L-aspartate + ATP -> L-aspartyl-4-phosphate + ADP pmids: [] rhea: [] right: - ADP - L-aspartyl-4-phosphate yeastcyc_id: ASPARTATEKIN-RXN - ec: - 1.2.1.11 genes: - *id232 left: - L-aspartate 4-semialdehyde - NADP+ - phosphate name: L-aspartate 4-semialdehyde + NADP+ + phosphate <- L-aspartyl-4-phosphate + NADPH + H+ pmids: [] rhea: [] right: - H+ - L-aspartyl-4-phosphate - NADPH yeastcyc_id: ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN - ec: - 2.1.1.14 genes: - *id262 left: - 5-methyltetrahydropteroyl tri-L-glutamate - L-homocysteine name: L-homocysteine + 5-methyltetrahydropteroyl tri-L-glutamate <-> L-methionine + tetrahydropteroyl tri-L-glutamate pmids: [] rhea: [] right: - L-methionine - tetrahydropteroyl tri-L-glutamate yeastcyc_id: HOMOCYSMET-RXN - ec: - 2.7.1.39 genes: - *id229 left: - ATP - L-homoserine name: L-homoserine + ATP -> O-phospho-L-homoserine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - O-phospho-L-homoserine yeastcyc_id: HOMOSERKIN-RXN - ec: - 1.1.1.3 genes: - *id233 left: - L-homoserine - NAD(P)+ name: L-homoserine + NAD(P)+ <- L-aspartate 4-semialdehyde + NAD(P)H + H+ pmids: [] rhea: [] right: - H+ - L-aspartate 4-semialdehyde - NAD(P)H yeastcyc_id: HOMOSERDEHYDROG-RXN - ec: - 2.3.1.31 genes: - *id263 left: - L-homoserine - acetyl-CoA name: L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A pmids: [] rhea: [] right: - O-acetyl-L-homoserine - coenzyme A yeastcyc_id: HOMOSERINE-O-ACETYLTRANSFERASE-RXN - ec: - 2.5.1.49 genes: - *id264 left: - O-acetyl-L-homoserine - hydrogen sulfide name: O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H+ pmids: [] rhea: [] right: - H+ - L-homocysteine - acetate yeastcyc_id: ACETYLHOMOSER-CYS-RXN - ec: - 4.2.3.1 genes: - *id230 left: - H2O - O-phospho-L-homoserine name: O-phospho-L-homoserine + H2O -> L-threonine + phosphate pmids: [] rhea: [] right: - L-threonine - phosphate yeastcyc_id: THRESYN-RXN - ec: - 6.3.2.17 genes: - *id265 left: - ATP - L-glutamate - a 5-methyltetrahydrofolate name: a 5-methyltetrahydrofolate + L-glutamate + ATP -> a 5-methyltetrahydrofolate + ADP + phosphate pmids: [] rhea: [] right: - ADP - a 5-methyltetrahydrofolate - phosphate yeastcyc_id: RXN3O-22 yeastcyc_id: P4-PWY-1 PANTOSYN2-PWY: all_genes: - *id155 - &id273 orf: YMR169C symbol: ALD3 uniprot: UniProtKB:P54114 - &id271 orf: YDR531W symbol: CAB1 uniprot: UniProtKB:Q04430 - &id266 orf: YIL083C symbol: CAB2 uniprot: UniProtKB:P40506 - &id267 orf: YKL088W symbol: CAB3 uniprot: UniProtKB:P36076 - &id274 orf: YGR277C symbol: CAB4 uniprot: UniProtKB:P53332 - &id272 orf: YDR196C symbol: CAB5 uniprot: UniProtKB:Q03941 - &id275 orf: YBR176W symbol: ECM31 uniprot: UniProtKB:P38122 - &id276 orf: YMR020W symbol: FMS1 uniprot: UniProtKB:P50264 - &id270 orf: YHR063C symbol: PAN5 uniprot: UniProtKB:P38787 - &id277 orf: YIL145C symbol: PAN6 uniprot: UniProtKB:P40459 - &id268 orf: YKR072C symbol: SIS2 uniprot: UniProtKB:P36024 - &id269 orf: YOR054C symbol: VHS3 uniprot: UniProtKB:Q08438 comment: 'Pantothenate (vitamin B5) is a metabolic precursor to the essential cofactor coenzyme A. It is synthesized de novo in plants, eubacteria, archaea, and many fungi, but not in animals who instead must acquire it from the environment. S. cerevisiae is able to synthesize pantothenate de novo, however some laboratory strains still require pantothenate supplementation in order to achieve optimal growth. Synthesis of pantothenate requires two precursors: pantoate and -alanine. The source of -alanine for this pathway varies by organism; whereas bacteria produce -alanine in one-step via the decarboxylation of aspartate, S. cerevisiae derives -alanine in two steps from spermine, a polyamine produced in the methionine salvage pathway. In the S. cerevisiae route, spermine is oxidized by amine oxidase (Fms1p) to form 3-aminopropanal, which is subsequently converted to -alanine by an aldehyde dehydrogenase (Ald2p or Ald3p). Pantoate is synthesized from 2-ketoisovalerate (2-KIV), an intermediate in the biosynthesis of branched-chain amino acids. This occurs in two steps in S. cerevisiae: hydroxymethylation of 2-KIV via Ecm31p to form ketopantoate, and reduction of ketopantoate to pantoate via Pan5p. After its production, pantoate can be condensed with -alanine in a reaction catalyzed by pantothenate synthetase (Pan6p) to form pantothenate. Pantothenate may then go on to react with cysteine and ATP in a five-step pathway leading up to the synthesis of coenzyme A. References: |CITS:[15565250]||CITS: [11154694]||CITS: [10373490]||CITS: [12586697]|' name: pantothenate and coenzyme A biosynthesis pmids: - '11154694' reactions: - ec: - 6.3.2.5 genes: - *id266 left: - (R)-4'-phosphopantothenate - CTP - L-cysteine name: (R)-4'-phosphopantothenate + L-cysteine + CTP -> (R)-4'-phosphopantothenoyl-L-cysteine + CMP + diphosphate + H+ pmids: [] rhea: [] right: - (R)-4'-phosphopantothenoyl-L-cysteine - CMP - H+ - diphosphate yeastcyc_id: P-PANTOCYSLIG-RXN - ec: - 4.1.1.36 genes: - *id267 - *id268 - *id269 left: - (R)-4'-phosphopantothenoyl-L-cysteine - H+ name: (R)-4'-phosphopantothenoyl-L-cysteine + H+ -> 4'-phosphopantetheine + CO2 pmids: [] rhea: [] right: - 4'-phosphopantetheine - CO2 yeastcyc_id: P-PANTOCYSDECARB-RXN - ec: - 1.1.1.169 genes: - *id270 left: - (R)-pantoate - NADP+ name: (R)-pantoate + NADP+ <- 2-dehydropantoate + NADPH + H+ pmids: [] rhea: [] right: - 2-dehydropantoate - H+ - NADPH yeastcyc_id: 2-DEHYDROPANTOATE-REDUCT-RXN - ec: - 2.7.1.33 genes: - *id271 left: - (R)-pantothenate - ATP name: (R)-pantothenate + ATP -> (R)-4'-phosphopantothenate + ADP + H+ pmids: [] rhea: [] right: - (R)-4'-phosphopantothenate - ADP - H+ yeastcyc_id: PANTOTHENATE-KIN-RXN - ec: - 2.7.1.24 genes: - *id272 left: - 3'-dephospho-CoA - ATP name: 3'-dephospho-CoA + ATP -> ADP + coenzyme A + H+ pmids: [] rhea: [] right: - ADP - H+ - coenzyme A yeastcyc_id: DEPHOSPHOCOAKIN-RXN - ec: - 1.2.1.3 genes: - *id155 - *id273 left: - 3-aminopropanal - H2O - NAD+ name: 3-aminopropanal + NAD+ + H2O -> β-alanine + NADH pmids: [] rhea: [] right: - NADH - β-alanine yeastcyc_id: 3-PROPANAL-DEHYDROGENASE-RXN - ec: - 2.7.7.3 genes: - *id274 left: - 4'-phosphopantetheine - ATP - H+ name: 4'-phosphopantetheine + ATP + H+ -> 3'-dephospho-CoA + diphosphate pmids: [] rhea: [] right: - 3'-dephospho-CoA - diphosphate yeastcyc_id: PANTEPADENYLYLTRAN-RXN - ec: - 2.1.2.11 genes: - *id275 left: - 3-methyl-2-oxobutanoate - H2O - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate + H2O -> 2-dehydropantoate + a tetrahydrofolate pmids: [] rhea: [] right: - 2-dehydropantoate - a tetrahydrofolate yeastcyc_id: 3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN - ec: - 1.5.3.16 - 1.5.3.17 genes: - *id276 left: - H2O - oxygen - spermine name: spermine + oxygen + H2O -> spermidine + 3-aminopropanal + hydrogen peroxide pmids: [] rhea: [] right: - 3-aminopropanal - hydrogen peroxide - spermidine yeastcyc_id: RXN-9015 - ec: - 6.3.2.1 genes: - *id277 left: - (R)-pantoate - ATP - β-alanine name: β-alanine + (R)-pantoate + ATP -> (R)-pantothenate + AMP + diphosphate + H+ pmids: [] rhea: [] right: - (R)-pantothenate - AMP - H+ - diphosphate yeastcyc_id: PANTOATE-BETA-ALANINE-LIG-RXN yeastcyc_id: PANTOSYN2-PWY PENTOSE-P-PWY: all_genes: - *id255 - *id256 - *id259 - *id260 - *id258 - *id254 - *id257 - *id261 comment: 'The pentose phosphate pathway is important for generating NADPH, which is a source of reducing energy, as well as a variety of sugar molecules that are required for the biosynthesis of nucleic acids and amino acids. |CITS:[8929392]||CITS:[8910528]||CITS:[9813062]||CITS:[ 11298766]||CITS:[1628611]||CITS:[15960801]||CITS:[7916691]||CITS:[14690456]|. This pathway is also important for protecting yeast from oxidative stress, since NADPH is an essential cofactor for glutathione- and thioredoxin-dependent enzymes that defend cells against oxidative damage |CITS:[8929392]||CITS:[8910528]||CITS:[11557322]||CITS:[16179340]|. The pentose phosphate pathway is of industrial interest for the fermentation of xylose to ethanol |CITS:[11916674]|. Xylose is the predominant sugar found in biomass such as agricultural wastes, wood, municipal solid wastes, and wastes from pulp and paper industries, and possibly could serve as a low-cost and abundant raw material for fuel ethanol production |CITS:[8534086]|. Saccharomyces cerevisiae does not naturally metabolize xylose, but recombinant S. cerevisiae strains containing the xylose reductase and xylitol dehydrogenase genes from Pichia stipitis are able to metabolize xylose via the pentose phosphate pathway |CITS:[15630585]||CITS:[8534086]|. Changes in the levels of enzymes in the pentose phosphate pathway effect the fitness, ethanol production, and amount of xylose metabolized by these recombinant xylose-utilizing strains. The pentose phosphate pathway is also of medical interest because mutations in the human homologs of some yeast pentose phosphate genes are associated with a variety of diseases. Zwf1p is homologus to human glucose-6-phosphate dehydrogenase (G6PD), which has been implicated in neonatal jaundice and haemolytic anemia. Sol3p and Sol4p have similarity to human PGLS, which is associated with 6- phosphogluconolactonase deficiency and may contribute to some forms of G6PD-associated hemolytic anemia |CITS:[10518023]|. Sol3p and Sol4p also have similarity to human H6PD, which is associated with cortisone reductase deficiency |CITS:[10518023]|. Gnd1p and Gnd2p have similarity to human PGD, mutation in which may also contribute to some forms of G6PD-associated hemolytic anemia |CITS:[10518023]|. Tal1p is similar to human TALDO1, mutation in which has been reported to be associated with transaldolase deficiency and hepatosplenomegaly |CITS:[ 8300619]|. Rki1p has similarity to human RPIA, which has been associated with ribose 5-phosphate isomerase deficiency, leukoencephalopathy and peripheral neuropathy |CITS:[16054529]|. ' name: pentose phosphate pathway pmids: [] reactions: - ec: - 3.1.1.31 genes: - *id259 - *id260 left: - 6-phospho D-glucono-1,5-lactone - H2O name: 6-phospho D-glucono-1,5-lactone + H2O -> D-gluconate 6-phosphate + H+ pmids: [] rhea: [] right: - D-gluconate 6-phosphate - H+ yeastcyc_id: 6PGLUCONOLACT-RXN - ec: - 2.2.1.1 genes: - *id254 left: - D-erythrose 4-phosphate - D-xylulose 5-phosphate name: D-erythrose 4-phosphate + D-xylulose 5-phosphate <-> β-D-fructofuranose 6-phosphate + D-glyceraldehyde 3-phosphate pmids: [] rhea: [] right: - D-glyceraldehyde 3-phosphate - β-D-fructofuranose 6-phosphate yeastcyc_id: 2TRANSKETO-RXN - ec: - 1.1.1.44 genes: [] left: - D-gluconate 6-phosphate - NADP+ name: D-gluconate 6-phosphate + NADP+ -> D-ribulose 5-phosphate + CO2 + NADPH pmids: [] rhea: [] right: - CO2 - D-ribulose 5-phosphate - NADPH yeastcyc_id: RXN-9952 - ec: - 1.1.1.49 genes: - *id261 left: - D-glucopyranose 6-phosphate - NADP+ name: D-glucopyranose 6-phosphate + NADP+ -> 6-phospho D-glucono-1,5-lactone + NADPH + H+ pmids: [] rhea: [] right: - 6-phospho D-glucono-1,5-lactone - H+ - NADPH yeastcyc_id: GLU6PDEHYDROG-RXN - ec: - 5.3.1.6 genes: - *id255 left: - D-ribose 5-phosphate name: D-ribose 5-phosphate <-> D-ribulose 5-phosphate pmids: [] rhea: [] right: - D-ribulose 5-phosphate yeastcyc_id: RIB5PISOM-RXN - ec: - 5.1.3.1 genes: - *id256 left: - D-ribulose 5-phosphate name: D-ribulose 5-phosphate <-> D-xylulose 5-phosphate pmids: [] rhea: [] right: - D-xylulose 5-phosphate yeastcyc_id: RIBULP3EPIM-RXN - ec: - 2.2.1.1 genes: - *id254 - *id257 left: - D-glyceraldehyde 3-phosphate - D-sedoheptulose 7-phosphate name: D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate <-> D-ribose 5-phosphate + D-xylulose 5-phosphate pmids: [] rhea: [] right: - D-ribose 5-phosphate - D-xylulose 5-phosphate yeastcyc_id: 1TRANSKETO-RXN - ec: - 2.2.1.2 genes: - *id258 left: - D-glyceraldehyde 3-phosphate - D-sedoheptulose 7-phosphate name: D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate <-> β-D-fructofuranose 6-phosphate + D-erythrose 4-phosphate pmids: [] rhea: [] right: - D-erythrose 4-phosphate - β-D-fructofuranose 6-phosphate yeastcyc_id: TRANSALDOL-RXN yeastcyc_id: PENTOSE-P-PWY PERIPLASMA-NAD-DEGRADATION: all_genes: - &id278 orf: YGL067W symbol: NPY1 uniprot: UniProtKB:P53164 comment: 'In some organisms, the metabolism of extracellular nicotinamide adenine dinucleotide (NAD+) plays an important role in purine salvage and uptake. In humans, for instance, extracellular NAD+ generated via cell lysis or other means can be salvaged for adenine through the following steps: 1) cleavage of NAD+ to AMP and nicotinamide mononucleotide (NMN) by NAD+ pyrophosphatase, 2) cleavage of AMP to release adenosine via 5-nucleotidase, 3) transport of extracellular adenosine into the cell via adenosine transporters, and 4) regeneration of adenine nucleotides from adenosine via phosphorylation. This process has been implicated human immune cell activation. Extracellular metabolism of NMN, but not NAD+, is known to occur in S. cerevisiae. This occurs via Pho5p, the major secreted acid phosphatase in yeast. Pho5p catalyzes the conversion of exogenous NMN in the periplasm to nicotinamide riboside (NR), a NAD+ precursor that can be imported into the cell and converted back to NAD+ via salvage pathways. Deletion of PHO5 prevents growth of a mutant disrupted in the NAD+ biosynthesis pathway on medium containing NMN. In addition to Pho5p, two other enzymes are known to play a role in catabolizing extracellular nucleotides in S. cerevisiae: the nucleotide pyrophosphatases/phosphodiesterases Npp1p and Npp2p. Both yeast enzymes belong to a superfamily of alkaline phosphatases that also includes extracellular 5-nucleotidases from mammals. References: |CITS: [BOGAN2010]||CITS: [19416965]||CITS: [16278456]|' name: periplasmic NAD degradation pmids: - '16278456' - '19416965' reactions: - ec: - 3.1.3.5 genes: [] left: - AMP - H2O name: AMP + H2O -> adenosine + phosphate pmids: [] rhea: [] right: - adenosine - phosphate yeastcyc_id: AMP-DEPHOSPHORYLATION-RXN - ec: - 3.6.1.22 genes: - *id278 left: - H2O - NAD+ name: NAD+ + H2O -> AMP + β-nicotinamide D-ribonucleotide + 2 H+ pmids: [] rhea: [] right: - AMP - H+ - β-nicotinamide D-ribonucleotide yeastcyc_id: NADPYROPHOSPHAT-RXN yeastcyc_id: PERIPLASMA-NAD-DEGRADATION PHOS-PWY: all_genes: - &id280 orf: YBR029C symbol: CDS1 uniprot: UniProtKB:P38221 - &id289 orf: YER026C symbol: CHO1 uniprot: UniProtKB:P08456 - &id284 orf: YGR157W symbol: CHO2 uniprot: UniProtKB:P05374 - &id292 orf: YLR133W symbol: CKI1 uniprot: UniProtKB:P20485 - &id285 orf: YNL130C symbol: CPT1 uniprot: UniProtKB:P17898 - &id279 orf: YDL142C symbol: CRD1 uniprot: UniProtKB:Q07560 - &id282 orf: YGR007W symbol: ECT1 uniprot: UniProtKB:P33412 - &id293 orf: YDR147W symbol: EKI1 uniprot: UniProtKB:Q03764 - &id286 orf: YHR123W symbol: EPT1 uniprot: UniProtKB:P22140 - &id283 orf: YJR073C symbol: OPI3 uniprot: UniProtKB:P05375 - &id281 orf: YGR202C symbol: PCT1 uniprot: UniProtKB:P13259 - &id291 orf: YCL004W symbol: PGS1 uniprot: UniProtKB:P25578 - &id290 orf: YPR113W symbol: PIS1 uniprot: UniProtKB:P06197 - &id287 orf: YNL169C symbol: PSD1 uniprot: UniProtKB:P39006 - &id288 orf: YGR170W symbol: PSD2 uniprot: UniProtKB:P53037 comment: 'Phospholipids are amphipathic molecules that consist of a glycerol backbone esterified to a phosphate group and two fatty acids. As a primary structural element of biological membranes, phospholipids play important roles in cell morphology and organelle function. The major phospholipids found in total cell extracts from S. cerevisiae are phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), and phosphatidylserine (PS); however, the phospholipid composition of yeast changes according to the carbon source used for growth. All major phospholipid classes in S. cerevisiae may trace their synthesis to a common precursor: cytidine diphosphate diacylglycerol (CDP-DAG). CDP-DAG is synthesized in a reaction catalyzed by CDP-DAG synthase, which converts phosphatidic acid (PA) to CDP-DAG using cytidine triphosphate (CTP) as the CDP donor. There are two distinct CDP-DAG synthases in S. cerevisiae: Cds1p, localized in the endoplasmic reticulum (ER), and Tam41p, localized in the mitochondrial matrix. In the ER, CDP-DAG generated by Cds1p can be converted to phosphatidylinositol (PI) or phosphatidylserine (PS) via PI synthase (Pis1p) or PS synthase (Cho1p), respectively. In the mitochondrion, CDP-DAG generated by Tam41p can be sequentially converted to phosphatidylglycerol (PG), which can be further converted to cardiolipin. Synthesis of PI, PG, and cardiolipin occurs through similar mechanisms in mammalian cells; however, unlike yeast, mammals primarily synthesize PS from other phospholipids and not from CDP-DAG. PS generated via Pis1p may undergo further processing in the mitochondria, where the enzyme PS decarboxylase (Psd1p) can convert it to phosphatidylethanolamine (PE). This represents the major route of PE synthesis in S. cerevisiae. The second route occurs via the CDP-ethanolamine branch of the Kennedy pathway. This pathway consists of three steps: 1) phosphorylation of ethanolamine to phosphoethanolamine by ethanolamine kinase (Eki1p) or choline kinase (Cki1p), 2) activation of phosphoethanolamine to CDP-ethanolamine by phosphoethanolamine cytidylyltransferase (Ect1p), and 3) transfer of a phosphoethanolamine moiety from CDP-ethanolamine to diacylglycerol by 1,2-diacylglycerol ethanolaminephosphotransferase (Ept1p). The other branch of the Kennedy pathway, the CDP-choline pathway, incorporates choline into phosphatidylcholine (PC) in three analogous steps. PC may also be synthesized from PE when the latter molecule undergoes three successive methylations by Cho2p and Opi3p. References: |CITS: [9885152]||CITS: [24520995]||CITS: [24866973]|' name: superpathway of phosphatidic acid and phospholipid biosynthesis pmids: - '24520995' - '24866973' - '9885152' reactions: - ec: - 3.1.3.27 genes: [] left: - 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate - H2O name: 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate + H2O -> an L-1-phosphatidyl-sn-glycerol + phosphate pmids: [] rhea: [] right: - an L-1-phosphatidyl-sn-glycerol - phosphate yeastcyc_id: PGPPHOSPHA-RXN - ec: - 2.7.8.- genes: - *id279 left: - an L-1-phosphatidyl-sn-glycerol name: 2 an L-1-phosphatidyl-sn-glycerol -> a cardiolipin + glycerol pmids: [] rhea: [] right: - a cardiolipin - glycerol yeastcyc_id: CARDIOLIPSYN-RXN - ec: - 2.7.7.41 genes: - *id280 left: - CTP - H+ - a 1,2-diacyl-sn-glycerol 3-phosphate name: CTP + a 1,2-diacyl-sn-glycerol 3-phosphate + H+ -> a CDP-diacylglycerol + diphosphate pmids: [] rhea: [] right: - a CDP-diacylglycerol - diphosphate yeastcyc_id: CDPDIGLYSYN-RXN - ec: - 2.7.7.15 genes: - *id281 left: - CTP - H+ - phosphocholine name: CTP + phosphocholine + H+ -> CDP-choline + diphosphate pmids: [] rhea: [] right: - CDP-choline - diphosphate yeastcyc_id: 2.7.7.15-RXN - ec: - 2.7.7.14 genes: - *id282 left: - CTP - H+ - O-phosphoethanolamine name: O-phosphoethanolamine + CTP + H+ -> CDP-ethanolamine + diphosphate pmids: - '16807089' - '8982874' rhea: [] right: - CDP-ethanolamine - diphosphate yeastcyc_id: 2.7.7.14-RXN - ec: - 2.1.1.71 genes: - *id283 left: - S-adenosyl-L-methionine - a phosphatidyl-N-dimethylethanolamine name: S-adenosyl-L-methionine + a phosphatidyl-N-dimethylethanolamine -> a phosphatidylcholine + S-adenosyl-L-homocysteine pmids: [] rhea: [] right: - S-adenosyl-L-homocysteine - a phosphatidylcholine yeastcyc_id: RXN3O-349 - ec: - 2.1.1.71 genes: - *id283 left: - S-adenosyl-L-methionine - a phosphatidyl-N-dimethylethanolamine name: S-adenosyl-L-methionine + a phosphatidyl-N-dimethylethanolamine -> a phosphatidylcholine + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a phosphatidylcholine yeastcyc_id: RXN4FS-2 - ec: - 2.1.1.71 genes: - *id283 left: - S-adenosyl-L-methionine - a phosphatidyl-N-methylethanolamine name: S-adenosyl-L-methionine + a phosphatidyl-N-methylethanolamine -> a phosphatidyl-N-dimethylethanolamine + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a phosphatidyl-N-dimethylethanolamine yeastcyc_id: 2.1.1.71-RXN - ec: - 2.1.1.17 genes: - *id284 left: - S-adenosyl-L-methionine - an L-1-phosphatidylethanolamine name: S-adenosyl-L-methionine + an L-1-phosphatidylethanolamine -> a phosphatidyl-N-methylethanolamine + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a phosphatidyl-N-methylethanolamine yeastcyc_id: 2.1.1.17-RXN - ec: - 2.7.8.2 genes: - *id285 left: - CDP-choline - a 1,2-diacyl-sn-glycerol name: a 1,2-diacyl-sn-glycerol + CDP-choline <-> a phosphatidylcholine + CMP + H+ pmids: [] rhea: [] right: - CMP - H+ - a phosphatidylcholine yeastcyc_id: RXN-5781 - ec: - 2.7.8.1 genes: - *id286 left: - CDP-ethanolamine - a 1,2-diacyl-sn-glycerol name: a 1,2-diacyl-sn-glycerol + CDP-ethanolamine -> an L-1-phosphatidylethanolamine + CMP + H+ pmids: - '16807089' - '2848840' rhea: [] right: - CMP - H+ - an L-1-phosphatidylethanolamine yeastcyc_id: ETHANOLAMINEPHOSPHOTRANSFERASE-RXN - ec: - 4.1.1.65 genes: - *id287 - *id288 left: - H+ - a 3-O-sn-phosphatidyl-L-serine name: a 3-O-sn-phosphatidyl-L-serine + H+ -> an L-1-phosphatidylethanolamine + CO2 pmids: [] rhea: [] right: - CO2 - an L-1-phosphatidylethanolamine yeastcyc_id: PHOSPHASERDECARB-RXN - ec: - 2.7.8.8 genes: - *id289 left: - L-serine - a CDP-diacylglycerol name: a CDP-diacylglycerol + L-serine <-> CMP + a 3-O-sn-phosphatidyl-L-serine + H+ pmids: [] rhea: [] right: - CMP - H+ - a 3-O-sn-phosphatidyl-L-serine yeastcyc_id: PHOSPHASERSYN-RXN - ec: - 2.7.8.11 genes: - *id290 left: - a CDP-diacylglycerol - myo-inositol name: a CDP-diacylglycerol + myo-inositol -> a 1-phosphatidyl-1D-myo-inositol + CMP + H+ pmids: [] rhea: [] right: - CMP - H+ - a 1-phosphatidyl-1D-myo-inositol yeastcyc_id: 2.7.8.11-RXN - ec: - 2.7.8.5 genes: - *id291 left: - a CDP-diacylglycerol - sn-glycerol 3-phosphate name: a CDP-diacylglycerol + sn-glycerol 3-phosphate -> CMP + 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate + H+ pmids: [] rhea: [] right: - 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate - CMP - H+ yeastcyc_id: PHOSPHAGLYPSYN-RXN - ec: - 2.7.1.32 genes: - *id292 left: - ATP - choline name: choline + ATP -> phosphocholine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - phosphocholine yeastcyc_id: CHOLINE-KINASE-RXN - ec: - 2.7.1.82 genes: - *id293 left: - ATP - ethanolamine name: ethanolamine + ATP -> O-phosphoethanolamine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - O-phosphoethanolamine yeastcyc_id: ETHANOLAMINE-KINASE-RXN yeastcyc_id: PHOS-PWY PHOSLIPSYN2-PWY-1: all_genes: - *id289 - *id284 - *id279 - *id283 - *id291 - *id287 - *id288 name: phospholipid biosynthesis pmids: - '16807089' reactions: - ec: - 3.1.3.27 genes: [] left: - 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate - H2O name: 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate + H2O -> an L-1-phosphatidyl-sn-glycerol + phosphate pmids: [] rhea: [] right: - an L-1-phosphatidyl-sn-glycerol - phosphate yeastcyc_id: PGPPHOSPHA-RXN - ec: - 2.7.8.- genes: - *id279 left: - an L-1-phosphatidyl-sn-glycerol name: 2 an L-1-phosphatidyl-sn-glycerol -> a cardiolipin + glycerol pmids: [] rhea: [] right: - a cardiolipin - glycerol yeastcyc_id: CARDIOLIPSYN-RXN - ec: - 2.1.1.71 genes: - *id283 left: - S-adenosyl-L-methionine - a phosphatidyl-N-dimethylethanolamine name: S-adenosyl-L-methionine + a phosphatidyl-N-dimethylethanolamine -> a phosphatidylcholine + S-adenosyl-L-homocysteine pmids: [] rhea: [] right: - S-adenosyl-L-homocysteine - a phosphatidylcholine yeastcyc_id: RXN3O-349 - ec: - 2.1.1.71 genes: - *id283 left: - S-adenosyl-L-methionine - a phosphatidyl-N-methylethanolamine name: S-adenosyl-L-methionine + a phosphatidyl-N-methylethanolamine -> a phosphatidyl-N-dimethylethanolamine + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a phosphatidyl-N-dimethylethanolamine yeastcyc_id: 2.1.1.71-RXN - ec: - 2.1.1.17 genes: - *id284 left: - S-adenosyl-L-methionine - an L-1-phosphatidylethanolamine name: S-adenosyl-L-methionine + an L-1-phosphatidylethanolamine -> a phosphatidyl-N-methylethanolamine + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a phosphatidyl-N-methylethanolamine yeastcyc_id: 2.1.1.17-RXN - ec: - 4.1.1.65 genes: - *id287 - *id288 left: - H+ - a 3-O-sn-phosphatidyl-L-serine name: a 3-O-sn-phosphatidyl-L-serine + H+ -> an L-1-phosphatidylethanolamine + CO2 pmids: [] rhea: [] right: - CO2 - an L-1-phosphatidylethanolamine yeastcyc_id: PHOSPHASERDECARB-RXN - ec: - 2.7.8.8 genes: - *id289 left: - L-serine - a CDP-diacylglycerol name: a CDP-diacylglycerol + L-serine <-> CMP + a 3-O-sn-phosphatidyl-L-serine + H+ pmids: [] rhea: [] right: - CMP - H+ - a 3-O-sn-phosphatidyl-L-serine yeastcyc_id: PHOSPHASERSYN-RXN - ec: - 2.7.8.5 genes: - *id291 left: - a CDP-diacylglycerol - sn-glycerol 3-phosphate name: a CDP-diacylglycerol + sn-glycerol 3-phosphate -> CMP + 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate + H+ pmids: [] rhea: [] right: - 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate - CMP - H+ yeastcyc_id: PHOSPHAGLYPSYN-RXN yeastcyc_id: PHOSLIPSYN2-PWY-1 PLPSAL-PWY: all_genes: - &id294 orf: YEL029C symbol: BUD16 uniprot: UniProtKB:P39988 - &id295 orf: YBR035C symbol: PDX3 uniprot: UniProtKB:P38075 comment: 'Pyridoxal phosphate (PLP) is the active form of vitamin B6 and is a cofactor in many reactions of amino acid metabolism. Pyridoxine (PN), pyridoxamine (PM), pyridoxal (PL), pyridoxine 5''-phosphate (PNP) and pyridoxamine 5''-phosphate (PMP) are all forms of vitamin B6 that can be converted to PLP via the PLP salvage pathway. Most unicellular organisms and plants can synthesize PLP, whereas mammals cannot and require vitamin B6 in their diet. Thus far, three PLP biosynthetic pathways have been characterized: the de novo PLP biosynthesis pathway as characterized in Escherichia coli |CITS: [12686115]|, the de novo PLP biosynthesis pathway as being studied in fungi |CITS: [15483325],[14764090]|, and the PLP salvage pathway |CITS: [15483325], [17696614],[8764513],[9537380]|. Saccharomyces cerevisiae synthesize PLP via the fungal type de novo PLP synthesis pathway and the PLP salvage pathway |CITS: [7896706], [17696614], [15483325], [14764090]|. Extracellular PN, PL and PM are transported into the cell by Tpn1p, a member of the purine-cytosine permease family |CITS: [12649274]|.' name: pyridoxal 5'-phosphate salvage I pmids: - '15483325' - '17696614' reactions: - ec: - 2.7.1.35 genes: - *id294 left: - ATP - pyridoxal name: ATP + pyridoxal -> pyridoxal 5'-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - pyridoxal 5'-phosphate yeastcyc_id: PYRIDOXKIN-RXN - ec: - 2.7.1.35 genes: - *id294 left: - ATP - pyridoxamine name: ATP + pyridoxamine -> ADP + pyridoxamine 5'-phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - pyridoxamine 5'-phosphate yeastcyc_id: PYRAMKIN-RXN - ec: - 2.7.1.35 genes: - *id294 left: - ATP - pyridoxine name: ATP + pyridoxine -> ADP + pyridoxine 5'-phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - pyridoxine 5'-phosphate yeastcyc_id: PNKIN-RXN - ec: - 1.4.3.5 genes: - *id295 left: - H2O - oxygen - pyridoxamine 5'-phosphate name: pyridoxamine 5'-phosphate + oxygen + H2O -> ammonium + hydrogen peroxide + pyridoxal 5'-phosphate pmids: [] rhea: [] right: - ammonium - hydrogen peroxide - pyridoxal 5'-phosphate yeastcyc_id: PMPOXI-RXN - ec: - 1.4.3.5 genes: - *id295 left: - oxygen - pyridoxine 5'-phosphate name: pyridoxine 5'-phosphate + oxygen -> hydrogen peroxide + pyridoxal 5'-phosphate pmids: [] rhea: [] right: - hydrogen peroxide - pyridoxal 5'-phosphate yeastcyc_id: PNPOXI-RXN yeastcyc_id: PLPSAL-PWY POLYAMSYN-YEAST-PWY: all_genes: - &id296 orf: YKL184W symbol: SPE1 uniprot: UniProtKB:P08432 - *id047 - *id083 - *id048 comment: 'Polyamines are low molecular weight aliphatic cations present in all types of living organisms. They are essential in all eukaryotes and likely essential in archaea, while in bacteria their requirement for growth varies. Polyamines are known to be involved in several biological processes, including post-translational modification of eIF5A in eukaryotes and biofilm formation in some bacteria. However, their role in the cell is not completely understood. The most common polyamines are putrescine, spermidine, and spermine. In S. cerevisiae, the biosynthesis of putrescine, spermidine, and spermine begins with two intermediates from amino acid metabolism: ornithine, an intermediate of arginine biosynthesis and degradation, and S-adenosylmethionine (AdoMet), a metabolite of methionine and a ubiquitous methyl group donor for many biological reactions. At the start of the pathway, ornithine is decarboxylated to putrescine by ornithine decarboxylase (Spe1p) while S-adenosylmethionine decarboxylase (Spe2p) decarboxylates AdoMet. Spermidine synthase (Spe3p) then catalyzes the transfer of an aminopropyl group from decarboxylated AdoMet to putrescine, converting the two substrates to 5-methylthioadenosine (MTA) and spermidine, respectively. In an analogous reaction, spermidine can go on to react with decarboxylated AdoMet via spermine synthase (Spe4p) to yield spermine and another molecule of MTA. Spermidine but not spermine is essential for growth in S. cerevisiae. MTA, a major byproduct of the polyamine biosynthesis pathway, is also the principal substrate for the methionine salvage pathway. The methionine salvage pathway recycles MTA produced during polyamine biosynthesis or other cellular processes back into methionine. In S. cerevisiae, the polyamine biosynthesis pathway and the methionine salvage pathway together are estimated to account for 11-19% of the methionine used by a methionine auxotroph grown on limiting methionine. References: |CITS: [27470594]||CITS: [3157043]||CITS: [9073064]||CITS: [9573363]||CITS: [16530730]|' name: superpathway of polyamine biosynthesis pmids: - '16530730' - '27470594' - '3157043' - '9073064' - '9573363' reactions: - ec: - 4.1.1.17 genes: - *id296 left: - H+ - L-ornithine name: L-ornithine + H+ -> CO2 + putrescine pmids: [] rhea: [] right: - CO2 - putrescine yeastcyc_id: ORNDECARBOX-RXN - ec: - 4.1.1.50 genes: - *id047 left: - H+ - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + H+ -> CO2 + S-adenosyl 3-(methylsulfanyl)propylamine pmids: [] rhea: [] right: - CO2 - S-adenosyl 3-(methylsulfanyl)propylamine yeastcyc_id: SAMDECARB-RXN - ec: - 2.5.1.16 genes: - *id083 left: - S-adenosyl 3-(methylsulfanyl)propylamine - putrescine name: putrescine + S-adenosyl 3-(methylsulfanyl)propylamine -> spermidine + S-methyl-5'-thioadenosine + H+ pmids: [] rhea: [] right: - H+ - S-methyl-5'-thioadenosine - spermidine yeastcyc_id: SPERMIDINESYN-RXN - ec: - 2.5.1.22 genes: - *id048 left: - S-adenosyl 3-(methylsulfanyl)propylamine - spermidine name: spermidine + S-adenosyl 3-(methylsulfanyl)propylamine -> spermine + S-methyl-5'-thioadenosine + H+ pmids: [] rhea: [] right: - H+ - S-methyl-5'-thioadenosine - spermine yeastcyc_id: SPERMINE-SYNTHASE-RXN yeastcyc_id: POLYAMSYN-YEAST-PWY PROSYN-PWY: all_genes: - &id297 orf: YDR300C symbol: PRO1 uniprot: UniProtKB:P32264 - &id298 orf: YOR323C symbol: PRO2 uniprot: UniProtKB:P54885 - *id045 comment: 'Proline is a non-essential amino acid belonging to the glutamate family of amino acids whose biosynthesis depends on the carbon skeleton of glutamic acid. Proline is synthesized from glutamate in the cytoplasm. The P5C reductase enzymatic reaction in this pathway is identical to the one in arginine degradation |CITS:[ 6997271]|. Since these two pathways converge at this step, the requirement for proline in pro1 and pro2 mutant strains can be satisfied by arginine. However, these pro-strains cannot grow on rich media because the presence of optimal nitrogen sources causes the repression of genes necessary for arginine degradation |CITS:[2824433]|, |CITS:[10640599]|. Many of the genes involved in S. cerevisiae amino acid biosynthesis are coregulated by a process known as the general amino acid control system. In response to starvation for any single amino acid, the expression of many biosynthetic enzymes is upregulated |CITS:[3045517]|. Mutational studies indicate that both PRO1 and PRO2 expression are regulated by general amino acid control, mediated by the transcriptional activator Gcn4p |CITS:[1350780]|. However, expression profiling by microarray analysis shows that only PRO2 is activated by Gcn4p |CITS:[11390663]|. In contrast, the expression of PRO3 appears to be constitutively expressed and under no form of regulation. ' name: L-proline biosynthesis I pmids: - '12513997' - '2824433' reactions: - ec: [] genes: [] left: - (S)-1-pyrroline-5-carboxylate - H+ - H2O name: (S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde pmids: [] rhea: [] right: - L-glutamate-5-semialdehyde yeastcyc_id: SPONTPRO-RXN - ec: - 2.7.2.11 genes: - *id297 left: - ATP - L-glutamate name: L-glutamate + ATP -> γ-L-glutamyl 5-phosphate + ADP pmids: [] rhea: [] right: - ADP - γ-L-glutamyl 5-phosphate yeastcyc_id: GLUTKIN-RXN - ec: - 1.2.1.41 genes: - *id298 left: - L-glutamate-5-semialdehyde - NADP+ - phosphate name: L-glutamate-5-semialdehyde + NADP+ + phosphate <- γ-L-glutamyl 5-phosphate + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - γ-L-glutamyl 5-phosphate yeastcyc_id: GLUTSEMIALDEHYDROG-RXN - ec: - 1.5.1.2 genes: - *id045 left: - L-proline - NAD(P)+ name: L-proline + NAD(P)+ <- (S)-1-pyrroline-5-carboxylate + NAD(P)H + 2 H+ pmids: - '6997271' rhea: [] right: - (S)-1-pyrroline-5-carboxylate - H+ - NAD(P)H yeastcyc_id: PYRROLINECARBREDUCT-RXN yeastcyc_id: PROSYN-PWY PROUT-PWY: all_genes: - *id046 comment: 'Although proline is the least-preferred nitrogen source for many lab strains of S. cerevisiae, it is the most abundant source of nitrogen in grapes, the natural environment of wild yeast |CITS: [10629046]|. When other sources of nitrogen like ammonia, asparagine or glutamine are unavailabe, S. cerevisiae degrade proline into glutmate via the proline utilization pathway in the mitochondria |CITS:[387737]|, |CITS:[387738]|. This degradation is catalyzed by proline oxidase and delta 1-pyrroline-5-carboxylate dehydrogenase, which are encoded by the nuclear genes PUT1 and PUT2 respectively |CITS: [3537723]|, |CITS: [ 6358862]|. Both PUT1 and PUT2 are positively regulated by the transcriptional activator Put3p |CITS:[14517252]|. Although Put3p is bound constitutively to the promoters of PUT1 and PUT2, transcriptional upregulation only occurs in the presense of proline and absence of a preferred nitrogen source |CITS:[10629046]|, |CITS:[1986247]|. PUT1 is also positively regulated by the GATA factors Gln3p and Nil1p/Gat1p |CITS: [7891726]|, |CITS:[12796300]|. The presence of a good nitrogen source, such as ammonia or glutamine, supresses the proline utilization pathway-an effect known as nitrogen catabolite repression (NCR) |CITS: [10640599]|. The transcription factors responsible for PUT1 and PUT2 repression by NCR are Ure2p, Dal80p, and Nil2p |CITS:[8416910]|, |CITS:[9171427]|.' name: L-proline degradation pmids: - '10629046' - '387737' reactions: - ec: [] genes: [] left: - (S)-1-pyrroline-5-carboxylate - H+ - H2O name: (S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde pmids: [] rhea: [] right: - L-glutamate-5-semialdehyde yeastcyc_id: SPONTPRO-RXN - ec: - 1.2.1.88 genes: [] left: - H2O - L-glutamate-5-semialdehyde - NAD+ name: L-glutamate-5-semialdehyde + NAD+ + H2O -> L-glutamate + NADH + 2 H+ pmids: [] rhea: [] right: - H+ - L-glutamate - NADH yeastcyc_id: RXN-14116 - ec: - 1.5.5.2 genes: - *id046 left: - L-proline - an electron-transfer quinone name: L-proline[in] + an electron-transfer quinone[membrane] -> (S)-1-pyrroline-5-carboxylate[in] + an electron-transfer quinol[membrane] + H+[in] pmids: - '387737' rhea: [] right: - (S)-1-pyrroline-5-carboxylate - H+ - an electron-transfer quinol yeastcyc_id: RXN-14903 yeastcyc_id: PROUT-PWY PRPP-PWY-1: all_genes: - *id092 - *id101 - *id086 - *id096 - *id097 - *id087 - *id088 - *id091 - *id093 - *id103 - *id089 - *id090 - *id049 - *id050 - *id102 - *id095 - *id223 - *id225 - *id224 - *id222 - *id016 - *id221 - *id226 - *id098 - *id099 - *id100 - &id302 orf: YKL181W symbol: PRS1 uniprot: UniProtKB:P32895 - &id303 orf: YER099C symbol: PRS2 uniprot: UniProtKB:P38620 - &id304 orf: YHL011C symbol: PRS3 uniprot: UniProtKB:P38689 - &id305 orf: YBL068W symbol: PRS4 uniprot: UniProtKB:P38063 - &id306 orf: YOL061W symbol: PRS5 uniprot: UniProtKB:Q12265 - *id104 - *id105 - *id106 - *id107 - &id300 orf: YKL216W symbol: URA1 uniprot: UniProtKB:P28272 - &id310 orf: YMR271C symbol: URA10 uniprot: UniProtKB:P30402 - *id051 - &id309 orf: YEL021W symbol: URA3 uniprot: UniProtKB:P03962 - &id299 orf: YLR420W symbol: URA4 uniprot: UniProtKB:P20051 - &id311 orf: YML106W symbol: URA5 uniprot: UniProtKB:P13298 - &id301 orf: YKL024C symbol: URA6 uniprot: UniProtKB:P15700 - &id307 orf: YBL039C symbol: URA7 uniprot: UniProtKB:P28274 - &id308 orf: YJR103W symbol: URA8 uniprot: UniProtKB:P38627 - *id094 name: superpathway of histidine, purine, and pyrimidine biosynthesis pmids: [] reactions: - ec: - 3.5.2.3 genes: - *id299 left: - (S)-dihydroorotate - H2O name: (S)-dihydroorotate + H2O <-> N-carbamoyl-L-aspartate + H+ pmids: [] rhea: [] right: - H+ - N-carbamoyl-L-aspartate yeastcyc_id: DIHYDROOROT-RXN - ec: - 1.3.98.1 genes: - *id300 left: - (S)-dihydroorotate - fumarate name: (S)-dihydroorotate + fumarate -> orotate + succinate pmids: [] rhea: [] right: - orotate - succinate yeastcyc_id: RXN-9929 - ec: - 5.3.1.16 genes: - *id221 left: - 1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide name: 1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide -> phosphoribulosylformimino-AICAR-phosphate pmids: [] rhea: [] right: - phosphoribulosylformimino-AICAR-phosphate yeastcyc_id: PRIBFAICARPISOM-RXN - ec: - 3.5.4.19 genes: - *id222 left: - 1-(5-phospho-β-D-ribosyl)-AMP - H2O name: 1-(5-phospho-β-D-ribosyl)-AMP + H2O -> 1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide pmids: [] rhea: [] right: - 1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide yeastcyc_id: HISTCYCLOHYD-RXN - ec: - 3.6.1.31 genes: - *id222 left: - 1-(5-phospho-β-D-ribosyl)-ATP - H2O name: 1-(5-phospho-β-D-ribosyl)-ATP + H2O -> 1-(5-phospho-β-D-ribosyl)-AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - 1-(5-phospho-β-D-ribosyl)-AMP - H+ - diphosphate yeastcyc_id: HISTPRATPHYD-RXN - ec: - 2.4.2.17 genes: - *id223 left: - 1-(5-phospho-β-D-ribosyl)-ATP - diphosphate name: 1-(5-phospho-β-D-ribosyl)-ATP + diphosphate <- ATP + 5-phospho-α-D-ribose 1-diphosphate + H+ pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - ATP - H+ yeastcyc_id: ATPPHOSPHORIBOSYLTRANS-RXN - ec: - 6.3.5.5 genes: - *id049 - *id050 - *id051 left: - ATP - H2O - L-glutamine - hydrogencarbonate name: 2 ATP + L-glutamine + hydrogencarbonate + H2O -> L-glutamate + carbamoyl phosphate + 2 ADP + phosphate + 2 H+ pmids: - '8626695' rhea: [] right: - ADP - H+ - L-glutamate - carbamoyl phosphate - phosphate yeastcyc_id: CARBPSYN-RXN - ec: - 4.3.2.2 genes: - *id086 left: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole name: 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <-> fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - fumarate yeastcyc_id: AICARSYN-RXN - ec: - 4.1.1.21 genes: - *id087 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - H+ name: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H+ <-> 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + CO2 pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - CO2 yeastcyc_id: AIRCARBOXY-RXN - ec: - 2.4.2.14 genes: - *id088 left: - 5-phospho-β-D-ribosylamine - L-glutamate - diphosphate name: 5-phospho-β-D-ribosylamine + L-glutamate + diphosphate <-> 5-phospho-α-D-ribose 1-diphosphate + L-glutamine + H2O pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - H2O - L-glutamine yeastcyc_id: PRPPAMIDOTRANS-RXN - ec: - 2.7.4.3 genes: - *id089 - *id090 left: - AMP - ATP name: AMP + ATP <-> 2 ADP pmids: [] rhea: [] right: - ADP yeastcyc_id: ADENYL-KIN-RXN - ec: - 6.3.3.1 genes: - *id091 left: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ATP name: ATP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine -> ADP + 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + phosphate + H+ pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - ADP - H+ - phosphate yeastcyc_id: AIRS-RXN - ec: - 6.3.2.6 genes: - *id092 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - ATP - L-aspartate name: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate -> ADP + 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole + phosphate + H+ pmids: [] rhea: [] right: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole - ADP - H+ - phosphate yeastcyc_id: SAICARSYN-RXN - ec: - 6.3.4.13 genes: - *id091 left: - 5-phospho-β-D-ribosylamine - ATP - glycine name: ATP + 5-phospho-β-D-ribosylamine + glycine -> ADP + N1-(5-phospho-β-D-ribosyl)glycinamide + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - N1-(5-phospho-β-D-ribosyl)glycinamide - phosphate yeastcyc_id: GLYRIBONUCSYN-RXN - ec: - 6.3.5.3 genes: - *id093 left: - ATP - H2O - L-glutamine - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide name: ATP + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + L-glutamine + H2O -> L-glutamate + ADP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine + phosphate + H+ pmids: [] rhea: [] right: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ADP - H+ - L-glutamate - phosphate yeastcyc_id: FGAMSYN-RXN - ec: - 2.7.4.14 - 2.7.4.22 - 2.7.4.4 genes: - *id301 left: - ATP - UMP name: ATP + UMP -> ADP + UDP pmids: [] rhea: [] right: - ADP - UDP yeastcyc_id: RXN-12002 - ec: - 4.2.1.19 genes: - *id224 left: - D-erythro-imidazole-glycerol-phosphate name: D-erythro-imidazole-glycerol-phosphate -> imidazole acetol-phosphate + H2O pmids: [] rhea: [] right: - H2O - imidazole acetol-phosphate yeastcyc_id: IMIDPHOSDEHYD-RXN - ec: - 2.7.6.1 genes: - *id302 - *id303 - *id304 - *id305 - *id306 left: - ATP - D-ribose 5-phosphate name: D-ribose 5-phosphate + ATP <-> 5-phospho-α-D-ribose 1-diphosphate + AMP + H+ pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - AMP - H+ yeastcyc_id: PRPPSYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - GDP name: GDP + ATP -> GTP + ADP pmids: [] rhea: [] right: - ADP - GTP yeastcyc_id: GDPKIN-RXN - ec: - 2.7.4.8 genes: - *id095 left: - ATP - GMP name: GMP + ATP <-> GDP + ADP pmids: [] rhea: [] right: - ADP - GDP yeastcyc_id: GUANYL-KIN-RXN - ec: - 3.5.4.10 genes: - *id096 - *id097 left: - H2O - IMP name: IMP + H2O <-> 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide yeastcyc_id: IMPCYCLOHYDROLASE-RXN - ec: - 1.1.1.205 genes: - *id098 - *id099 - *id100 left: - H2O - IMP - NAD+ name: IMP + NAD+ + H2O <-> XMP + NADH + H+ pmids: - '12746440' rhea: [] right: - H+ - NADH - XMP yeastcyc_id: IMP-DEHYDROG-RXN - ec: - 6.3.4.4 genes: - *id101 left: - GTP - IMP - L-aspartate name: L-aspartate + IMP + GTP -> adenylo-succinate + GDP + phosphate + 2 H+ pmids: [] rhea: [] right: - GDP - H+ - adenylo-succinate - phosphate yeastcyc_id: ADENYLOSUCCINATE-SYNTHASE-RXN - ec: - 2.1.3.2 genes: - *id051 left: - L-aspartate - carbamoyl phosphate name: L-aspartate + carbamoyl phosphate <-> N-carbamoyl-L-aspartate + phosphate + H+ pmids: [] rhea: [] right: - H+ - N-carbamoyl-L-aspartate - phosphate yeastcyc_id: ASPCARBTRANS-RXN - ec: - 6.3.4.2 genes: - *id307 - *id308 left: - ATP - H2O - L-glutamine - UTP name: L-glutamine + UTP + ATP + H2O -> ADP + CTP + L-glutamate + phosphate + 2 H+ pmids: [] rhea: [] right: - ADP - CTP - H+ - L-glutamate - phosphate yeastcyc_id: CTPSYN-RXN - ec: - 2.6.1.9 genes: - *id016 left: - 2-oxoglutarate - L-histidinol phosphate name: L-histidinol phosphate + 2-oxoglutarate <- imidazole acetol-phosphate + L-glutamate pmids: [] rhea: [] right: - L-glutamate - imidazole acetol-phosphate yeastcyc_id: HISTAMINOTRANS-RXN - ec: - 3.1.3.15 genes: - *id225 left: - H2O - L-histidinol phosphate name: L-histidinol phosphate + H2O -> histidinol + phosphate pmids: [] rhea: [] right: - histidinol - phosphate yeastcyc_id: HISTIDPHOS-RXN - ec: - 2.7.4.6 genes: [] left: - ATP - UDP name: UDP + ATP -> UTP + ADP pmids: [] rhea: [] right: - ADP - UTP yeastcyc_id: UDPKIN-RXN - ec: - 6.3.5.2 genes: - *id102 left: - ATP - H2O - L-glutamine - XMP name: XMP + L-glutamine + ATP + H2O -> L-glutamate + GMP + AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - AMP - GMP - H+ - L-glutamate - diphosphate yeastcyc_id: GMP-SYN-GLUT-RXN - ec: - 2.1.2.3 genes: - *id096 - *id097 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide <-> a tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide - a tetrahydrofolate yeastcyc_id: AICARTRANSFORM-RXN - ec: - 2.1.2.2 genes: - *id103 left: - N1-(5-phospho-β-D-ribosyl)glycinamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + N1-(5-phospho-β-D-ribosyl)glycinamide <-> a tetrahydrofolate + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + H+ pmids: [] rhea: [] right: - H+ - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide - a tetrahydrofolate yeastcyc_id: GART-RXN - ec: - 4.3.2.2 genes: - *id086 left: - adenylo-succinate name: adenylo-succinate <-> fumarate + AMP pmids: [] rhea: [] right: - AMP - fumarate yeastcyc_id: AMPSYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dADP name: dADP + ATP -> dATP + ADP pmids: [] rhea: [] right: - ADP - dATP yeastcyc_id: DADPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dADP name: dADP + an oxidized thioredoxin + H2O <- ADP + a reduced thioredoxin pmids: [] rhea: [] right: - ADP - a reduced thioredoxin yeastcyc_id: ADPREDUCT-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dGDP name: dGDP + ATP -> dGTP + ADP pmids: [] rhea: [] right: - ADP - dGTP yeastcyc_id: DGDPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dGDP name: dGDP + an oxidized thioredoxin + H2O <- GDP + a reduced thioredoxin pmids: [] rhea: [] right: - GDP - a reduced thioredoxin yeastcyc_id: GDPREDUCT-RXN - ec: - 1.1.98.6 genes: [] left: - ATP - H+ - formate name: formate + ATP + H+ -> CO2 + dATP + H2O pmids: [] rhea: [] right: - CO2 - H2O - dATP yeastcyc_id: RXN0-745 - ec: - 1.1.98.6 genes: [] left: - GTP - H+ - formate name: formate + GTP + H+ -> dGTP + CO2 + H2O pmids: [] rhea: [] right: - CO2 - H2O - dGTP yeastcyc_id: RXN0-746 - ec: [] genes: - *id222 left: - H2O - NAD+ - histidinal name: histidinal + NAD+ + H2O -> L-histidine + NADH + 2 H+ pmids: [] rhea: [] right: - H+ - L-histidine - NADH yeastcyc_id: HISTALDEHYD-RXN - ec: [] genes: - *id222 left: - NAD+ - histidinol name: histidinol + NAD+ -> histidinal + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - histidinal yeastcyc_id: HISTOLDEHYD-RXN - ec: - 4.1.1.23 genes: - *id309 left: - H+ - orotidine 5'-phosphate name: orotidine 5'-phosphate + H+ -> CO2 + UMP pmids: [] rhea: [] right: - CO2 - UMP yeastcyc_id: OROTPDECARB-RXN - ec: - 2.4.2.10 genes: - *id310 - *id311 left: - diphosphate - orotidine 5'-phosphate name: orotidine 5'-phosphate + diphosphate <-> 5-phospho-α-D-ribose 1-diphosphate + orotate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - orotate yeastcyc_id: OROPRIBTRANS-RXN - ec: - 4.3.2.10 genes: - *id226 left: - L-glutamine - phosphoribulosylformimino-AICAR-phosphate name: phosphoribulosylformimino-AICAR-phosphate + L-glutamine -> L-glutamate + D-erythro-imidazole-glycerol-phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + H+ pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - D-erythro-imidazole-glycerol-phosphate - H+ - L-glutamate yeastcyc_id: GLUTAMIDOTRANS-RXN yeastcyc_id: PRPP-PWY-1 PWY-1801-1: all_genes: - &id314 orf: YOR388C symbol: FDH1 uniprot: UniProtKB:Q08911 - &id312 orf: YDL168W symbol: SFA1 uniprot: UniProtKB:P32771 - &id313 orf: YJL068C symbol: null uniprot: UniProtKB:P40363 comment: 'Formaldehyde is formed by oxidative demethylation reactions in many plants and methylotrophic organisms, but Saccharomyces cerevisiae is a nonmethylotrophic yeast and cannot metabolize methanol to formaldehyde. However, S. cerevisiae is exposed to exogenous formaldehyde from plant material or in polluted air and water. Concentrations of formaldehyde of 1mM or higher are cytostatic or cytotoxic to haploid wild-type cells. Any free formaldehyde in vivo spontaneously reacts with glutathione to form S-hydroxymethylglutathione |CITS:[12913179]|, |CITS:[8625422]|, |CITS:[10427036]|. The level of enzymes involved in the degradation of formaldehyde, such as Sfa1p and Yjl068p, determine the level of formaldehyde toxicity, and cells overproducing Sfa1p are resistant to formaldehyde and null mutants in either sfa1 or yjl068c are hypersensitive to formaldehyde. Sfa1p is induced in response to chemicals such as formaldehyde (FA), ethanol and methyl methanesulphonate, and Yjl068p is also induced in response to chemical stresses |CITS:[7689168]|, |CITS:[8625422]|, |CITS:[10427036]|, |CITS:[8483449]|, |CITS:[2557161]|, |CITS:[9990050]|, |CITS:[11562456]|. Formate dehydrogenase is encoded by FDH1/YOR388C and FDH2. In some strain backgrounds of S. cerevisiae, FDH2 is encoded by a continuous open reading frame comprised of YPL275W and YPL276W. However, in the systematic sequence of S288C, FDH2 is represented by these two separate open reading frames due to an in frame stop codon |CITS:[11921099]|. ' name: formaldehyde oxidation II (glutathione-dependent) pmids: [] reactions: - ec: - 4.4.1.22 genes: [] left: - S-(hydroxymethyl)glutathione name: S-(hydroxymethyl)glutathione <- formaldehyde + glutathione pmids: [] rhea: [] right: - formaldehyde - glutathione yeastcyc_id: RXN-2961 - ec: - 1.1.1.284 genes: - *id312 left: - NAD(P)+ - S-(hydroxymethyl)glutathione name: S-(hydroxymethyl)glutathione + NAD(P)+ -> S-formylglutathione + NAD(P)H + H+ pmids: [] rhea: [] right: - H+ - NAD(P)H - S-formylglutathione yeastcyc_id: RXN-2962 - ec: - 3.1.2.12 genes: - *id313 left: - H2O - S-formylglutathione name: S-formylglutathione + H2O -> formate + glutathione + H+ pmids: [] rhea: [] right: - H+ - formate - glutathione yeastcyc_id: S-FORMYLGLUTATHIONE-HYDROLASE-RXN - ec: - 1.17.1.9 genes: - *id314 left: - NAD+ - formate name: formate + NAD+ -> CO2 + NADH pmids: [] rhea: [] right: - CO2 - NADH yeastcyc_id: 1.2.1.2-RXN yeastcyc_id: PWY-1801-1 PWY-2201: all_genes: - *id021 - &id315 orf: YER183C symbol: FAU1 uniprot: UniProtKB:P40099 - *id031 - *id032 - *id033 - *id034 - *id023 - *id024 - *id022 - *id025 - *id018 - *id019 name: folate transformations I pmids: [] reactions: - ec: - 2.1.1.13 genes: [] left: - L-homocysteine - a 5-methyltetrahydrofolate name: L-homocysteine + a 5-methyltetrahydrofolate -> L-methionine + a tetrahydrofolate pmids: [] rhea: [] right: - L-methionine - a tetrahydrofolate yeastcyc_id: HOMOCYSMETB12-RXN - ec: - 2.1.2.1 genes: - *id018 - *id019 left: - L-serine - a tetrahydrofolate name: L-serine + a tetrahydrofolate <-> glycine + a 5,10-methylenetetrahydrofolate + H2O pmids: [] rhea: [] right: - H2O - a 5,10-methylenetetrahydrofolate - glycine yeastcyc_id: GLYOHMETRANS-RXN - ec: - 6.3.3.2 genes: - *id315 left: - ATP - a (6S)-5-formyltetrahydrofolate name: a (6S)-5-formyltetrahydrofolate + ATP -> a 5,10-methenyltetrahydrofolate + ADP + phosphate pmids: [] rhea: [] right: - ADP - a 5,10-methenyltetrahydrofolate - phosphate yeastcyc_id: 5-FORMYL-THF-CYCLO-LIGASE-RXN - ec: - 3.5.1.10 genes: [] left: - H2O - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + H2O -> a tetrahydrofolate + formate + H+ pmids: [] rhea: [] right: - H+ - a tetrahydrofolate - formate yeastcyc_id: FORMYLTHFDEFORMYL-RXN - ec: - 3.5.4.9 genes: - *id021 - *id022 left: - H2O - a 5,10-methenyltetrahydrofolate name: a 5,10-methenyltetrahydrofolate + H2O <-> a 10-formyltetrahydrofolate + H+ pmids: [] rhea: [] right: - H+ - a 10-formyltetrahydrofolate yeastcyc_id: METHENYLTHFCYCLOHYDRO-RXN - ec: - 1.5.1.15 genes: - *id025 left: - NAD+ - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NAD+ -> a 5,10-methenyltetrahydrofolate + NADH pmids: - '8608153' rhea: [] right: - NADH - a 5,10-methenyltetrahydrofolate yeastcyc_id: 1.5.1.15-RXN - ec: - 1.5.1.5 genes: - *id021 - *id022 left: - NADP+ - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NADP+ <-> a 5,10-methenyltetrahydrofolate + NADPH pmids: [] rhea: [] right: - NADPH - a 5,10-methenyltetrahydrofolate yeastcyc_id: METHYLENETHFDEHYDROG-NADP-RXN - ec: - 1.5.7.1 genes: [] left: - a 5-methyltetrahydrofolate - an oxidized ferredoxin [iron-sulfur] cluster name: a 5-methyltetrahydrofolate + 2 an oxidized ferredoxin [iron-sulfur] cluster <- a 5,10-methylenetetrahydrofolate + 2 a reduced ferredoxin [iron-sulfur] cluster + 2 H+ pmids: [] rhea: [] right: - H+ - a 5,10-methylenetetrahydrofolate - a reduced ferredoxin [iron-sulfur] cluster yeastcyc_id: RXN-5061 - ec: - 1.5.1.20 genes: - *id023 - *id024 left: - NAD+ - a 5-methyltetrahydrofolate name: a 5-methyltetrahydrofolate + NAD+ <- a 5,10-methylenetetrahydrofolate + NADH + H+ pmids: - '10600168' rhea: [] right: - H+ - NADH - a 5,10-methylenetetrahydrofolate yeastcyc_id: 1.5.1.20-RXN - ec: - 6.3.4.3 genes: - *id021 - *id022 left: - ATP - a tetrahydrofolate - formate name: a tetrahydrofolate + ATP + formate <-> a 10-formyltetrahydrofolate + ADP + phosphate pmids: - '1916088' rhea: [] right: - ADP - a 10-formyltetrahydrofolate - phosphate yeastcyc_id: FORMATETHFLIG-RXN - ec: - 2.1.1.19 genes: [] left: - a tetrahydrofolate - trimethyl sulfonium name: a tetrahydrofolate + trimethyl sulfonium <- dimethyl sulfide + a 5-methyltetrahydrofolate + H+ pmids: [] rhea: [] right: - H+ - a 5-methyltetrahydrofolate - dimethyl sulfide yeastcyc_id: 2.1.1.19-RXN - ec: [] genes: - *id031 - *id032 - *id033 - *id034 left: - NAD+ - a tetrahydrofolate - glycine name: glycine + a tetrahydrofolate + NAD+ -> a 5,10-methylenetetrahydrofolate + ammonium + CO2 + NADH pmids: - '1916088' rhea: [] right: - CO2 - NADH - a 5,10-methylenetetrahydrofolate - ammonium yeastcyc_id: GCVMULTI-RXN yeastcyc_id: PWY-2201 PWY-2301: all_genes: - &id316 orf: YHR046C symbol: INM1 uniprot: UniProtKB:P38710 - &id317 orf: YDR287W symbol: INM2 uniprot: UniProtKB:Q05533 - &id318 orf: YJL153C symbol: INO1 uniprot: UniProtKB:P11986 name: myo-inositol biosynthesis pmids: - '10096091' - '10844654' - '2642902' reactions: - ec: - 3.1.3.25 genes: - *id316 - *id317 left: - 1D-myo-inositol 3-monophosphate - H2O name: 1D-myo-inositol 3-monophosphate + H2O -> myo-inositol + phosphate pmids: - '10096091' - '10844654' rhea: [] right: - myo-inositol - phosphate yeastcyc_id: MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN - ec: - 5.5.1.4 genes: - *id318 left: - D-glucopyranose 6-phosphate name: D-glucopyranose 6-phosphate -> 1D-myo-inositol 3-monophosphate pmids: [] rhea: [] right: - 1D-myo-inositol 3-monophosphate yeastcyc_id: MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN yeastcyc_id: PWY-2301 PWY-3322: all_genes: - &id319 orf: YDL215C symbol: GDH2 uniprot: UniProtKB:P33327 comment: 'In S. cerevisiae cells, the amino group of glutamate and the amide group of glutamine are the source of nitrogen for all other macromolecules |CITS: [1975578]|. In order to provide ammonia for the synthesis of glutamine during growth on glutamate-yielding nitrogen sources, cells degrade glutamate into ammonia. The main pathway for S. cerevisiae glutamate degradation is catalyzed by the NAD dependent glutamate dehydrogenase encoded by GDH2 |CITS:[1975578]|. Transcriptional regulation of GDH2 is dependent upon six different sequence elements present in the promoter |CITS:[1682801]|. Two elements behave as upstream activation sites (UAS) while the remaining four sites inhibit the effects of the two UASs |CITS: [1652057]|. One UAS has been shown to activate transcription during growth on nonfermentable carbon sources or on limiting amounts of glucose |CITS:[1652057]|. The other UAS is under the control of nitrogen catabolite repression (NCR) |CITS: [4394512]|. Under nitrogen-poor conditions, GDH2 expression is upregulated by the transcriptional activator Gln3p and the co-activator Hfi1p |CITS:[1990286]|, |CITS:[8416910]|, |CITS:[10048020]|. Conversely, in the presence of an optimal nitrogen source such as glutamine, GDH2 transcription is repressed by the transcription factor Ure2p |CITS:[1990286]|. Unrelated to NCR, GDH2 gene expression is regulated by ammonia concentrations. An increase in intracellular ammonia leads to a decrease in GDH2 expression |CITS:[12851403]| but an increase in extracellular ammonia leads to an increase in GDH2 transcription and Gdh2p activity |CITS:[7592450]|. Gdh2p enzyme activity also appears to be regulated by phosphorylation through cAMP-dependent and cAMP-independent protein kinases and subsequent proteolysis |CITS:[6319381]|, |CITS:[7009211]|. ' name: glutamate degradation IX pmids: - '1975578' reactions: - ec: - 1.4.1.2 genes: - *id319 left: - H2O - L-glutamate - NAD+ name: L-glutamate + NAD+ + H2O -> 2-oxoglutarate + ammonium + NADH + H+ pmids: [] rhea: [] right: - 2-oxoglutarate - H+ - NADH - ammonium yeastcyc_id: GLUTAMATE-DEHYDROGENASE-RXN yeastcyc_id: PWY-3322 PWY-46: all_genes: - *id296 name: putrescine biosynthesis III pmids: [] reactions: - ec: - 4.1.1.17 genes: - *id296 left: - H+ - L-ornithine name: L-ornithine + H+ -> CO2 + putrescine pmids: [] rhea: [] right: - CO2 - putrescine yeastcyc_id: ORNDECARBOX-RXN yeastcyc_id: PWY-46 PWY-5041: all_genes: - *id262 - &id322 orf: YER043C symbol: SAH1 uniprot: UniProtKB:P39954 - &id320 orf: YLR180W symbol: SAM1 uniprot: UniProtKB:P10659 - &id321 orf: YDR502C symbol: SAM2 uniprot: UniProtKB:P19358 name: S-adenosyl-L-methionine cycle II pmids: - '9409150' reactions: - ec: - 2.5.1.6 genes: - *id320 - *id321 left: - ATP - H2O - L-methionine name: ATP + L-methionine + H2O -> S-adenosyl-L-methionine + phosphate + diphosphate pmids: [] rhea: [] right: - S-adenosyl-L-methionine - diphosphate - phosphate yeastcyc_id: S-ADENMETSYN-RXN - ec: - 2.1.1.14 genes: - *id262 left: - 5-methyltetrahydropteroyl tri-L-glutamate - L-homocysteine name: L-homocysteine + 5-methyltetrahydropteroyl tri-L-glutamate <-> L-methionine + tetrahydropteroyl tri-L-glutamate pmids: [] rhea: [] right: - L-methionine - tetrahydropteroyl tri-L-glutamate yeastcyc_id: HOMOCYSMET-RXN - ec: - 3.3.1.1 genes: - *id322 left: - H2O - S-adenosyl-L-homocysteine name: S-adenosyl-L-homocysteine + H2O -> L-homocysteine + adenosine pmids: [] rhea: [] right: - L-homocysteine - adenosine yeastcyc_id: ADENOSYLHOMOCYSTEINASE-RXN - ec: - 2.1.1.- genes: [] left: - S-adenosyl-L-methionine - a demethylated methyl donor name: S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a methylated methyl donor yeastcyc_id: RXN-7605 yeastcyc_id: PWY-5041 PWY-5080-1: all_genes: - &id325 orf: YCR034W symbol: ELO2 uniprot: UniProtKB:P25358 - &id326 orf: YLR372W symbol: ELO3 uniprot: UniProtKB:P40319 - &id324 orf: YBR159W symbol: IFA38 uniprot: UniProtKB:P38286 - &id323 orf: YJL097W symbol: PHS1 uniprot: UniProtKB:P40857 - &id327 orf: YDL015C symbol: TSC13 uniprot: UniProtKB:Q99190 name: very long chain fatty acid biosynthesis I pmids: - '17719534' - '17719544' - '18272525' reactions: - ec: - 4.2.1.17 genes: - *id323 left: - a 3-hydroxyacyl-CoA name: a 3-hydroxyacyl-CoA -> a trans-2-enoyl-CoA + H2O pmids: [] rhea: [] right: - H2O - a trans-2-enoyl-CoA yeastcyc_id: RXN3O-9813 - ec: - 1.1.1.36 genes: - *id324 left: - H+ - NADPH - a 3-oxoacyl-CoA name: a 3-oxoacyl-CoA + NADPH + H+ -> a 3-hydroxyacyl-CoA + NADP+ pmids: [] rhea: [] right: - NADP+ - a 3-hydroxyacyl-CoA yeastcyc_id: RXN3O-9812 - ec: - 2.3.1.- genes: - *id325 - *id326 left: - a long-chain acyl-CoA - malonyl-CoA name: a long-chain acyl-CoA + malonyl-CoA -> a 3-oxoacyl-CoA + CO2 + coenzyme A pmids: [] rhea: [] right: - CO2 - a 3-oxoacyl-CoA - coenzyme A yeastcyc_id: RXN3O-9811 - ec: - 1.3.1.93 genes: - *id327 left: - H+ - NADPH - a trans-2-enoyl-CoA name: a trans-2-enoyl-CoA + NADPH + H+ -> a long-chain acyl-CoA + NADP+ pmids: [] rhea: [] right: - NADP+ - a long-chain acyl-CoA yeastcyc_id: RXN3O-9814 yeastcyc_id: PWY-5080-1 PWY-5084: all_genes: - &id328 orf: YIL125W symbol: KGD1 uniprot: UniProtKB:P20967 - &id329 orf: YDR148C symbol: KGD2 uniprot: UniProtKB:P19262 - *id034 name: 2-oxoglutarate decarboxylation to succinyl-CoA pmids: - '2072900' reactions: - ec: - 1.2.4.2 genes: - *id328 left: - 2-oxoglutarate - H+ - a [2-oxoglutarate dehydrogenase E2 protein] N6-lipoyl-L-lysine name: 2-oxoglutarate + a [2-oxoglutarate dehydrogenase E2 protein] N6-lipoyl-L-lysine + H+ -> a [2-oxoglutarate dehydrogenase E2 protein] N6-S-succinyldihydrolipoyl-L-lysine + CO2 pmids: [] rhea: [] right: - CO2 - a [2-oxoglutarate dehydrogenase E2 protein] N6-S-succinyldihydrolipoyl-L-lysine yeastcyc_id: 2OXOGLUTDECARB-RXN - ec: - 1.8.1.4 genes: - *id034 left: - NAD+ - a [2-oxoglutarate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine name: a [2-oxoglutarate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine + NAD+ -> a [2-oxoglutarate dehydrogenase E2 protein] N6-lipoyl-L-lysine + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - a [2-oxoglutarate dehydrogenase E2 protein] N6-lipoyl-L-lysine yeastcyc_id: RXN-7716 - ec: - 2.3.1.61 genes: - *id329 left: - a [2-oxoglutarate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine - succinyl-CoA name: succinyl-CoA + a [2-oxoglutarate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine <-> a [2-oxoglutarate dehydrogenase E2 protein] N6-S-succinyldihydrolipoyl-L-lysine + coenzyme A pmids: - '2072900' rhea: [] right: - a [2-oxoglutarate dehydrogenase E2 protein] N6-S-succinyldihydrolipoyl-L-lysine - coenzyme A yeastcyc_id: RXN0-1147 yeastcyc_id: PWY-5084 PWY-5123: all_genes: - *id126 - *id131 name: trans, trans-farnesyl diphosphate biosynthesis pmids: [] reactions: - ec: - 2.5.1.1 genes: - *id126 left: - dimethylallyl diphosphate - isopentenyl diphosphate name: dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - geranyl diphosphate yeastcyc_id: GPPSYN-RXN - ec: - 2.5.1.10 genes: - *id126 left: - geranyl diphosphate - isopentenyl diphosphate name: geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate pmids: [] rhea: [] right: - (2E,6E)-farnesyl diphosphate - diphosphate yeastcyc_id: FPPSYN-RXN - ec: - 5.3.3.2 genes: - *id131 left: - isopentenyl diphosphate name: isopentenyl diphosphate <-> dimethylallyl diphosphate pmids: [] rhea: [] right: - dimethylallyl diphosphate yeastcyc_id: IPPISOM-RXN yeastcyc_id: PWY-5123 PWY-5177: all_genes: - *id119 name: glutaryl-CoA degradation pmids: [] reactions: - ec: [] genes: [] left: - (E)-glutaconyl-CoA - H+ name: (E)-glutaconyl-CoA + H+ -> CO2 + crotonyl-CoA pmids: [] rhea: [] right: - CO2 - crotonyl-CoA yeastcyc_id: GLUTACONYL-COA-DECARBOXYLASE-RXN - ec: - 4.2.1.150 genes: [] left: - (S)-3-hydroxybutanoyl-CoA name: (S)-3-hydroxybutanoyl-CoA <- crotonyl-CoA + H2O pmids: [] rhea: [] right: - H2O - crotonyl-CoA yeastcyc_id: RXN-11667 - ec: - 1.1.1.35 genes: [] left: - (S)-3-hydroxybutanoyl-CoA - NAD+ name: (S)-3-hydroxybutanoyl-CoA + NAD+ <-> acetoacetyl-CoA + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - acetoacetyl-CoA yeastcyc_id: RXN-11662 - ec: - 2.3.1.9 genes: - *id119 left: - acetyl-CoA name: 2 acetyl-CoA <-> acetoacetyl-CoA + coenzyme A pmids: [] rhea: [] right: - acetoacetyl-CoA - coenzyme A yeastcyc_id: ACETYL-COA-ACETYLTRANSFER-RXN - ec: [] genes: [] left: - H+ - an oxidized electron-transfer flavoprotein - glutaryl-CoA name: glutaryl-CoA + an oxidized electron-transfer flavoprotein + H+ <-> (E)-glutaconyl-CoA + a reduced electron-transfer flavoprotein pmids: [] rhea: [] right: - (E)-glutaconyl-CoA - a reduced electron-transfer flavoprotein yeastcyc_id: GLUTARYL-COA-DEHYDROG-RXN yeastcyc_id: PWY-5177 PWY-5194-1: all_genes: - &id330 orf: YKR069W symbol: MET1 uniprot: UniProtKB:P36150 - &id331 orf: YBR213W symbol: MET8 uniprot: UniProtKB:P15807 comment: 'Sulfite and nitrite reductases catalyze the six-electron reduction of sulphite to sulfide and nitrite to ammonia, respectively, which are key enzymatic steps in the assimilation of sulfur and nitrogen into all life forms |CITS: [8994874]|. Siroheme, a modified cyclic tetrapyrrole, similar in structure to heme, chlorophyll and cobalamin, is used as a prosthetic group by sulfite and nitrite reductases |CITS: [4583265]|. Similar to many cyclic tetrapyrroles, siroheme coordinates with a metal in its central cavity. While siroheme and heme coordinate an iron atom, chlorophyll and cobalamin coordinate maganesium and cobalt, respectively. Assimilatory sulfite reductases are found in bacteria, plants and fungi, but not in animals, while dissimilatory sulfite reductases are found in diverse sulfate-reducing eubacteria and some species of thermophilic archaebacteria |CITS: [8994874]|. Assimilatory nitrite reductases are also found in bacteria, plants, and fungi |CITS: [8994874]|, but not in the yeast Saccharomyces cerevisiae. Thus, in S. cerevisiae siroheme is used exclusively in sulfite reductase. The biologically important modified tetrapyrroles, such as siroheme, heme, chlorophyll and cobalamin share a common biosynthetic pathway up to the synthesis of the first macrocyclic intermediate uroporphyrinogen-III |CITS: [2077690]|. Siroheme is biosynthesized from uroporphyringoen-III in four enzymatic steps: two transmethylations, a dehydrogenation, and a ferrochelation |CITS: [10051442]|. In S. cerevisiae the two transmethylations are catalyzed by Met1p, a uroporphyrin III methyltransferase that requires S-adenosyl-L-methionine (AdoMet) as a methyl donor, and the dehydrogenation and ferrochelation reactions are catalyzed by the bifunctional enzyme Met8p |CITS: [10051442], [9003798], [11980703]|. In Escherichia coli K12 a single trifunctional enzyme, siroheme synthase (CysG), catalyzes all four siroheme biosynthetic reactions |CITS: [7945210]|.' name: siroheme biosynthesis pmids: [] reactions: - ec: - 2.1.1.107 genes: - *id330 left: - S-adenosyl-L-methionine - uroporphyrinogen-III name: 2 S-adenosyl-L-methionine + uroporphyrinogen-III -> 2 S-adenosyl-L-homocysteine + precorrin-2 + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - precorrin-2 yeastcyc_id: RXN-13403 - ec: - 1.3.1.76 genes: - *id331 left: - NAD+ - precorrin-2 name: precorrin-2 + NAD+ -> sirohydrochlorin + NADH + 2 H+ pmids: [] rhea: [] right: - H+ - NADH - sirohydrochlorin yeastcyc_id: DIMETHUROPORDEHYDROG-RXN - ec: - 4.99.1.4 genes: - *id331 left: - Fe2+ - sirohydrochlorin name: sirohydrochlorin + Fe2+ -> siroheme + 2 H+ pmids: [] rhea: [] right: - H+ - siroheme yeastcyc_id: SIROHEME-FERROCHELAT-RXN yeastcyc_id: PWY-5194-1 PWY-5340: all_genes: - &id332 orf: YKL001C symbol: MET14 uniprot: UniProtKB:Q02196 - &id333 orf: YJR010W symbol: MET3 uniprot: UniProtKB:P08536 name: sulfate activation (for sulfonation) pmids: [] reactions: - ec: - 2.7.1.25 genes: - *id332 left: - ATP - adenosine 5'-phosphosulfate name: adenosine 5'-phosphosulfate + ATP <-> 3'-phosphoadenylyl-sulfate + ADP + H+ pmids: [] rhea: [] right: - 3'-phosphoadenylyl-sulfate - ADP - H+ yeastcyc_id: ADENYLYLSULFKIN-RXN - ec: - 2.7.7.4 genes: - *id333 left: - ATP - H+ - sulfate name: sulfate + ATP + H+ <-> adenosine 5'-phosphosulfate + diphosphate pmids: [] rhea: [] right: - adenosine 5'-phosphosulfate - diphosphate yeastcyc_id: SULFATE-ADENYLYLTRANS-RXN yeastcyc_id: PWY-5340 PWY-5344: all_genes: - *id264 - *id263 name: L-homocysteine biosynthesis pmids: [] reactions: - ec: - 2.3.1.31 genes: - *id263 left: - L-homoserine - acetyl-CoA name: L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A pmids: [] rhea: [] right: - O-acetyl-L-homoserine - coenzyme A yeastcyc_id: HOMOSERINE-O-ACETYLTRANSFERASE-RXN - ec: - 2.5.1.49 genes: - *id264 left: - O-acetyl-L-homoserine - hydrogen sulfide name: O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H+ pmids: [] rhea: [] right: - H+ - L-homocysteine - acetate yeastcyc_id: ACETYLHOMOSER-CYS-RXN yeastcyc_id: PWY-5344 PWY-5651: all_genes: - *id245 - *id249 - *id250 - *id248 - *id244 - *id251 name: L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde pmids: [] reactions: - ec: - 3.7.1.3 genes: - *id244 left: - 3-hydroxy-L-kynurenine - H2O name: 3-hydroxy-L-kynurenine + H2O -> 3-hydroxyanthranilate + L-alanine + H+ pmids: [] rhea: [] right: - 3-hydroxyanthranilate - H+ - L-alanine yeastcyc_id: 3-HYDROXY-KYNURENINASE-RXN - ec: - 1.13.11.6 genes: - *id245 left: - 3-hydroxyanthranilate - oxygen name: 3-hydroxyanthranilate + oxygen -> 2-amino-3-carboxymuconate-6-semialdehyde + H+ pmids: [] rhea: [] right: - 2-amino-3-carboxymuconate-6-semialdehyde - H+ yeastcyc_id: 1.13.11.6-RXN - ec: - 1.14.13.9 genes: - *id248 left: - H+ - L-kynurenine - NADPH - oxygen name: L-kynurenine + NADPH + oxygen + H+ -> 3-hydroxy-L-kynurenine + NADP+ + H2O pmids: [] rhea: [] right: - 3-hydroxy-L-kynurenine - H2O - NADP+ yeastcyc_id: KYNURENINE-3-MONOOXYGENASE-RXN - ec: - 1.13.11.11 - 1.13.11.52 genes: - *id249 left: - L-tryptophan - oxygen name: L-tryptophan + oxygen -> N-Formyl-L-kynurenine pmids: [] rhea: [] right: - N-Formyl-L-kynurenine yeastcyc_id: RXN-8665 - ec: - 3.5.1.9 genes: - *id250 - *id251 left: - H2O - N-Formyl-L-kynurenine name: N-Formyl-L-kynurenine + H2O -> L-kynurenine + formate + H+ pmids: [] rhea: [] right: - H+ - L-kynurenine - formate yeastcyc_id: ARYLFORMAMIDASE-RXN yeastcyc_id: PWY-5651 PWY-5653: all_genes: - *id247 - *id252 - *id253 - *id246 name: NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde pmids: [] reactions: - ec: [] genes: [] left: - 2-amino-3-carboxymuconate-6-semialdehyde name: 2-amino-3-carboxymuconate-6-semialdehyde -> quinolinate + H2O pmids: [] rhea: [] right: - H2O - quinolinate yeastcyc_id: RXN-5721 - ec: - 6.3.5.1 genes: - *id246 left: - ATP - H2O - L-glutamine - nicotinate adenine dinucleotide name: ATP + nicotinate adenine dinucleotide + L-glutamine + H2O -> L-glutamate + AMP + NAD+ + diphosphate + H+ pmids: [] rhea: [] right: - AMP - H+ - L-glutamate - NAD+ - diphosphate yeastcyc_id: NAD-SYNTH-GLN-RXN - ec: - 2.4.2.19 genes: - *id247 left: - CO2 - diphosphate - β-nicotinate D-ribonucleotide name: CO2 + β-nicotinate D-ribonucleotide + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + quinolinate + 2 H+ pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - H+ - quinolinate yeastcyc_id: QUINOPRIBOTRANS-RXN - ec: - 2.7.7.18 genes: - *id252 - *id253 left: - ATP - H+ - β-nicotinate D-ribonucleotide name: β-nicotinate D-ribonucleotide + ATP + H+ -> nicotinate adenine dinucleotide + diphosphate pmids: [] rhea: [] right: - diphosphate - nicotinate adenine dinucleotide yeastcyc_id: NICONUCADENYLYLTRAN-RXN yeastcyc_id: PWY-5653 PWY-5669: all_genes: - *id289 - *id287 - *id288 name: phosphatidylethanolamine biosynthesis I pmids: [] reactions: - ec: - 4.1.1.65 genes: - *id287 - *id288 left: - H+ - a 3-O-sn-phosphatidyl-L-serine name: a 3-O-sn-phosphatidyl-L-serine + H+ -> an L-1-phosphatidylethanolamine + CO2 pmids: [] rhea: [] right: - CO2 - an L-1-phosphatidylethanolamine yeastcyc_id: PHOSPHASERDECARB-RXN - ec: - 2.7.8.8 genes: - *id289 left: - L-serine - a CDP-diacylglycerol name: a CDP-diacylglycerol + L-serine <-> CMP + a 3-O-sn-phosphatidyl-L-serine + H+ pmids: [] rhea: [] right: - CMP - H+ - a 3-O-sn-phosphatidyl-L-serine yeastcyc_id: PHOSPHASERSYN-RXN yeastcyc_id: PWY-5669 PWY-5670-1: all_genes: - *id133 - *id118 name: epoxysqualene biosynthesis pmids: [] reactions: - ec: - 2.5.1.103 genes: - *id118 left: - (2E,6E)-farnesyl diphosphate name: 2 (2E,6E)-farnesyl diphosphate -> presqualene diphosphate + diphosphate pmids: - '2068081' - '3277535' rhea: [] right: - diphosphate - presqualene diphosphate yeastcyc_id: RXN-12263 - ec: [] genes: - *id118 left: - H+ - NAD(P)H - presqualene diphosphate name: presqualene diphosphate + NAD(P)H + H+ -> squalene + NAD(P)+ + diphosphate pmids: [] rhea: [] right: - NAD(P)+ - diphosphate - squalene yeastcyc_id: RXN66-281 - ec: - 1.14.14.17 genes: - *id133 left: - a reduced electron acceptor - oxygen - squalene name: squalene + a reduced electron acceptor + oxygen -> (3S)-2,3-epoxy-2,3-dihydrosqualene + an oxidized electron acceptor + H2O pmids: [] rhea: [] right: - (3S)-2,3-epoxy-2,3-dihydrosqualene - H2O - an oxidized electron acceptor yeastcyc_id: RXN3O-9816 yeastcyc_id: PWY-5670-1 PWY-5686-1: all_genes: - *id049 - *id050 - *id300 - *id310 - *id051 - *id309 - *id299 - *id311 name: UMP biosynthesis I pmids: [] reactions: - ec: - 3.5.2.3 genes: - *id299 left: - (S)-dihydroorotate - H2O name: (S)-dihydroorotate + H2O <-> N-carbamoyl-L-aspartate + H+ pmids: [] rhea: [] right: - H+ - N-carbamoyl-L-aspartate yeastcyc_id: DIHYDROOROT-RXN - ec: - 1.3.98.1 genes: - *id300 left: - (S)-dihydroorotate - fumarate name: (S)-dihydroorotate + fumarate -> orotate + succinate pmids: [] rhea: [] right: - orotate - succinate yeastcyc_id: RXN-9929 - ec: - 6.3.5.5 genes: - *id049 - *id050 - *id051 left: - ATP - H2O - L-glutamine - hydrogencarbonate name: 2 ATP + L-glutamine + hydrogencarbonate + H2O -> L-glutamate + carbamoyl phosphate + 2 ADP + phosphate + 2 H+ pmids: - '8626695' rhea: [] right: - ADP - H+ - L-glutamate - carbamoyl phosphate - phosphate yeastcyc_id: CARBPSYN-RXN - ec: - 2.1.3.2 genes: - *id051 left: - L-aspartate - carbamoyl phosphate name: L-aspartate + carbamoyl phosphate <-> N-carbamoyl-L-aspartate + phosphate + H+ pmids: [] rhea: [] right: - H+ - N-carbamoyl-L-aspartate - phosphate yeastcyc_id: ASPCARBTRANS-RXN - ec: - 4.1.1.23 genes: - *id309 left: - H+ - orotidine 5'-phosphate name: orotidine 5'-phosphate + H+ -> CO2 + UMP pmids: [] rhea: [] right: - CO2 - UMP yeastcyc_id: OROTPDECARB-RXN - ec: - 2.4.2.10 genes: - *id310 - *id311 left: - diphosphate - orotidine 5'-phosphate name: orotidine 5'-phosphate + diphosphate <-> 5-phospho-α-D-ribose 1-diphosphate + orotate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - orotate yeastcyc_id: OROPRIBTRANS-RXN yeastcyc_id: PWY-5686-1 PWY-5694: all_genes: - *id039 - *id042 - *id040 name: allantoin degradation to glyoxylate I pmids: [] reactions: - ec: - 3.5.2.5 genes: - *id039 left: - (S)-(+)-allantoin - H2O name: (S)-(+)-allantoin + H2O -> allantoate + H+ pmids: [] rhea: [] right: - H+ - allantoate yeastcyc_id: ALLANTOINASE-RXN - ec: - 4.3.2.3 genes: - *id040 left: - (S)-ureidoglycolate name: (S)-ureidoglycolate -> urea + glyoxylate pmids: [] rhea: [] right: - glyoxylate - urea yeastcyc_id: UREIDOGLYCOLATE-LYASE-RXN - ec: - 3.5.3.4 genes: - *id042 left: - H2O - allantoate name: allantoate + H2O -> (S)-ureidoglycolate + urea pmids: [] rhea: [] right: - (S)-ureidoglycolate - urea yeastcyc_id: ALLANTOICASE-RXN yeastcyc_id: PWY-5694 PWY-5697: all_genes: - *id039 - *id042 name: allantoin degradation to ureidoglycolate I (urea producing) pmids: [] reactions: - ec: - 3.5.2.5 genes: - *id039 left: - (S)-(+)-allantoin - H2O name: (S)-(+)-allantoin + H2O -> allantoate + H+ pmids: [] rhea: [] right: - H+ - allantoate yeastcyc_id: ALLANTOINASE-RXN - ec: - 3.5.3.4 genes: - *id042 left: - H2O - allantoate name: allantoate + H2O -> (S)-ureidoglycolate + urea pmids: [] rhea: [] right: - (S)-ureidoglycolate - urea yeastcyc_id: ALLANTOICASE-RXN yeastcyc_id: PWY-5697 PWY-5703: all_genes: - *id041 name: urea degradation I pmids: [] reactions: - ec: - 6.3.4.6 genes: - *id041 left: - ATP - CO2 - H2O - urea name: CO2 + urea + ATP + H2O -> ADP + urea-1-carboxylate + phosphate + 2 H+ pmids: [] rhea: [] right: - ADP - H+ - phosphate - urea-1-carboxylate yeastcyc_id: UREA-CARBOXYLASE-RXN - ec: - 3.5.1.54 genes: - *id041 left: - H+ - H2O - urea-1-carboxylate name: urea-1-carboxylate + 3 H+ + H2O -> 2 ammonium + 2 CO2 pmids: [] rhea: [] right: - CO2 - ammonium yeastcyc_id: ALLOPHANATE-HYDROLASE-RXN yeastcyc_id: PWY-5703 PWY-5760-1: all_genes: - *id155 - *id273 - *id276 name: β-alanine biosynthesis IV pmids: - '12586697' reactions: - ec: - 1.2.1.3 genes: - *id155 - *id273 left: - 3-aminopropanal - H2O - NAD+ name: 3-aminopropanal + NAD+ + H2O -> β-alanine + NADH pmids: [] rhea: [] right: - NADH - β-alanine yeastcyc_id: 3-PROPANAL-DEHYDROGENASE-RXN - ec: - 1.5.3.16 - 1.5.3.17 genes: - *id276 left: - H2O - oxygen - spermine name: spermine + oxygen + H2O -> spermidine + 3-aminopropanal + hydrogen peroxide pmids: [] rhea: [] right: - 3-aminopropanal - hydrogen peroxide - spermidine yeastcyc_id: RXN-9015 yeastcyc_id: PWY-5760-1 PWY-5971-1: all_genes: - *id134 - *id135 comment: 'Fatty acids are essential to all organisms except for archaea; they are major constituents of cellular membranes, and are used for energy storage and for posttranslational protein modifications. Most organisms are capable of synthesizing long chain (C12:0-C16:0) saturated fatty acids de novo. Although the initiation and termination reactions may vary, the cyclic series of chain-lengthening reactions are essentially the same across all organisms. The fatty acid chain, which starts as a 2-carbon chain from acetyl-CoA, is extended two carbons at a time by the addition of an acetyl group from malonyl-CoA. When the final length of the fatty acid is achieved, fatty acid synthesis is terminated. Each cycle of chain elongation involves 5 reactions with the following enzymatic activities: malonyl transferase (EC: 2.3.1.39), ketoacyl synthase (EC: 2.3.1.41), ketoacyl reductase (EC: 1.1.1.100), 3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61), and enoyl-acyl reductase (EC: 1.3.1.10). In yeast, fatty acid biosynthesis is terminated with the release of fatty acyl-CoAs from fatty acid synthase (FAS), the enzyme complex that carries out de novo fatty acid biosynthesis. Palmitoyl- (C16) and stearoyl-CoA (C18) are the main products in yeast, while myristoyl-CoA (C14) is only produced in small amounts |CITS: [Lynen69]|. To synthesize palmitoyl-CoA (C16) one acetyl-CoA and 7 malonyl-CoA molecules are required. The elongation substrate, malonyl-CoA is synthesized from the carboxylation of acetyl-CoA (EC 6.4.1.2) by the biotin-containing enzyme, acetyl-CoA carboxylase (Acc1p) |CITS: [1350093]|). Acetyl-CoA carboxylase is activated by the biotin:apoprotein ligase (Bpl1p) |CITS: [7649444]|). There are two types of FAS systems based on the organization of the catalytic sites. Fungi, animals, and some bacteria have type I FASs, which are large multi-functional proteins that contain all of the requisite catalytic active sites for fatty acid biosynthesis within domains on a single polypeptide (alpha) or on two polypeptides (alpha and beta). Fungal FASs are alpha6beta6 heterododecamers, animal FASs are alpha2 homodimers, and some type I bacterial FASs are alpha6 |CITS: [17448991]|. Bacteria, plants and mitochondria, on the other hand, have type II FAS systems, which are comprised of independent proteins, whereby each protein catalyzes a single step in the cyclic series of reactions |CITS: [15952903]|. The yeast FAS complex catalyzes a total of 8 reactions. The alpha subunit(Fas2p) catalyzes 3 reactions, ketoacyl synthase (EC: 2.3.1.41),ketoacyl reductase (EC: 1.1.1.100) and self pantetheinylation and the yeast beta subunit (Fas1p) catalyzes 5 reactions, acetyltransferase (EC 2.3.1.38), malonyl transferase (EC: 2.3.1.39),3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61),enoyl-acyl reductase (EC: 1.3.1.10), and palmitoyl transferase (EC:2.3.1.-) |CITS: [365179], [1100391], [10785388], [3528750], [374077]|. FASs are regulated at the transcriptional and translational level as well as posttranslationally. In yeast, FAS is a housekeeping enzyme that is expressed constitutively at a low level, but its expression is also activated by the general yeast transcription factors Rap1, Abf1 and Reb1 |CITS: [7925441]| and theinositol/choline-responsive transcription factor heterodimer, Ino2p-Ino4p |CITS: [1461729][7862526]|. The coordinate expression of the two subunits also appears to be regulated by Fas1p controlling the expression of FAS2 |CITS: [11713312]|. The FAS subunits are further regulated by proteolytic degradation of excess subunits. While the intact FAS multimeric complex (alpha6beta6 ) is stable, its individual subunits are rapidly degraded |CITS: [1735446][8262967]|.' name: myristate biosynthesis pmids: [] reactions: - ec: - 1.3.1.10 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - H+ - NADPH - a (2E)-dec-2-enoyl-[acp] name: a (2E)-dec-2-enoyl-[acp] + NADPH + H+ -> a decanoyl-[acp] + NADP+ pmids: [] rhea: [] right: - NADP+ - a decanoyl-[acp] yeastcyc_id: RXN-9530 - ec: - 1.3.1.10 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - H+ - NADPH - a (2E)-dodec-2-enoyl-[acp] name: a (2E)-dodec-2-enoyl-[acp] + NADPH + H+ -> a dodecanoyl-[acp] + NADP+ pmids: [] rhea: [] right: - NADP+ - a dodecanoyl-[acp] yeastcyc_id: RXN-9534 - ec: - 1.3.1.10 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - H+ - NADPH - a (2E)-hex-2-enoyl-[acp] name: a (2E)-hex-2-enoyl-[acp] + NADPH + H+ -> a hexanoyl-[acp] + NADP+ pmids: [] rhea: [] right: - NADP+ - a hexanoyl-[acp] yeastcyc_id: RXN-9521 - ec: - 1.3.1.10 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - H+ - NADPH - a (2E)-oct-2-enoyl-[acp] name: a (2E)-oct-2-enoyl-[acp] + NADPH + H+ -> an octanoyl-[acp] + NADP+ pmids: [] rhea: [] right: - NADP+ - an octanoyl-[acp] yeastcyc_id: RXN-9526 - ec: - 1.3.1.10 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - H+ - NADPH - a (2E)-tetradec-2-enoyl-[acp] name: a (2E)-tetradec-2-enoyl-[acp] + NADPH + H+ -> a myristoyl-[acp] + NADP+ pmids: [] rhea: [] right: - NADP+ - a myristoyl-[acp] yeastcyc_id: RXN-9538 - ec: - 2.3.1.86 - 4.2.1.59 genes: - *id134 left: - a (3R)-3-hydroxydecanoyl-[acp] name: a (3R)-3-hydroxydecanoyl-[acp] -> a (2E)-dec-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-dec-2-enoyl-[acp] yeastcyc_id: RXN-9655 - ec: - 2.3.1.86 genes: [] left: - NADP+ - a (3R)-3-hydroxydecanoyl-[acp] name: a (3R)-3-hydroxydecanoyl-[acp] + NADP+ <- a 3-oxodecanoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxodecanoyl-[acp] yeastcyc_id: RXN-9528 - ec: - 2.3.1.86 - 4.2.1.59 genes: - *id134 left: - a (3R)-3-hydroxydodecanoyl-[acp] name: a (3R)-3-hydroxydodecanoyl-[acp] -> a (2E)-dodec-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-dodec-2-enoyl-[acp] yeastcyc_id: RXN-9533 - ec: - 2.3.1.86 genes: [] left: - NADP+ - a (3R)-3-hydroxydodecanoyl-[acp] name: a (3R)-3-hydroxydodecanoyl-[acp] + NADP+ <- a 3-oxododecanoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxododecanoyl-[acp] yeastcyc_id: RXN-9532 - ec: - 2.3.1.86 - 4.2.1.59 genes: - *id134 left: - a (3R)-3-hydroxyhexanoyl-[acp] name: a (3R)-3-hydroxyhexanoyl-[acp] -> a (2E)-hex-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-hex-2-enoyl-[acp] yeastcyc_id: RXN-9520 - ec: - 2.3.1.86 genes: [] left: - NADP+ - a (3R)-3-hydroxyhexanoyl-[acp] name: a (3R)-3-hydroxyhexanoyl-[acp] + NADP+ <- a 3-oxohexanoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxohexanoyl-[acp] yeastcyc_id: RXN-9518 - ec: - 2.3.1.86 - 4.2.1.59 genes: - *id134 left: - a (3R)-3-hydroxyoctanoyl-[acp] name: a (3R)-3-hydroxyoctanoyl-[acp] -> a (2E)-oct-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-oct-2-enoyl-[acp] yeastcyc_id: 4.2.1.59-RXN - ec: - 2.3.1.86 genes: [] left: - NADP+ - a (3R)-3-hydroxyoctanoyl-[acp] name: a (3R)-3-hydroxyoctanoyl-[acp] + NADP+ <- a 3-oxooctanoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxooctanoyl-[acp] yeastcyc_id: RXN-9524 - ec: - 2.3.1.85 - 2.3.1.86 - 4.2.1.59 - 4.2.1.61 genes: - *id134 left: - a (3R)-3-hydroxytetradecanoyl-[acp] name: a (3R)-3-hydroxytetradecanoyl-[acp] -> a (2E)-tetradec-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-tetradec-2-enoyl-[acp] yeastcyc_id: RXN-9537 - ec: - 2.3.1.86 genes: [] left: - NADP+ - a (3R)-3-hydroxytetradecanoyl-[acp] name: a (3R)-3-hydroxytetradecanoyl-[acp] + NADP+ <- a 3-oxotetradecanoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxotetradecanoyl-[acp] yeastcyc_id: RXN-9536 - ec: - 2.3.1.179 genes: - *id135 left: - H+ - a butanoyl-[acp] - a malonyl-[acp] name: a butanoyl-[acp] + a malonyl-[acp] + H+ -> a 3-oxohexanoyl-[acp] + CO2 + acyl-carrier protein pmids: [] rhea: [] right: - CO2 - a 3-oxohexanoyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: RXN-9516 - ec: - 2.3.1.179 genes: - *id135 left: - H+ - a decanoyl-[acp] - a malonyl-[acp] name: a decanoyl-[acp] + a malonyl-[acp] + H+ -> a 3-oxododecanoyl-[acp] + CO2 + acyl-carrier protein pmids: [] rhea: [] right: - CO2 - a 3-oxododecanoyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: RXN-9531 - ec: - 2.3.1.179 genes: - *id135 left: - H+ - a dodecanoyl-[acp] - a malonyl-[acp] name: a dodecanoyl-[acp] + a malonyl-[acp] + H+ -> a 3-oxotetradecanoyl-[acp] + CO2 + acyl-carrier protein pmids: [] rhea: [] right: - CO2 - a 3-oxotetradecanoyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: RXN-9535 - ec: - 2.3.1.179 genes: - *id135 left: - H+ - a hexanoyl-[acp] - a malonyl-[acp] name: a hexanoyl-[acp] + a malonyl-[acp] + H+ -> a 3-oxooctanoyl-[acp] + CO2 + acyl-carrier protein pmids: [] rhea: [] right: - CO2 - a 3-oxooctanoyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: RXN-9523 - ec: - 2.3.1.- genes: - *id134 left: - a myristoyl-[acp] - coenzyme A name: a myristoyl-[acp] + coenzyme A -> acyl-carrier protein + myristoyl-CoA pmids: [] rhea: [] right: - a soluble [acyl-carrier protein] - myristoyl-CoA yeastcyc_id: RXN3O-8214 - ec: - 2.3.1.179 genes: - *id135 left: - H+ - a malonyl-[acp] - an octanoyl-[acp] name: an octanoyl-[acp] + a malonyl-[acp] + H+ -> a 3-oxodecanoyl-[acp] + CO2 + acyl-carrier protein pmids: [] rhea: [] right: - CO2 - a 3-oxodecanoyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: RXN-9527 - ec: - 3.1.2.2 genes: [] left: - H2O - myristoyl-CoA name: myristoyl-CoA + H2O -> myristate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - myristate yeastcyc_id: RXN-9626 yeastcyc_id: PWY-5971-1 PWY-6074-1: all_genes: - *id132 - *id121 - *id120 - *id122 - *id123 name: zymosterol biosynthesis pmids: [] reactions: - ec: - 1.14.13.72 genes: - *id120 left: - 4,4-dimethylzymosterol - NAD(P)H - oxygen name: 4,4-dimethylzymosterol + NAD(P)H + oxygen -> 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + H2O pmids: [] rhea: [] right: - 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9821 - ec: - 1.3.1.70 genes: - *id121 left: - 4,4-dimethylzymosterol - NADP+ name: 4,4-dimethylzymosterol + NADP+ <- 4,4-dimethyl-cholesta-8,14,24-trienol + NADPH + H+ pmids: [] rhea: [] right: - 4,4-dimethyl-cholesta-8,14,24-trienol - H+ - NADPH yeastcyc_id: RXN66-306 - ec: - 1.1.1.170 genes: - *id122 left: - 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)+ name: 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ -> 3-dehydro-4-methylzymosterol + CO2 + NAD(P)H pmids: [] rhea: [] right: - 3-dehydro-4-methylzymosterol - CO2 - NAD(P)H yeastcyc_id: RXN66-313 - ec: - 1.1.1.170 genes: - *id122 left: - 4α-carboxy-5α-cholesta-8,24-dien-3β-ol - NAD(P)+ name: 4α-carboxy-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ -> zymosterone + CO2 + NAD(P)H pmids: [] rhea: [] right: - CO2 - NAD(P)H - zymosterone yeastcyc_id: RXN66-318 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)H - oxygen name: 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)H + oxygen -> 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + H2O pmids: [] rhea: [] right: - 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9823 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-formyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)H - oxygen name: 4α-formyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)H + oxygen -> 4α-carboxy-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + H2O pmids: [] rhea: [] right: - 4α-carboxy-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9826 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)H - oxygen name: 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)H + oxygen -> 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + 2 H2O pmids: [] rhea: [] right: - 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9822 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)H - oxygen name: 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)H + oxygen -> 4α-formyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + 2 H2O pmids: [] rhea: [] right: - 4α-formyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9825 - ec: - 1.14.13.72 genes: - *id120 left: - 4α-methyl-zymosterol - NAD(P)H - oxygen name: 4α-methyl-zymosterol + NAD(P)H + oxygen -> 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ + H2O pmids: [] rhea: [] right: - 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol - H2O - NAD(P)+ yeastcyc_id: RXN3O-9824 - ec: - 1.1.1.270 genes: - *id123 left: - 4α-methyl-zymosterol - NADP+ name: 4α-methyl-zymosterol + NADP+ <- 3-dehydro-4-methylzymosterol + NADPH + H+ pmids: [] rhea: [] right: - 3-dehydro-4-methylzymosterol - H+ - NADPH yeastcyc_id: RXN66-314 - ec: - 1.14.13.70 genes: - *id132 left: - H+ - NADPH - lanosterol - oxygen name: lanosterol + 3 NADPH + 3 oxygen + 3 H+ -> 4,4-dimethyl-cholesta-8,14,24-trienol + formate + 3 NADP+ + 4 H2O pmids: [] rhea: [] right: - 4,4-dimethyl-cholesta-8,14,24-trienol - H2O - NADP+ - formate yeastcyc_id: RXN3O-9820 - ec: - 1.1.1.270 genes: - *id123 left: - NADP+ - zymosterol name: zymosterol + NADP+ <- zymosterone + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - zymosterone yeastcyc_id: RXN66-319 yeastcyc_id: PWY-6074-1 PWY-6075-1: all_genes: - *id130 - *id127 - *id129 - *id128 - *id124 name: ergosterol biosynthesis I pmids: [] reactions: - ec: - 2.1.1.41 genes: - *id124 left: - S-adenosyl-L-methionine - zymosterol name: S-adenosyl-L-methionine + zymosterol -> S-adenosyl-L-homocysteine + fecosterol + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - fecosterol yeastcyc_id: RXN3O-178 - ec: [] genes: - *id127 left: - H+ - NADPH - episterol - oxygen name: episterol + NADPH + oxygen + H+ -> ergosta-5,7,24(28)-trien-3β-ol + NADP+ + 2 H2O pmids: [] rhea: [] right: - H2O - NADP+ - ergosta-5,7,24(28)-trien-3β-ol yeastcyc_id: RXN3O-9827 - ec: [] genes: - *id128 left: - H+ - NADPH - ergosta-5,7,24(28)-trien-3β-ol - oxygen name: ergosta-5,7,24(28)-trien-3β-ol + NADPH + oxygen + H+ -> ergosta-5,7,22,24(28)-tetraen-3-β-ol + NADP+ + 2 H2O pmids: [] rhea: [] right: - H2O - NADP+ - ergosta-5,7,22,24(28)-tetraen-3-β-ol yeastcyc_id: RXN3O-9828 - ec: - 1.3.1.71 genes: - *id129 left: - NADP+ - ergosterol name: ergosterol + NADP+ <- ergosta-5,7,22,24(28)-tetraen-3-β-ol + NADPH + H+ pmids: - '10722850' rhea: [] right: - H+ - NADPH - ergosta-5,7,22,24(28)-tetraen-3-β-ol yeastcyc_id: 1.3.1.71-RXN - ec: [] genes: - *id130 left: - fecosterol name: fecosterol -> episterol pmids: [] rhea: [] right: - episterol yeastcyc_id: RXN3O-203 yeastcyc_id: PWY-6075-1 PWY-6122-1: all_genes: - *id088 - *id091 - *id093 - *id103 name: 5-aminoimidazole ribonucleotide biosynthesis II pmids: [] reactions: - ec: - 2.4.2.14 genes: - *id088 left: - 5-phospho-β-D-ribosylamine - L-glutamate - diphosphate name: 5-phospho-β-D-ribosylamine + L-glutamate + diphosphate <-> 5-phospho-α-D-ribose 1-diphosphate + L-glutamine + H2O pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - H2O - L-glutamine yeastcyc_id: PRPPAMIDOTRANS-RXN - ec: - 6.3.3.1 genes: - *id091 left: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ATP name: ATP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine -> ADP + 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + phosphate + H+ pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - ADP - H+ - phosphate yeastcyc_id: AIRS-RXN - ec: - 6.3.4.13 genes: - *id091 left: - 5-phospho-β-D-ribosylamine - ATP - glycine name: ATP + 5-phospho-β-D-ribosylamine + glycine -> ADP + N1-(5-phospho-β-D-ribosyl)glycinamide + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - N1-(5-phospho-β-D-ribosyl)glycinamide - phosphate yeastcyc_id: GLYRIBONUCSYN-RXN - ec: - 6.3.5.3 genes: - *id093 left: - ATP - H2O - L-glutamine - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide name: ATP + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + L-glutamine + H2O -> L-glutamate + ADP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine + phosphate + H+ pmids: [] rhea: [] right: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ADP - H+ - L-glutamate - phosphate yeastcyc_id: FGAMSYN-RXN - ec: - 2.1.2.2 genes: - *id103 left: - N1-(5-phospho-β-D-ribosyl)glycinamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + N1-(5-phospho-β-D-ribosyl)glycinamide <-> a tetrahydrofolate + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + H+ pmids: [] rhea: [] right: - H+ - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide - a tetrahydrofolate yeastcyc_id: GART-RXN yeastcyc_id: PWY-6122-1 PWY-6123-1: all_genes: - *id092 - *id086 - *id096 - *id097 - *id087 name: inosine-5'-phosphate biosynthesis I pmids: [] reactions: - ec: - 4.3.2.2 genes: - *id086 left: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole name: 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <-> fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - fumarate yeastcyc_id: AICARSYN-RXN - ec: - 4.1.1.21 genes: - *id087 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - H+ name: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H+ <-> 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + CO2 pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - CO2 yeastcyc_id: AIRCARBOXY-RXN - ec: - 6.3.2.6 genes: - *id092 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - ATP - L-aspartate name: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate -> ADP + 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole + phosphate + H+ pmids: [] rhea: [] right: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole - ADP - H+ - phosphate yeastcyc_id: SAICARSYN-RXN - ec: - 3.5.4.10 genes: - *id096 - *id097 left: - H2O - IMP name: IMP + H2O <-> 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide yeastcyc_id: IMPCYCLOHYDROLASE-RXN - ec: - 2.1.2.3 genes: - *id096 - *id097 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide <-> a tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide - a tetrahydrofolate yeastcyc_id: AICARTRANSFORM-RXN yeastcyc_id: PWY-6123-1 PWY-6125: all_genes: - *id102 - *id095 - *id098 - *id099 - *id100 - *id104 - *id105 - *id106 - *id107 - *id094 name: superpathway of guanosine nucleotides de novo biosynthesis II pmids: [] reactions: - ec: - 2.7.4.6 genes: - *id094 left: - ATP - GDP name: GDP + ATP -> GTP + ADP pmids: [] rhea: [] right: - ADP - GTP yeastcyc_id: GDPKIN-RXN - ec: - 2.7.4.8 genes: - *id095 left: - ATP - GMP name: GMP + ATP <-> GDP + ADP pmids: [] rhea: [] right: - ADP - GDP yeastcyc_id: GUANYL-KIN-RXN - ec: - 1.1.1.205 genes: - *id098 - *id099 - *id100 left: - H2O - IMP - NAD+ name: IMP + NAD+ + H2O <-> XMP + NADH + H+ pmids: - '12746440' rhea: [] right: - H+ - NADH - XMP yeastcyc_id: IMP-DEHYDROG-RXN - ec: - 6.3.5.2 genes: - *id102 left: - ATP - H2O - L-glutamine - XMP name: XMP + L-glutamine + ATP + H2O -> L-glutamate + GMP + AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - AMP - GMP - H+ - L-glutamate - diphosphate yeastcyc_id: GMP-SYN-GLUT-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dGDP name: dGDP + ATP -> dGTP + ADP pmids: [] rhea: [] right: - ADP - dGTP yeastcyc_id: DGDPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dGDP name: dGDP + an oxidized thioredoxin + H2O <- GDP + a reduced thioredoxin pmids: [] rhea: [] right: - GDP - a reduced thioredoxin yeastcyc_id: GDPREDUCT-RXN - ec: - 1.1.98.6 genes: [] left: - GTP - H+ - formate name: formate + GTP + H+ -> dGTP + CO2 + H2O pmids: [] rhea: [] right: - CO2 - H2O - dGTP yeastcyc_id: RXN0-746 yeastcyc_id: PWY-6125 PWY-6126-1: all_genes: - *id101 - *id086 - *id089 - *id090 - *id104 - *id105 - *id106 - *id107 - *id094 name: superpathway of adenosine nucleotides de novo biosynthesis II pmids: [] reactions: - ec: - 2.7.4.3 genes: - *id089 - *id090 left: - AMP - ATP name: AMP + ATP <-> 2 ADP pmids: [] rhea: [] right: - ADP yeastcyc_id: ADENYL-KIN-RXN - ec: - 6.3.4.4 genes: - *id101 left: - GTP - IMP - L-aspartate name: L-aspartate + IMP + GTP -> adenylo-succinate + GDP + phosphate + 2 H+ pmids: [] rhea: [] right: - GDP - H+ - adenylo-succinate - phosphate yeastcyc_id: ADENYLOSUCCINATE-SYNTHASE-RXN - ec: - 4.3.2.2 genes: - *id086 left: - adenylo-succinate name: adenylo-succinate <-> fumarate + AMP pmids: [] rhea: [] right: - AMP - fumarate yeastcyc_id: AMPSYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dADP name: dADP + ATP -> dATP + ADP pmids: [] rhea: [] right: - ADP - dATP yeastcyc_id: DADPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dADP name: dADP + an oxidized thioredoxin + H2O <- ADP + a reduced thioredoxin pmids: [] rhea: [] right: - ADP - a reduced thioredoxin yeastcyc_id: ADPREDUCT-RXN - ec: - 1.1.98.6 genes: [] left: - ATP - H+ - formate name: formate + ATP + H+ -> CO2 + dATP + H2O pmids: [] rhea: [] right: - CO2 - H2O - dATP yeastcyc_id: RXN0-745 yeastcyc_id: PWY-6126-1 PWY-6132: all_genes: - *id112 name: lanosterol biosynthesis pmids: [] reactions: - ec: - 5.4.99.7 genes: - *id112 left: - (3S)-2,3-epoxy-2,3-dihydrosqualene name: (3S)-2,3-epoxy-2,3-dihydrosqualene -> lanosterol pmids: [] rhea: [] right: - lanosterol yeastcyc_id: LANOSTEROL-SYNTHASE-RXN yeastcyc_id: PWY-6132 PWY-6147: all_genes: - *id010 - *id012 name: 6-hydroxymethyl-dihydropterin diphosphate biosynthesis I pmids: [] reactions: - ec: - 2.7.6.3 genes: - *id010 left: - 6-(hydroxymethyl)-7,8-dihydropterin - ATP name: 6-(hydroxymethyl)-7,8-dihydropterin + ATP -> (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H+ pmids: [] rhea: [] right: - (7,8-dihydropterin-6-yl)methyl diphosphate - AMP - H+ yeastcyc_id: H2PTERIDINEPYROPHOSPHOKIN-RXN - ec: - 4.1.2.25 genes: - *id010 left: - 7,8-dihydroneopterin name: 7,8-dihydroneopterin -> glycolaldehyde + 6-(hydroxymethyl)-7,8-dihydropterin pmids: [] rhea: [] right: - 6-(hydroxymethyl)-7,8-dihydropterin - glycolaldehyde yeastcyc_id: H2NEOPTERINALDOL-RXN - ec: - 3.6.1.- genes: [] left: - 7,8-dihydroneopterin 3'-phosphate - H2O name: 7,8-dihydroneopterin 3'-phosphate + H2O -> 7,8-dihydroneopterin + phosphate pmids: [] rhea: [] right: - 7,8-dihydroneopterin - phosphate yeastcyc_id: DIHYDRONEOPTERIN-MONO-P-DEPHOS-RXN - ec: - 3.6.1.67 genes: [] left: - 7,8-dihydroneopterin 3'-triphosphate - H2O name: 7,8-dihydroneopterin 3'-triphosphate + H2O -> 7,8-dihydroneopterin 3'-phosphate + diphosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydroneopterin 3'-phosphate - H+ - diphosphate yeastcyc_id: H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN - ec: - 3.5.4.16 genes: - *id012 left: - GTP - H2O name: GTP + H2O -> formate + 7,8-dihydroneopterin 3'-triphosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydroneopterin 3'-triphosphate - H+ - formate yeastcyc_id: GTP-CYCLOHYDRO-I-RXN yeastcyc_id: PWY-6147 PWY-6482-1: all_genes: - &id335 orf: YIL103W symbol: DPH1 uniprot: UniProtKB:P40487 - &id336 orf: YKL191W symbol: DPH2 uniprot: UniProtKB:P32461 - &id334 orf: YLR172C symbol: DPH5 uniprot: UniProtKB:P32469 - &id337 orf: YBL071W-A symbol: KTI11 uniprot: UniProtKB:Q3E840 - &id338 orf: YBR246W symbol: RRT2 uniprot: UniProtKB:P38332 name: diphthamide biosynthesis pmids: - '1508200' - '15485916' - '3042777' - '6339504' - '8406038' reactions: - ec: [] genes: - *id334 left: - S-adenosyl-L-methionine - a 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2] name: S-adenosyl-L-methionine + a 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2] -> a 2-[(3S)-3-carboxy-3-(methylammonio)propyl]-L-histidine-[translation elongation factor 2] + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a 2-[(3S)-3-carboxy-3-(methylammonio)propyl]-L-histidine-[translation elongation factor 2] yeastcyc_id: RXN-11370 - ec: [] genes: - *id334 left: - S-adenosyl-L-methionine - a 2-[(3S)-3-carboxy-3-(dimethylammonio)propyl]-L-histidine-[translation elongation factor 2] name: S-adenosyl-L-methionine + a 2-[(3S)-3-carboxy-3-(dimethylammonio)propyl]-L-histidine-[translation elongation factor 2] -> a diphthine-[translation elongation factor 2] + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a diphthine-[translation elongation factor 2] yeastcyc_id: RXN-11373 - ec: [] genes: - *id334 left: - S-adenosyl-L-methionine - a 2-[(3S)-3-carboxy-3-(methylammonio)propyl]-L-histidine-[translation elongation factor 2] name: S-adenosyl-L-methionine + a 2-[(3S)-3-carboxy-3-(methylammonio)propyl]-L-histidine-[translation elongation factor 2] -> a 2-[(3S)-3-carboxy-3-(dimethylammonio)propyl]-L-histidine-[translation elongation factor 2] + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a 2-[(3S)-3-carboxy-3-(dimethylammonio)propyl]-L-histidine-[translation elongation factor 2] yeastcyc_id: RXN-11374 - ec: [] genes: - *id335 - *id336 - *id337 left: - S-adenosyl-L-methionine - an L-histidine-[translation elongation factor 2] name: S-adenosyl-L-methionine + an L-histidine-[translation elongation factor 2] -> a 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2] + S-methyl-5'-thioadenosine + H+ pmids: [] rhea: [] right: - H+ - S-methyl-5'-thioadenosine - a 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2] yeastcyc_id: RXN-11371 - ec: - 6.3.1.14 genes: - *id338 left: - ATP - a diphthine-[translation elongation factor 2] - ammonium name: a diphthine-[translation elongation factor 2] + ammonium + ATP -> a diphthamide-[translation elongation factor 2] + AMP + diphosphate + H+ pmids: - '22188241' rhea: [] right: - AMP - H+ - a diphthamide-[translation elongation factor 2] - diphosphate yeastcyc_id: DIPHTINE--AMMONIA-LIGASE-RXN yeastcyc_id: PWY-6482-1 PWY-6543: all_genes: - *id014 - *id009 name: 4-aminobenzoate biosynthesis pmids: [] reactions: - ec: - 4.1.3.38 genes: - *id009 left: - 4-amino-4-deoxychorismate name: 4-amino-4-deoxychorismate -> 4-aminobenzoate + pyruvate + H+ pmids: [] rhea: [] right: - 4-aminobenzoate - H+ - pyruvate yeastcyc_id: ADCLY-RXN - ec: - 2.6.1.85 genes: - *id014 left: - L-glutamine - chorismate name: L-glutamine + chorismate <-> 4-amino-4-deoxychorismate + L-glutamate pmids: [] rhea: [] right: - 4-amino-4-deoxychorismate - L-glutamate yeastcyc_id: PABASYN-RXN yeastcyc_id: PWY-6543 PWY-6614: all_genes: - *id027 - *id010 - *id013 name: tetrahydrofolate biosynthesis pmids: [] reactions: - ec: - 2.5.1.15 genes: - *id010 left: - (7,8-dihydropterin-6-yl)methyl diphosphate - 4-aminobenzoate name: 4-aminobenzoate + (7,8-dihydropterin-6-yl)methyl diphosphate -> 7,8-dihydropteroate + diphosphate pmids: [] rhea: [] right: - 7,8-dihydropteroate - diphosphate yeastcyc_id: H2PTEROATESYNTH-RXN - ec: - 6.3.2.12 genes: - *id013 left: - 7,8-dihydropteroate - ATP - L-glutamate name: L-glutamate + 7,8-dihydropteroate + ATP -> ADP + 7,8-dihydrofolate monoglutamate + phosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydrofolate monoglutamate - ADP - H+ - phosphate yeastcyc_id: DIHYDROFOLATESYNTH-RXN - ec: - 1.5.1.3 genes: - *id027 left: - NADP+ - a tetrahydrofolate name: a tetrahydrofolate + NADP+ <- a 7,8-dihydrofolate + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 7,8-dihydrofolate yeastcyc_id: DIHYDROFOLATEREDUCT-RXN yeastcyc_id: PWY-6614 PWY-7176: all_genes: - *id301 - *id307 - *id308 name: UTP and CTP de novo biosynthesis pmids: [] reactions: - ec: - 2.7.4.14 - 2.7.4.22 - 2.7.4.4 genes: - *id301 left: - ATP - UMP name: ATP + UMP -> ADP + UDP pmids: [] rhea: [] right: - ADP - UDP yeastcyc_id: RXN-12002 - ec: - 6.3.4.2 genes: - *id307 - *id308 left: - ATP - H2O - L-glutamine - UTP name: L-glutamine + UTP + ATP + H2O -> ADP + CTP + L-glutamate + phosphate + 2 H+ pmids: [] rhea: [] right: - ADP - CTP - H+ - L-glutamate - phosphate yeastcyc_id: CTPSYN-RXN - ec: - 2.7.4.6 genes: [] left: - ATP - UDP name: UDP + ATP -> UTP + ADP pmids: [] rhea: [] right: - ADP - UTP yeastcyc_id: UDPKIN-RXN yeastcyc_id: PWY-7176 PWY-7219: all_genes: - *id101 - *id086 - *id089 - *id090 name: adenosine ribonucleotides de novo biosynthesis pmids: [] reactions: - ec: - 2.7.4.3 genes: - *id089 - *id090 left: - AMP - ATP name: AMP + ATP <-> 2 ADP pmids: [] rhea: [] right: - ADP yeastcyc_id: ADENYL-KIN-RXN - ec: - 6.3.4.4 genes: - *id101 left: - GTP - IMP - L-aspartate name: L-aspartate + IMP + GTP -> adenylo-succinate + GDP + phosphate + 2 H+ pmids: [] rhea: [] right: - GDP - H+ - adenylo-succinate - phosphate yeastcyc_id: ADENYLOSUCCINATE-SYNTHASE-RXN - ec: - 4.3.2.2 genes: - *id086 left: - adenylo-succinate name: adenylo-succinate <-> fumarate + AMP pmids: [] rhea: [] right: - AMP - fumarate yeastcyc_id: AMPSYN-RXN yeastcyc_id: PWY-7219 PWY-7220-1: all_genes: - *id104 - *id105 - *id106 - *id107 - *id094 name: adenosine deoxyribonucleotides de novo biosynthesis II pmids: [] reactions: - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dADP name: dADP + ATP -> dATP + ADP pmids: [] rhea: [] right: - ADP - dATP yeastcyc_id: DADPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dADP name: dADP + an oxidized thioredoxin + H2O <- ADP + a reduced thioredoxin pmids: [] rhea: [] right: - ADP - a reduced thioredoxin yeastcyc_id: ADPREDUCT-RXN - ec: - 1.1.98.6 genes: [] left: - ATP - H+ - formate name: formate + ATP + H+ -> CO2 + dATP + H2O pmids: [] rhea: [] right: - CO2 - H2O - dATP yeastcyc_id: RXN0-745 yeastcyc_id: PWY-7220-1 PWY-7221: all_genes: - *id102 - *id095 - *id098 - *id099 - *id100 - *id094 name: guanosine ribonucleotides de novo biosynthesis pmids: [] reactions: - ec: - 2.7.4.6 genes: - *id094 left: - ATP - GDP name: GDP + ATP -> GTP + ADP pmids: [] rhea: [] right: - ADP - GTP yeastcyc_id: GDPKIN-RXN - ec: - 2.7.4.8 genes: - *id095 left: - ATP - GMP name: GMP + ATP <-> GDP + ADP pmids: [] rhea: [] right: - ADP - GDP yeastcyc_id: GUANYL-KIN-RXN - ec: - 1.1.1.205 genes: - *id098 - *id099 - *id100 left: - H2O - IMP - NAD+ name: IMP + NAD+ + H2O <-> XMP + NADH + H+ pmids: - '12746440' rhea: [] right: - H+ - NADH - XMP yeastcyc_id: IMP-DEHYDROG-RXN - ec: - 6.3.5.2 genes: - *id102 left: - ATP - H2O - L-glutamine - XMP name: XMP + L-glutamine + ATP + H2O -> L-glutamate + GMP + AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - AMP - GMP - H+ - L-glutamate - diphosphate yeastcyc_id: GMP-SYN-GLUT-RXN yeastcyc_id: PWY-7221 PWY-7222-1: all_genes: - *id104 - *id105 - *id106 - *id107 - *id094 name: guanosine deoxyribonucleotides de novo biosynthesis II pmids: [] reactions: - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dGDP name: dGDP + ATP -> dGTP + ADP pmids: [] rhea: [] right: - ADP - dGTP yeastcyc_id: DGDPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dGDP name: dGDP + an oxidized thioredoxin + H2O <- GDP + a reduced thioredoxin pmids: [] rhea: [] right: - GDP - a reduced thioredoxin yeastcyc_id: GDPREDUCT-RXN - ec: - 1.1.98.6 genes: [] left: - GTP - H+ - formate name: formate + GTP + H+ -> dGTP + CO2 + H2O pmids: [] rhea: [] right: - CO2 - H2O - dGTP yeastcyc_id: RXN0-746 yeastcyc_id: PWY-7222-1 PWY-781: all_genes: - &id340 orf: YFR030W symbol: MET10 uniprot: UniProtKB:P39692 - *id332 - &id339 orf: YPR167C symbol: MET16 uniprot: UniProtKB:P18408 - *id333 - &id341 orf: YJR137C symbol: MET5 uniprot: UniProtKB:P47169 comment: 'Sulfur is found in many important biological compounds, including the amino acids methionine and cysteine, the coenzymes biotin and coenzyme A, and other metabolites such as glutathione. Although most of these compounds contain reduced sulfur, in nature the major form of inorganic sulfur available to many microorganisms is sulfate. In order to use sulfate to synthesize organic sulfur compounds, particularly sulfur amino acids and their derivatives, plants and many microorganisms import and reduce sulfate via the sulfate assimilation pathway. In S. cerevisiae, the sulfate assimilation pathway consists of sulfates uptake via Sul1p and Sul2p, activation to adenylate compounds, reduction to sulfide, and subsequent incorporation into carbon chains. The importance of activating sulfate to adenylyl sulfate (APS) and phosphoadenylyl sulfate (PAPS) stems from the fact that physiological reducing agents (e.g. NADPH, NADH) are not large enough in E0'' to reduce sulfate directly. Adenylation lowers sulfate''s electropotential, enabling cells to circumvent what would otherwise be an endergonic reaction. After its conversion to PAPS, sulfate is reduced to sulfite by PAPS reductase (Met16p) and again to sulfide by sulfite reductase (Met5p and Met10p). The subsequent incorporation of sulfide into a carbon chain varies by organism; in S. cerevisiae, sulfide can react with O-acetylhomoserine via Met17p to form homocysteine, the major intermediate in the biosynthesis and interconversion of methionine and cysteine. In plants and enteric bacteria, sulfide can react with O-acetylserine to form cysteine directly. The induction of all genes involved in the S. cerevisiae sulfate assimilation pathway depends upon the leucine-zipper transcriptional activator Met4p. Met4p induces MET gene expression in cysteine-limiting conditions, while under cysteine-rich conditions Met4p transcriptional activity is negatively regulated by the ubiquitin ligase SCF(Met30). Furthermore, sulfur transport is inhibited in this organism by intracellular sulfate and sulfur metabolites such as APS and cysteine. References: |CITS: [9409150]||CITS: [16102596]||CITS: [22419079]||CITS: [BIOCHEMISTRYSULFURCYCLE]|' name: sulfate assimilation pathway pmids: - '16102596' - '22419079' - '9409150' reactions: - ec: - 1.8.4.8 genes: - *id339 left: - H+ - adenosine 3',5'-bisphosphate - an oxidized thioredoxin - sulfite name: adenosine 3',5'-bisphosphate + sulfite + an oxidized thioredoxin + 2 H+ <-> 3'-phosphoadenylyl-sulfate + a reduced thioredoxin pmids: - '3060034' rhea: [] right: - 3'-phosphoadenylyl-sulfate - a reduced thioredoxin yeastcyc_id: 1.8.4.8-RXN - ec: - 2.7.1.25 genes: - *id332 left: - ATP - adenosine 5'-phosphosulfate name: adenosine 5'-phosphosulfate + ATP <-> 3'-phosphoadenylyl-sulfate + ADP + H+ pmids: [] rhea: [] right: - 3'-phosphoadenylyl-sulfate - ADP - H+ yeastcyc_id: ADENYLYLSULFKIN-RXN - ec: - 1.8.1.2 genes: - *id340 - *id341 left: - H2O - NADP+ - hydrogen sulfide name: hydrogen sulfide + 3 NADP+ + 3 H2O <- sulfite + 3 NADPH + 5 H+ pmids: [] rhea: [] right: - H+ - NADPH - sulfite yeastcyc_id: SULFITE-REDUCT-RXN - ec: - 2.7.7.4 genes: - *id333 left: - ATP - H+ - sulfate name: sulfate + ATP + H+ <-> adenosine 5'-phosphosulfate + diphosphate pmids: [] rhea: [] right: - adenosine 5'-phosphosulfate - diphosphate yeastcyc_id: SULFATE-ADENYLYLTRANS-RXN yeastcyc_id: PWY-781 PWY-821-1: all_genes: - *id084 - *id085 - *id232 - *id231 - *id233 - *id340 - *id332 - *id339 - *id264 - *id263 - *id333 - *id341 - *id262 - *id265 - *id320 - *id321 - *id228 - *id227 name: superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) pmids: - '9409150' reactions: - ec: - 2.5.1.6 genes: - *id320 - *id321 left: - ATP - H2O - L-methionine name: ATP + L-methionine + H2O -> S-adenosyl-L-methionine + phosphate + diphosphate pmids: [] rhea: [] right: - S-adenosyl-L-methionine - diphosphate - phosphate yeastcyc_id: S-ADENMETSYN-RXN - ec: - 2.7.2.4 genes: - *id231 left: - ATP - L-aspartate name: L-aspartate + ATP -> L-aspartyl-4-phosphate + ADP pmids: [] rhea: [] right: - ADP - L-aspartyl-4-phosphate yeastcyc_id: ASPARTATEKIN-RXN - ec: - 1.2.1.11 genes: - *id232 left: - L-aspartate 4-semialdehyde - NADP+ - phosphate name: L-aspartate 4-semialdehyde + NADP+ + phosphate <- L-aspartyl-4-phosphate + NADPH + H+ pmids: [] rhea: [] right: - H+ - L-aspartyl-4-phosphate - NADPH yeastcyc_id: ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN - ec: - 4.4.1.13 genes: - *id227 left: - H2O - L-cystathionine name: L-cystathionine + H2O -> L-homocysteine + pyruvate + ammonium pmids: [] rhea: [] right: - L-homocysteine - ammonium - pyruvate yeastcyc_id: CYSTATHIONINE-BETA-LYASE-RXN - ec: - 4.4.1.1 genes: - *id084 left: - H2O - L-cystathionine name: L-cystathionine + H2O <-> 2-oxobutanoate + L-cysteine + ammonia pmids: [] rhea: [] right: - 2-oxobutanoate - L-cysteine - ammonia yeastcyc_id: CYSTAGLY-RXN - ec: [] genes: - *id228 left: - L-cysteine - O-acetyl-L-homoserine name: L-cysteine + O-acetyl-L-homoserine -> L-cystathionine + acetate pmids: [] rhea: [] right: - L-cystathionine - acetate yeastcyc_id: RXN-721 - ec: - 2.1.1.14 genes: - *id262 left: - 5-methyltetrahydropteroyl tri-L-glutamate - L-homocysteine name: L-homocysteine + 5-methyltetrahydropteroyl tri-L-glutamate <-> L-methionine + tetrahydropteroyl tri-L-glutamate pmids: [] rhea: [] right: - L-methionine - tetrahydropteroyl tri-L-glutamate yeastcyc_id: HOMOCYSMET-RXN - ec: - 4.2.1.22 genes: - *id085 left: - L-homocysteine - L-serine name: L-homocysteine + L-serine <-> L-cystathionine + H2O pmids: [] rhea: [] right: - H2O - L-cystathionine yeastcyc_id: CYSTATHIONINE-BETA-SYNTHASE-RXN - ec: - 1.1.1.3 genes: - *id233 left: - L-homoserine - NAD(P)+ name: L-homoserine + NAD(P)+ <- L-aspartate 4-semialdehyde + NAD(P)H + H+ pmids: [] rhea: [] right: - H+ - L-aspartate 4-semialdehyde - NAD(P)H yeastcyc_id: HOMOSERDEHYDROG-RXN - ec: - 2.3.1.31 genes: - *id263 left: - L-homoserine - acetyl-CoA name: L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A pmids: [] rhea: [] right: - O-acetyl-L-homoserine - coenzyme A yeastcyc_id: HOMOSERINE-O-ACETYLTRANSFERASE-RXN - ec: - 2.5.1.49 genes: - *id264 left: - O-acetyl-L-homoserine - hydrogen sulfide name: O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H+ pmids: [] rhea: [] right: - H+ - L-homocysteine - acetate yeastcyc_id: ACETYLHOMOSER-CYS-RXN - ec: - 6.3.2.17 genes: - *id265 left: - ATP - L-glutamate - a 5-methyltetrahydrofolate name: a 5-methyltetrahydrofolate + L-glutamate + ATP -> a 5-methyltetrahydrofolate + ADP + phosphate pmids: [] rhea: [] right: - ADP - a 5-methyltetrahydrofolate - phosphate yeastcyc_id: RXN3O-22 - ec: - 1.8.4.8 genes: - *id339 left: - H+ - adenosine 3',5'-bisphosphate - an oxidized thioredoxin - sulfite name: adenosine 3',5'-bisphosphate + sulfite + an oxidized thioredoxin + 2 H+ <-> 3'-phosphoadenylyl-sulfate + a reduced thioredoxin pmids: - '3060034' rhea: [] right: - 3'-phosphoadenylyl-sulfate - a reduced thioredoxin yeastcyc_id: 1.8.4.8-RXN - ec: - 2.7.1.25 genes: - *id332 left: - ATP - adenosine 5'-phosphosulfate name: adenosine 5'-phosphosulfate + ATP <-> 3'-phosphoadenylyl-sulfate + ADP + H+ pmids: [] rhea: [] right: - 3'-phosphoadenylyl-sulfate - ADP - H+ yeastcyc_id: ADENYLYLSULFKIN-RXN - ec: - 1.8.1.2 genes: - *id340 - *id341 left: - H2O - NADP+ - hydrogen sulfide name: hydrogen sulfide + 3 NADP+ + 3 H2O <- sulfite + 3 NADPH + 5 H+ pmids: [] rhea: [] right: - H+ - NADPH - sulfite yeastcyc_id: SULFITE-REDUCT-RXN - ec: - 2.7.7.4 genes: - *id333 left: - ATP - H+ - sulfate name: sulfate + ATP + H+ <-> adenosine 5'-phosphosulfate + diphosphate pmids: [] rhea: [] right: - adenosine 5'-phosphosulfate - diphosphate yeastcyc_id: SULFATE-ADENYLYLTRANS-RXN yeastcyc_id: PWY-821-1 PWY-901: all_genes: - &id342 orf: YML004C symbol: GLO1 uniprot: UniProtKB:P50107 - &id343 orf: YDR272W symbol: GLO2 uniprot: UniProtKB:Q05584 - &id344 orf: YOR040W symbol: GLO4 uniprot: UniProtKB:Q12320 comment: 'Methylglyoxal is toxic compound that is formed as a by-product of glycolysis from triose phosphates through the action of triose-phosphate isomerase. One route by which methylglyoxal can be catabolized is a glyoxalase system in which methylglyoxal is condensed with glutathione to give S-D-lactoylglutathione by the action of glyoxalase I (GLO1) |CITS: [8824231]|, and the glutathione thiolester is then hydrolyzed to lactic acid and glutathione by glyoxalase II (GLO2 and GLO4) |CITS: [9261170]|. The GLO2 gene is expressed on both glucose and glycerol and the active Glo2p protein is localized in the cytoplasm. The GLO4 gene is only active on glycerol and the active Glo4p is localized in the mitochondrial matrix |CITS: [9261170]|. Deletion of either GLO1 or GLO2 and GLO4 results in increased sensitivity to exogenous methylglyoxal |CITS: [8824231]||CITS: [9261170]|.' name: methylglyoxal catabolism pmids: - '8824231' - '9261170' reactions: - ec: - 4.4.1.5 genes: - *id342 left: - (R)-S-lactoylglutathione name: (R)-S-lactoylglutathione <- methylglyoxal + glutathione pmids: [] rhea: [] right: - glutathione - methylglyoxal yeastcyc_id: GLYOXI-RXN - ec: - 3.1.2.6 genes: - *id343 - *id344 left: - (R)-S-lactoylglutathione - H2O name: (R)-S-lactoylglutathione + H2O -> glutathione + (R)-lactate + H+ pmids: [] rhea: [] right: - (R)-lactate - H+ - glutathione yeastcyc_id: GLYOXII-RXN yeastcyc_id: PWY-901 PWY-922: all_genes: - *id119 - *id113 - *id125 - *id116 - *id114 - *id115 - *id131 - *id117 name: mevalonate pathway I pmids: [] reactions: - ec: - 2.7.1.36 genes: - *id113 left: - (R)-mevalonate - ATP name: (R)-mevalonate + ATP <-> (R)-mevalonate 5-phosphate + ADP + H+ pmids: [] rhea: [] right: - (R)-mevalonate 5-phosphate - ADP - H+ yeastcyc_id: MEVALONATE-KINASE-RXN - ec: - 1.1.1.34 genes: - *id114 - *id115 left: - (R)-mevalonate - NADP+ - coenzyme A name: (R)-mevalonate + coenzyme A + 2 NADP+ <-> (S)-3-hydroxy-3-methylglutaryl-CoA + 2 NADPH + 2 H+ pmids: [] rhea: [] right: - (S)-3-hydroxy-3-methylglutaryl-CoA - H+ - NADPH yeastcyc_id: 1.1.1.34-RXN - ec: - 2.7.4.2 genes: - *id116 left: - (R)-mevalonate 5-phosphate - ATP name: (R)-mevalonate 5-phosphate + ATP <-> (R)-mevalonate diphosphate + ADP pmids: [] rhea: [] right: - (R)-mevalonate diphosphate - ADP yeastcyc_id: PHOSPHOMEVALONATE-KINASE-RXN - ec: - 4.1.1.33 genes: - *id117 left: - (R)-mevalonate diphosphate - ATP name: (R)-mevalonate diphosphate + ATP -> CO2 + isopentenyl diphosphate + ADP + phosphate pmids: [] rhea: [] right: - ADP - CO2 - isopentenyl diphosphate - phosphate yeastcyc_id: DIPHOSPHOMEVALONTE-DECARBOXYLASE-RXN - ec: - 2.3.1.9 genes: - *id119 left: - acetyl-CoA name: 2 acetyl-CoA <-> acetoacetyl-CoA + coenzyme A pmids: [] rhea: [] right: - acetoacetyl-CoA - coenzyme A yeastcyc_id: ACETYL-COA-ACETYLTRANSFER-RXN - ec: - 2.3.3.10 genes: - *id125 left: - H2O - acetoacetyl-CoA - acetyl-CoA name: acetoacetyl-CoA + acetyl-CoA + H2O <-> (S)-3-hydroxy-3-methylglutaryl-CoA + coenzyme A + H+ pmids: [] rhea: [] right: - (S)-3-hydroxy-3-methylglutaryl-CoA - H+ - coenzyme A yeastcyc_id: HYDROXYMETHYLGLUTARYL-COA-SYNTHASE-RXN - ec: - 5.3.3.2 genes: - *id131 left: - isopentenyl diphosphate name: isopentenyl diphosphate <-> dimethylallyl diphosphate pmids: [] rhea: [] right: - dimethylallyl diphosphate yeastcyc_id: IPPISOM-RXN yeastcyc_id: PWY-922 PWY0-162: all_genes: - *id049 - *id050 - *id300 - *id310 - *id051 - *id309 - *id299 - *id311 - *id301 - *id307 - *id308 name: superpathway of pyrimidine ribonucleotides de novo biosynthesis pmids: [] reactions: - ec: - 3.5.2.3 genes: - *id299 left: - (S)-dihydroorotate - H2O name: (S)-dihydroorotate + H2O <-> N-carbamoyl-L-aspartate + H+ pmids: [] rhea: [] right: - H+ - N-carbamoyl-L-aspartate yeastcyc_id: DIHYDROOROT-RXN - ec: - 1.3.98.1 genes: - *id300 left: - (S)-dihydroorotate - fumarate name: (S)-dihydroorotate + fumarate -> orotate + succinate pmids: [] rhea: [] right: - orotate - succinate yeastcyc_id: RXN-9929 - ec: - 6.3.5.5 genes: - *id049 - *id050 - *id051 left: - ATP - H2O - L-glutamine - hydrogencarbonate name: 2 ATP + L-glutamine + hydrogencarbonate + H2O -> L-glutamate + carbamoyl phosphate + 2 ADP + phosphate + 2 H+ pmids: - '8626695' rhea: [] right: - ADP - H+ - L-glutamate - carbamoyl phosphate - phosphate yeastcyc_id: CARBPSYN-RXN - ec: - 2.7.4.14 - 2.7.4.22 - 2.7.4.4 genes: - *id301 left: - ATP - UMP name: ATP + UMP -> ADP + UDP pmids: [] rhea: [] right: - ADP - UDP yeastcyc_id: RXN-12002 - ec: - 2.1.3.2 genes: - *id051 left: - L-aspartate - carbamoyl phosphate name: L-aspartate + carbamoyl phosphate <-> N-carbamoyl-L-aspartate + phosphate + H+ pmids: [] rhea: [] right: - H+ - N-carbamoyl-L-aspartate - phosphate yeastcyc_id: ASPCARBTRANS-RXN - ec: - 6.3.4.2 genes: - *id307 - *id308 left: - ATP - H2O - L-glutamine - UTP name: L-glutamine + UTP + ATP + H2O -> ADP + CTP + L-glutamate + phosphate + 2 H+ pmids: [] rhea: [] right: - ADP - CTP - H+ - L-glutamate - phosphate yeastcyc_id: CTPSYN-RXN - ec: - 2.7.4.6 genes: [] left: - ATP - UDP name: UDP + ATP -> UTP + ADP pmids: [] rhea: [] right: - ADP - UTP yeastcyc_id: UDPKIN-RXN - ec: - 4.1.1.23 genes: - *id309 left: - H+ - orotidine 5'-phosphate name: orotidine 5'-phosphate + H+ -> CO2 + UMP pmids: [] rhea: [] right: - CO2 - UMP yeastcyc_id: OROTPDECARB-RXN - ec: - 2.4.2.10 genes: - *id310 - *id311 left: - diphosphate - orotidine 5'-phosphate name: orotidine 5'-phosphate + diphosphate <-> 5-phospho-α-D-ribose 1-diphosphate + orotate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - orotate yeastcyc_id: OROPRIBTRANS-RXN yeastcyc_id: PWY0-162 PWY0-662: all_genes: - *id302 - *id303 - *id304 - *id305 - *id306 name: PRPP biosynthesis pmids: [] reactions: - ec: - 2.7.6.1 genes: - *id302 - *id303 - *id304 - *id305 - *id306 left: - ATP - D-ribose 5-phosphate name: D-ribose 5-phosphate + ATP <-> 5-phospho-α-D-ribose 1-diphosphate + AMP + H+ pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - AMP - H+ yeastcyc_id: PRPPSYN-RXN yeastcyc_id: PWY0-662 PWY3O-0: all_genes: - *id146 - *id147 comment: 'Fructose is a six-carbon ketose that can be used as a fermentable carbon source in S. cerevisiae. Utilization of fructose begins with its uptake via hexose transporter (Hxt) family proteins. Of the 20 different Hxt-related proteins in S. cerevisiae, Hxt1p-4p, 6p, and 7p are the most important for glucose, fructose, and mannose uptake. Once inside the cell, fructose is phosphorylated to fructose-6-phosphate (F6P) by the hexokinases Hxk1p and Hxk2p. Although both kinases can catalyze this reaction, only HXK2 is expressed when fructose is the carbon source. HXK1 expression occurs in the presence of non-fermentable carbon sources or galactose. F6P, in addition to being an intermediate in glycolysis, may also be utilized in yeast to synthesize UDP-N-acetyl-D-glucosamine, a building block for major structural components of the fungal cell wall. References: |CITS: [16408321]||CITS: [9299703]||CITS: [7732723]|' name: fructose degradation pmids: - '16408321' - '7732723' - '9299703' reactions: - ec: - 2.7.1.4 genes: - *id146 - *id147 left: - ATP - D-fructose name: D-fructose + ATP -> keto-D-fructose 6-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - keto-D-fructose 6-phosphate yeastcyc_id: RXN3O-9790 - ec: [] genes: [] left: - keto-D-fructose 6-phosphate name: keto-D-fructose 6-phosphate <-> β-D-fructofuranose 6-phosphate pmids: [] rhea: [] right: - β-D-fructofuranose 6-phosphate yeastcyc_id: RXN-14812 yeastcyc_id: PWY3O-0 PWY3O-1: all_genes: - &id350 orf: YNL141W symbol: AAH1 uniprot: UniProtKB:P53909 - &id351 orf: YJR105W symbol: ADO1 uniprot: UniProtKB:P47143 - &id345 orf: YML035C symbol: AMD1 uniprot: UniProtKB:P15274 - &id346 orf: YML022W symbol: APT1 uniprot: UniProtKB:P49435 - &id347 orf: YDR441C symbol: APT2 uniprot: UniProtKB:P36973 - &id352 orf: YDL238C symbol: GUD1 uniprot: UniProtKB:Q07729 - &id348 orf: YDR399W symbol: HPT1 uniprot: UniProtKB:Q04178 - &id353 orf: YLR209C symbol: PNP1 uniprot: UniProtKB:Q05788 - &id349 orf: YJR133W symbol: XPT1 uniprot: UniProtKB:P47165 comment: 'In yeast and most eukaryotes, purine nucleotides levels are maintained via a combination of de novo synthesis and salvage pathways. The salvage pathways utilize purine bases and nucleosides taken up from the environment or formed from metabolism to synthesize purine nucleoside monophosphates. Compared to the de novo pathway, where 5-phosphoribosyl-1-pyrophosphate (PRPP) is converted to the adenylic/guanylic nucleotide precursor inosine 5-monophosphate (IMP) over many ATP-consuming steps, the salvage pathways synthesize IMP, GMP, and AMP directly from PRPP and a purine base via the action of purine phosphoribosyltransferases. There are three main phosphoribosyltransferases involved in purine salvage in S. cerevisiae: i) Hpt1p, which produces GMP and IMP from guanine and hypoxanthine, respectively; ii) Apt1p, which synthesizes AMP from adenine; and iii) Xpt1p, which synthesizes XMP from xanthine. XMP can be further converted to GMP via the GMP synthase Gua1p. The salvage pathways represent the preferred route of synthesis when purines are abundant in the growth medium. In S. cerevisiae, most of the ADE genes responsible for de novo synthesis of IMP and AMP are repressed by extracellular adenine, whereas extracellular guanine strongly represses the IMD genes responsible for the rate-limiting step of GMP synthesis. References: |CITS:[17052198 ]||CITS: [9864350]||CITS: [10217799]||CITS: [22419079]|' name: salvage pathways of purines and their nucleosides pmids: - '10217799' - '11223943' - '15565584' - '1577682' - '17052198' - '22419079' - '9864350' reactions: - ec: - 3.5.4.17 - 3.5.4.6 genes: - *id345 left: - AMP - H+ - H2O name: AMP + H+ + H2O -> IMP + ammonium pmids: [] rhea: [] right: - IMP - ammonium yeastcyc_id: AMP-DEAMINASE-RXN - ec: - 2.4.2.7 genes: - *id346 - *id347 left: - AMP - diphosphate name: AMP + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + adenine pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - adenine yeastcyc_id: ADENPRIBOSYLTRAN-RXN - ec: - 2.4.2.8 genes: - *id348 left: - GMP - diphosphate name: GMP + diphosphate <- guanine + 5-phospho-α-D-ribose 1-diphosphate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - guanine yeastcyc_id: GUANPRIBOSYLTRAN-RXN - ec: - 2.4.2.8 genes: - *id348 left: - IMP - diphosphate name: IMP + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + hypoxanthine pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - hypoxanthine yeastcyc_id: HYPOXANPRIBOSYLTRAN-RXN - ec: - 2.4.2.22 genes: - *id349 left: - XMP - diphosphate name: XMP + diphosphate <- xanthine + 5-phospho-α-D-ribose 1-diphosphate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - xanthine yeastcyc_id: XANPRIBOSYLTRAN-RXN - ec: - 3.5.4.2 genes: - *id350 left: - H+ - H2O - adenine name: adenine + H+ + H2O -> ammonium + hypoxanthine pmids: [] rhea: [] right: - ammonium - hypoxanthine yeastcyc_id: ADENINE-DEAMINASE-RXN - ec: - 2.7.1.20 genes: - *id351 left: - ATP - adenosine name: adenosine + ATP -> AMP + ADP + H+ pmids: [] rhea: [] right: - ADP - AMP - H+ yeastcyc_id: ADENOSINE-KINASE-RXN - ec: - 3.5.4.3 genes: - *id352 left: - H+ - H2O - guanine name: guanine + H+ + H2O -> ammonium + xanthine pmids: [] rhea: [] right: - ammonium - xanthine yeastcyc_id: GUANINE-DEAMINASE-RXN - ec: - 2.4.2.1 genes: - *id353 left: - inosine - phosphate name: inosine + phosphate -> α-D-ribose-1-phosphate + hypoxanthine pmids: [] rhea: [] right: - hypoxanthine - α-D-ribose-1-phosphate yeastcyc_id: INOPHOSPHOR-RXN yeastcyc_id: PWY3O-1 PWY3O-10: all_genes: - &id354 orf: YNR016C symbol: ACC1 uniprot: UniProtKB:Q00955 - *id137 - *id134 - *id135 - &id355 orf: YMR207C symbol: HFA1 uniprot: UniProtKB:P32874 - &id356 orf: YOR221C symbol: MCT1 uniprot: UniProtKB:Q12283 comment: 'Fatty acids are essential to all organisms except for archaea; they are major constituents of cellular membranes, and are used for energy storage and for posttranslational protein modifications. Most organisms are capable of synthesizing long chain (C12:0-C16:0) saturated fatty acids de novo. Although the initiation and termination reactions may vary, the cyclic series of chain-lengthening reactions are essentially the same across all organisms. The fatty acid chain, which starts as a 2-carbon chain from acetyl-CoA, is extended two carbons at a time by the addition of an acetyl group from malonyl-CoA. When the final length of the fatty acid is achieved, fatty acid synthesis is terminated. Each cycle of chain elongation involves 5 reactions with the following enzymatic activities: malonyl transferase (EC: 2.3.1.39), ketoacyl synthase (EC: 2.3.1.41), ketoacyl reductase (EC: 1.1.1.100), 3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61), and enoyl-acyl reductase (EC: 1.3.1.10). In yeast, fatty acid biosynthesis is terminated with the release of fatty acyl-CoAs from fatty acid synthase (FAS), the enzyme complex that carries out de novo fatty acid biosynthesis. Palmitoyl- (C16) and stearoyl-CoA (C18) are the main products in yeast, while myristoyl-CoA (C14) is only produced in small amounts |CITS: [Lynen69]|. To synthesize palmitoyl-CoA (C16) one acetyl-CoA and 7 malonyl-CoA molecules are required. The elongation substrate, malonyl-CoA is synthesized from the carboxylation of acetyl-CoA (EC 6.4.1.2) by the biotin-containing enzyme, acetyl-CoA carboxylase (Acc1p) |CITS: [1350093]|). Acetyl-CoA carboxylase is activated by the biotin:apoprotein ligase (Bpl1p) |CITS: [7649444]|). There are two types of FAS systems based on the organization of the catalytic sites. Fungi, animals, and some bacteria have type I FASs, which are large multi-functional proteins that contain all of the requisite catalytic active sites for fatty acid biosynthesis within domains on a single polypeptide (alpha) or on two polypeptides (alpha and beta). Fungal FASs are alpha6beta6 heterododecamers, animal FASs are alpha2 homodimers, and some type I bacterial FASs are alpha6 |CITS: [17448991]|. Bacteria, plants and mitochondria, on the other hand, have type II FAS systems, which are comprised of independent proteins, whereby each protein catalyzes a single step in the cyclic series of reactions |CITS: [15952903]|. The yeast FAS complex catalyzes a total of 8 reactions. The alpha subunit(Fas2p) catalyzes 3 reactions, ketoacyl synthase (EC: 2.3.1.41),ketoacyl reductase (EC: 1.1.1.100) and self pantetheinylation and the yeast beta subunit (Fas1p) catalyzes 5 reactions, acetyltransferase (EC 2.3.1.38), malonyl transferase (EC: 2.3.1.39),3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61),enoyl-acyl reductase (EC: 1.3.1.10), and palmitoyl transferase (EC:2.3.1.-) |CITS: [365179], [1100391], [10785388], [3528750], [374077]|. FASs are regulated at the transcriptional and translational level as well as posttranslationally. In yeast, FAS is a housekeeping enzyme that is expressed constitutively at a low level, but its expression is also activated by the general yeast transcription factors Rap1, Abf1 and Reb1 |CITS: [7925441]| and theinositol/choline-responsive transcription factor heterodimer, Ino2p-Ino4p |CITS: [1461729][7862526]|. The coordinate expression of the two subunits also appears to be regulated by Fas1p controlling the expression of FAS2 |CITS: [11713312]|. The FAS subunits are further regulated by proteolytic degradation of excess subunits. While the intact FAS multimeric complex (alpha6beta6 ) is stable, its individual subunits are rapidly degraded |CITS: [1735446][8262967]|.' name: fatty acid biosynthesis, initial steps pmids: - '18059524' reactions: - ec: - 1.3.1.10 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - H+ - NADPH - a (2E)-but-2-enoyl-[acp] name: a (2E)-but-2-enoyl-[acp] + NADPH + H+ -> a butanoyl-[acp] + NADP+ pmids: [] rhea: [] right: - NADP+ - a butanoyl-[acp] yeastcyc_id: RXN-9515 - ec: - 2.3.1.86 - 4.2.1.59 genes: - *id134 left: - a (3R)-3-hydroxybutanoyl-[acp] name: a (3R)-3-hydroxybutanoyl-[acp] -> a (2E)-but-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-but-2-enoyl-[acp] yeastcyc_id: 4.2.1.58-RXN - ec: - 2.3.1.86 genes: - *id135 left: - NADP+ - a (3R)-3-hydroxybutanoyl-[acp] name: a (3R)-3-hydroxybutanoyl-[acp] + NADP+ <- an acetoacetyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - an acetoacetyl-[acp] yeastcyc_id: RXN-9514 - ec: - 6.4.1.2 genes: - *id354 - *id355 left: - ATP - acetyl-CoA - hydrogencarbonate name: acetyl-CoA + ATP + hydrogencarbonate -> ADP + malonyl-CoA + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - malonyl-CoA - phosphate yeastcyc_id: ACETYL-COA-CARBOXYLTRANSFER-RXN - ec: - 2.3.1.86 genes: - *id134 left: - a soluble [acyl-carrier protein] - acetyl-CoA name: acyl-carrier protein + acetyl-CoA -> an acetyl-[acp] + coenzyme A pmids: [] rhea: [] right: - an acetyl-[acp] - coenzyme A yeastcyc_id: ACP-S-ACETYLTRANSFER-RXN - ec: - 2.3.1.86 genes: - *id134 - *id356 left: - a soluble [acyl-carrier protein] - malonyl-CoA name: acyl-carrier protein + malonyl-CoA -> a malonyl-[acp] + coenzyme A pmids: [] rhea: [] right: - a malonyl-[acp] - coenzyme A yeastcyc_id: MALONYL-COA-ACP-TRANSACYL-RXN - ec: - 2.3.1.179 genes: - *id137 - *id135 left: - H+ - a malonyl-[acp] - an acetyl-[acp] name: an acetyl-[acp] + a malonyl-[acp] + H+ -> an acetoacetyl-[acp] + acyl-carrier protein + CO2 pmids: [] rhea: [] right: - CO2 - a soluble [acyl-carrier protein] - an acetoacetyl-[acp] yeastcyc_id: 3-OXOACYL-ACP-SYNTH-BASE-RXN yeastcyc_id: PWY3O-10 PWY3O-103: all_genes: - *id280 comment: 'Cytidine diphosphate diacylglycerol (CDP-DAG) is a liponucleotide and the precursor to all major phospholipids in S. cerevisiae. It is synthesized in a reaction catalyzed by CDP-DAG synthase, which converts phosphatidic acid (PA) to CDP-DAG using cytidine triphosphate (CTP) as the CDP donor. There are two distinct CDP-DAG synthases in S. cerevisiae: Cds1p, localized in the endoplasmic reticulum (ER), and Tam41p, localized in the mitochondrial matrix. Both localizations represent the site of action for the CDP-DAG pathway of phospholipid biosynthesis in yeast. At the ER site, CDP-DAG generated by Cds1p can be converted to phosphatidylinositol (PI) or phosphatidylserine (PS) via PI synthase (Pis1p) and PS synthase (Cho1p), respectively. At the mitochondrial site, CDP-DAG generated by Tam41p can be sequentially converted to phosphatidylglycerol (PG) and further converted to cardiolipin. Synthesis of PI, PG, and cardiolipin occurs through similar mechanisms in mammalian cells; however, unlike yeast, mammals primarily synthesize PS from other phospholipids and not from CDP-DAG. References: |CITS:[24866973]||CITS: [23623749]||CITS: [16943180]||CITS: [21382416]|' name: CDP-diacylglycerol biosynthesis pmids: - '16943180' - '21382416' - '23623749' - '24866973' reactions: - ec: - 2.7.7.41 genes: - *id280 left: - CTP - H+ - a 1,2-diacyl-sn-glycerol 3-phosphate name: CTP + a 1,2-diacyl-sn-glycerol 3-phosphate + H+ -> a CDP-diacylglycerol + diphosphate pmids: [] rhea: [] right: - a CDP-diacylglycerol - diphosphate yeastcyc_id: CDPDIGLYSYN-RXN yeastcyc_id: PWY3O-103 PWY3O-1109: all_genes: [] comment: 'This is the proposed pathway for p-hydroxybenzoate biosynthesis in S. cerevisiae based on genetic studies and incorporation of radiolabeled intermediates.|CITS: [11583838]|' name: p-hydroxybenzoate biosynthesis pmids: [] reactions: - ec: [] genes: [] left: - (E)-4-coumaroyl-CoA - H2O - NAD+ - coenzyme A name: (E)-4-coumaroyl-CoA + coenzyme A + NAD+ + H2O -> 4-hydroxybenzoyl-CoA + acetyl-CoA + NADH + H+ pmids: [] rhea: [] right: - 4-hydroxybenzoyl-CoA - H+ - NADH - acetyl-CoA yeastcyc_id: RXN3O-1120 - ec: [] genes: [] left: - (R)-3-(4-hydroxyphenyl)lactate name: (R)-3-(4-hydroxyphenyl)lactate -> 4-coumarate + H2O pmids: [] rhea: [] right: - 4-coumarate - H2O yeastcyc_id: RXN3O-1118 - ec: - 1.1.1.110 genes: [] left: - (R)-3-(4-hydroxyphenyl)lactate - NAD+ name: (R)-3-(4-hydroxyphenyl)lactate + NAD+ <- 3-(4-hydroxyphenyl)pyruvate + NADH + H+ pmids: [] rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - H+ - NADH yeastcyc_id: HYDROXYPHENYLPYRUVATE-REDUCTASE-RXN - ec: - 6.2.1.12 genes: [] left: - 4-coumarate - ATP - coenzyme A name: 4-coumarate + ATP + coenzyme A -> (E)-4-coumaroyl-CoA + AMP + diphosphate pmids: [] rhea: [] right: - (E)-4-coumaroyl-CoA - AMP - diphosphate yeastcyc_id: 4-COUMARATE--COA-LIGASE-RXN - ec: [] genes: [] left: - 4-hydroxybenzoyl-CoA - acetyl-CoA name: 4-hydroxybenzoyl-CoA + acetyl-CoA -> 4-hydroxybenzoate pmids: [] rhea: [] right: - 4-hydroxybenzoate yeastcyc_id: RXN3O-1121 - ec: [] genes: [] left: - L-tyrosine name: L-tyrosine -> 3-(4-hydroxyphenyl)pyruvate + ammonia pmids: [] rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - ammonia yeastcyc_id: RXN3O-1116 - ec: - 4.1.3.40 genes: [] left: - chorismate name: chorismate -> 4-hydroxybenzoate + pyruvate pmids: [] rhea: [] right: - 4-hydroxybenzoate - pyruvate yeastcyc_id: CHORPYRLY-RXN yeastcyc_id: PWY3O-1109 PWY3O-114: all_genes: - &id357 orf: YFR044C symbol: DUG1 uniprot: UniProtKB:P43616 - &id358 orf: YLR299W symbol: ECM38 uniprot: UniProtKB:Q05902 - *id198 - *id199 comment: 'The tripeptide glutathione (GSH: L-γ-glutamyl-L-cysteinylglycine) is a prevalent intracellular thiol that is able to act as a cellular redox buffer due to its low redox potential (as reviewed in |CITS: [12702279]|). GSH is involved in many biological processes including: protein and DNA synthesis; amino acid transport; enzyme regulation; protection of cells against reactive oxygen compounds and free radicals, xenobiotics and heavy metals (as reviewed in |CITS: [12702279]|). GSH can also be used as a source of sulfur and cysteine in |CITS: [1674526], [10514563]|. Plants and animals metabolize GSH via the γ-glutamyl cycle. Whether or not this complete cycle exists in yeast and other microorganisms is open to debate |CITS: [5076], [JASPERS85]|. The two enzymes catalyzing the synthesis of GSH from its constituent amino acids, γ-glutamylcysteine synthetase (Gsh1p) and GSH synthetase (Gsh2p), are present in yeast (as reviewed in |CITS: [12702279]|). Yeast was also found to have γ-glutamyl transpeptidase (Ecm38p) and cysteinylglycine dipeptidase (CGase) |CITS: [JASPERS85]|, two vacuolar-membrane-bound enzymes that are proposed to catalyze the complete hydrolysis of GSH to its constitutive amino acids |CITS: [6143574], [11672438]|. Although enzymatic activity for CGase was observed in S. cerevisiae |CITS: [JASPERS85]|, the open reading frame for CGase has yet to be identified in S. cerevisiae. The presence of the remaining two γ-glutamyl cycle enzymes, γ-glutamyl cyclotransferase and 5-oxoprolinase, is still in question |CITS: [5076], [JASPERS85]|, suggesting that yeast may only have a truncated γ-glutamyl cycle. S. cerevisiae also has been proposed to have an alternative pathway for degrading GSH that involves a novel GSH degradosomal protein complex comprised of the three gene products Dug1p, Dug2p, and Dug3p |CITS: [17179087]|.' name: superpathway of glutathione metabolism (truncated γ-glutamyl cycle) pmids: - '10514563' - '12702279' - '16102596' - '4144403' - '5076' reactions: - ec: - 6.3.2.2 genes: - *id198 left: - ATP - L-cysteine - L-glutamate name: L-cysteine + L-glutamate + ATP -> γ-L-glutamyl-L-cysteine + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - phosphate - γ-L-glutamyl-L-cysteine yeastcyc_id: GLUTCYSLIG-RXN - ec: - 3.4.13.18 genes: - *id357 left: - H2O - L-cysteinylglycine name: L-cysteinylglycine + H2O -> L-cysteine + glycine pmids: - '19346245' rhea: [] right: - L-cysteine - glycine yeastcyc_id: RXN-6622 - ec: - 2.3.2.2 genes: - *id358 left: - a proteinogenic amino acid - glutathione name: glutathione + a proteinogenic amino acid -> an α-(γ-L-glutamyl)-L-amino acid + L-cysteinylglycine pmids: [] rhea: [] right: - L-cysteinylglycine - an α-(γ-L-glutamyl)-L-amino acid yeastcyc_id: RXN-6601 - ec: - 6.3.2.3 genes: - *id199 left: - ATP - glycine - γ-L-glutamyl-L-cysteine name: glycine + γ-L-glutamyl-L-cysteine + ATP -> glutathione + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - glutathione - phosphate yeastcyc_id: GLUTATHIONE-SYN-RXN yeastcyc_id: PWY3O-114 PWY3O-123: all_genes: - &id360 orf: YPR183W symbol: DPM1 uniprot: UniProtKB:P14020 - &id359 orf: YER003C symbol: PMI40 uniprot: UniProtKB:P29952 - &id362 orf: YDL055C symbol: PSA1 uniprot: UniProtKB:P41940 - &id361 orf: YFL045C symbol: SEC53 uniprot: UniProtKB:P07283 comment: 'In the dolichol pathway of N-linked glycosylation, an oligosaccharide consisting of two N-acetylglucosamine (GlcNAc), nine mannosyl, and three glucosyl residues (abbreviated GlcNAc2Man9Glc3) is assembled on the lipid carrier dolichol-pyrophosphate (Dol-PP). The ordered assembly of this lipid-linked oligosaccharide (LLO) begins on the cytoplasmic face of the endoplasmic reticulum (ER) and concludes within the lumen of the ER. Two distinct molecules provide the mannose units required for assembly of the LLO: GDP-mannose and Dol-P-mannose. GDP-mannose provides the first five mannose units attached to the LLO during the cytoplasmic phase, whereas Dol-P-mannose provides the final four units during the ER lumenal phase. In S. cerevisiae, Dol-P-mannose is synthesized from GDP-mannose and dolichyl phosphate (Dol-P) while GDP-mannose is synthesized from GDP and fructose-6-phosphate. The pathway for the synthesis of GDP-mannose from fructose-6-phosphate (F6P) occurs in three steps in S. cerevisiae: isomerization of F6P to mannose-6-phosphate by phosphomannoisomerase (Pmi40p), conversion of mannose-6-phosphate to mannose-1-phosphate by phosphomannomutase (Sec53p), and conversion of mannose-1-phosphate and GDP to GDP-mannose via mannose-1-phosphate guanylyltransferase (Psa1p). During the cytoplasmic phase of LLO biosynthesis, GDP-mannose molecules are used by a series of glycosyltransferases (Alg1p, Alg2p, and Alg11p) to add five mannosyl residues to Dol-PP-GlcNAc2. Alternatively, GDP-mannose can donate its sugar unit to Dol-P via Dol-P-mannose synthase (Dpm1p), forming Dol-P-mannose. Molecules of Dol-P-mannose are used by a second group of glycosyltransferases (Alg3p, Alg9p, and Alg12p) during the ER lumenal phase to add the four final mannoses to Dol-PP-GlcNAc2Man5. References: |CITS:[23751184]||CITS: [9878760]|' name: dolichyl phosphate D-mannose biosynthesis pmids: - '23751184' - '9878760' reactions: - ec: - 5.3.1.8 genes: - *id359 left: - D-mannopyranose 6-phosphate name: D-mannopyranose 6-phosphate <-> β-D-fructofuranose 6-phosphate pmids: [] rhea: [] right: - β-D-fructofuranose 6-phosphate yeastcyc_id: MANNPISOM-RXN - ec: - 2.4.1.83 genes: - *id360 left: - GDP-α-D-mannose - a dolichyl phosphate name: a dolichyl phosphate + GDP-α-D-mannose -> a dolichyl β-D-mannosyl phosphate + GDP pmids: [] rhea: [] right: - GDP - a dolichyl β-D-mannosyl phosphate yeastcyc_id: 2.4.1.83-RXN - ec: - 5.4.2.8 genes: - *id361 left: - α-D-mannose 1-phosphate name: α-D-mannose 1-phosphate <- D-mannopyranose 6-phosphate pmids: [] rhea: [] right: - D-mannopyranose 6-phosphate yeastcyc_id: PHOSMANMUT-RXN - ec: - 2.7.7.22 genes: - *id362 left: - GDP - H+ - α-D-mannose 1-phosphate name: α-D-mannose 1-phosphate + GDP + H+ -> GDP-α-D-mannose + phosphate pmids: [] rhea: [] right: - GDP-α-D-mannose - phosphate yeastcyc_id: MANNPGUANYLTRANGDP-RXN yeastcyc_id: PWY3O-123 PWY3O-13: all_genes: - *id190 - *id191 - *id138 - *id189 - &id363 orf: YDL066W symbol: IDP1 uniprot: UniProtKB:P21954 - &id364 orf: YLR174W symbol: IDP2 uniprot: UniProtKB:P41939 - &id365 orf: YNL009W symbol: IDP3 uniprot: UniProtKB:P53982 comment: 'The utilization of ammonia to synthesize glutamate occurs through two pathways in most microorganisms. In the first pathway, glutamate is synthesized through the reductive amination of -ketoglutarate by glutamate dehydrogenase. Two NADPH-dependent glutamate dehydrogenases exist in S. cerevisiae: Gdh1p and Gdh3p. GDH1 is highly expressed when either ethanol or glucose is used as the carbon source, whereas GDH3 is glucose-repressed and induced only in ethanol. The second route of glutamate biosynthesis involves the combined action of glutamine synthetase (Gln1p) and glutamate synthase (Glt1p). In the first step, glutamate reacts with a molecule of ammonia in a reaction catalyzed by Gln1p to form glutamine. In the second, glutamine reacts with -ketoglutarate via Glt1p to form two molecules of glutamate, resulting in a net gain of one for each glutamate molecule that enters the pathway. References: |CITS:[22419079]||CITS: [11562373]|' name: superpathway of glutamate biosynthesis pmids: - '11562373' - '22419079' - '8672488' reactions: - ec: - 1.4.1.14 genes: - *id189 left: - L-glutamate - NAD+ name: 2 L-glutamate + NAD+ <- L-glutamine + 2-oxoglutarate + NADH + H+ pmids: [] rhea: [] right: - 2-oxoglutarate - H+ - L-glutamine - NADH yeastcyc_id: GLUTAMATE-SYNTHASE-NADH-RXN - ec: - 1.1.1.42 genes: - *id363 - *id364 - *id365 left: - D-threo-isocitrate - NADP+ name: D-threo-isocitrate + NADP+ <-> 2-oxoglutarate + CO2 + NADPH pmids: [] rhea: [] right: - 2-oxoglutarate - CO2 - NADPH yeastcyc_id: ISOCITDEH-RXN - ec: - 1.4.1.4 genes: - *id190 - *id191 left: - H2O - L-glutamate - NADP+ name: L-glutamate + NADP+ + H2O <-> ammonium + 2-oxoglutarate + NADPH + H+ pmids: [] rhea: [] right: - 2-oxoglutarate - H+ - NADPH - ammonium yeastcyc_id: GLUTDEHYD-RXN - ec: - 6.3.1.2 genes: - *id138 left: - ATP - L-glutamate - ammonium name: ammonium + L-glutamate + ATP -> L-glutamine + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - L-glutamine - phosphate yeastcyc_id: GLUTAMINESYN-RXN yeastcyc_id: PWY3O-13 PWY3O-15: all_genes: - &id366 orf: YNL192W symbol: CHS1 uniprot: UniProtKB:P08004 - &id367 orf: YBR038W symbol: CHS2 uniprot: UniProtKB:P14180 - &id368 orf: YBR023C symbol: CHS3 uniprot: UniProtKB:P29465 comment: Chitin, a linear polymer of N-acetyl glucosamine (GlcNAc) residues joined by beta-(1,4) linkages, is a minor but essential structural component of fungal cell walls. The majority (90%) of chitin in the cell wall is synthesized by chitin synthase III (CSIII), one of the three chitin synthases in S. cerevisiae (as reviewed in |CITS:[8257107]|). Each of the three chitin synthases (CSI, CSII, and CSIII) are nonessential, but the lack of all three leads to cell lethality (|CITS:[2050738]|). The genes encoding the catalytic subunits of CSI, CSII, and CSIII are CHS1, CHS2, and CHS3, respectively. Skt5p (Chs4/Cal2/Csd4) has been shown to physically interact with Chs3p, and is indispensable for its enzymatic activity in vivo (|CITS:[ 17142567]|). Chitin is deacetylated to form chitosan, a component of the yeast spore wall (ascospore). name: chitin biosynthesis pmids: - '12228806' - '16760306' reactions: - ec: - 2.4.1.16 genes: - *id366 - *id367 - *id368 left: - UDP-N-acetyl-α-D-glucosamine - chitin name: UDP-N-acetyl-α-D-glucosamine + [1,4-(N-acetyl-β-D-glucosaminyl)]n -> UDP + [1,4-(N-acetyl-β-D-glucosaminyl)](n+1) pmids: [] rhea: [] right: - UDP - chitin yeastcyc_id: CHITIN-SYNTHASE-RXN yeastcyc_id: PWY3O-15 PWY3O-1565: all_genes: - &id369 orf: YPL227C symbol: ALG5 uniprot: UniProtKB:P40350 - *id203 - *id204 - &id370 orf: YKL035W symbol: UGP1 uniprot: UniProtKB:P32861 - &id371 orf: YHL012W symbol: null uniprot: UniProtKB:P38709 comment: 'In the dolichol pathway of N-linked glycosylation, an oligosaccharide consisting of two N-acetylglucosamine (GlcNAc), nine mannosyl, and three glucosyl residues (abbreviated GlcNAc2Man9Glc3) is assembled on the lipid carrier dolichol-pyrophosphate (Dol-PP). This assembly is catalyzed by several groups of glycosyltransferases, each using a different nucleotide-activated or Dol-P-bound sugar as their donor substrate. One such substrate is Dol-P-glucose, which provides glucose residues for assembly of the terminal Glc3 cap on the lipid-linked oligosaccharide (LLO). In S. cerevisiae, Dol-P-glucose is synthesized from glucose-6-phosphate (G6P) in three steps: conversion of G6P to glucose-1-phosphate by phosphoglucomutase (Pgm1p or Pgm2p), formation of UDP-glucose from glucose-1-phosphate and UTP via UDP-glucose pyrophosphorylase (Ugp1p), and transfer of glucose from UDP-glucose to Dol-P by UDP-glucose:dolichyl-phosphate glucosyltransferase (Alg5p). After its production, Dol-P-glucose may serve as substrate for the glycosyltransferases Alg6p, Alg8p, and Die2p/Alg10p within the lumen of the endoplasmic reticulum (ER). These enzymes catalyze the sequential addition of three glucose residues, each derived from a molecule of Dol-P-glucose, to the growing LLO during the final steps of LLO biosynthesis. References: |CITS:[23751184]||CITS: [9878760]|' name: dolichyl glucosyl phosphate biosynthesis pmids: - '23751184' - '9878760' reactions: - ec: - 2.4.1.117 genes: - *id369 left: - UDP-α-D-glucose - a dolichyl phosphate name: UDP-α-D-glucose + a dolichyl phosphate -> a dolichyl β-D-glucosyl phosphate + UDP pmids: [] rhea: [] right: - UDP - a dolichyl β-D-glucosyl phosphate yeastcyc_id: 2.4.1.117-RXN - ec: - 5.4.2.2 genes: - *id203 - *id204 left: - α-D-glucopyranose 1-phosphate name: α-D-glucopyranose 1-phosphate <-> D-glucopyranose 6-phosphate pmids: [] rhea: [] right: - D-glucopyranose 6-phosphate yeastcyc_id: PHOSPHOGLUCMUT-RXN - ec: - 2.7.7.64 - 2.7.7.9 genes: - *id370 - *id371 left: - H+ - UTP - α-D-glucopyranose 1-phosphate name: α-D-glucopyranose 1-phosphate + UTP + H+ -> UDP-α-D-glucose + diphosphate pmids: [] rhea: [] right: - UDP-α-D-glucose - diphosphate yeastcyc_id: GLUC1PURIDYLTRANS-RXN yeastcyc_id: PWY3O-1565 PWY3O-17: all_genes: - &id376 orf: YDL244W symbol: THI13 uniprot: UniProtKB:Q07748 - &id372 orf: YOL055C symbol: THI20 uniprot: UniProtKB:Q08224 - &id373 orf: YPL258C symbol: THI21 uniprot: UniProtKB:Q08975 - &id375 orf: YGR144W symbol: THI4 uniprot: UniProtKB:P32318 - &id374 orf: YPL214C symbol: THI6 uniprot: UniProtKB:P41835 - &id377 orf: YOR143C symbol: THI80 uniprot: UniProtKB:P35202 comment: 'Thiamin (vitamin B1) is an essential compound for all organisms. The major bioactive form of thiamin, thiamin diphosphate (TDP), is a cofactor for many enzymes involved in carbohydrate and amino acid metabolism. Bacteria, plants, and fungi are able to synthesize thiamin de novo, while animals must acquire it from the environment. Thiamin is formed from the ring structures of two aromatic compounds: 4-amino-5-hydroxymethyl-2-methylpyrimidine diphosphate (HMP-PP) and 5-(2-hydroxyethyl)-4-methylthiazole phosphate (HET-P). In S. cerevisiae, thiamin diphosphate is synthesized from HMP-PP and HET-P in three steps. First, HMP-PP and HET-P are condensed by Thi6p to yield thiamin monophosphate (TMP). Second, TMP is dephosphorylated to yield thiamine. This step is presumed to be catalyzed by nonspecific phosphatases in the cytosol. Third, thiamine is pyrophosphorylated by thiamin pyrophosphokinase (Thi80p) to yield TDP. The thiazole and pyrimidine heterocycles of thiamin are derived from HET-P and HMP-PP, respectively. The underlying mechanisms for the synthesis of the thiazole and pyrimidine precursors in yeast are not yet fully understood. In S. cerevisiae, the thiazole is formed from NAD, glycine, and a cysteine residue from the active site of thiazole synthase (Thi4p). This unusual suicide mechanism results in a single turnover capacity for Thi4p. Likewise, the pyrimidine ring is formed from histidine and pyridoxal phosphate via the action of THI5 family enzymes, and may also involve a suicide mechanism where histidine is supplied from the active site of Thi5p. The single turnover capacity of Thi4p and Thi5p is speculated to balance the provision of thiazole and pyramidine heterocycles and provide an alternate regulatory mechanism for thiamin biosynthesis in yeast (see |CITS: [23048037]|). References: |CITS:[18161008]||CITS: [17309261]||CITS: [22031445]||CITS: [22568620]||CITS: [23048037]|' name: thiamine biosynthesis pmids: - '17309261' - '18161008' - '22031445' - '22568620' - '23048037' reactions: - ec: [] genes: [] left: [] name: null pmids: - '8394314' rhea: [] right: [] yeastcyc_id: null - ec: - 2.7.4.7 genes: - *id372 - *id373 left: - 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine - ATP name: 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + ATP -> 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + ADP pmids: [] rhea: [] right: - 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine - ADP yeastcyc_id: PYRIMSYN3-RXN - ec: - 2.5.1.3 genes: - *id374 left: - 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine - 4-methyl-5-(2-phosphooxyethyl)thiazole - H+ name: 4-methyl-5-(2-phosphooxyethyl)thiazole + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + H+ -> thiamine phosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - thiamine phosphate yeastcyc_id: THI-P-SYN-RXN - ec: [] genes: - *id375 left: - ADP-5-ethyl-4-methylthiazole-2-carboxylate - H2O name: ADP-5-ethyl-4-methylthiazole-2-carboxylate + H2O -> AMP + 4-methyl-5-(2-phosphooxyethyl)thiazole + CO2 + H+ pmids: [] rhea: [] right: - 4-methyl-5-(2-phosphooxyethyl)thiazole - AMP - CO2 - H+ yeastcyc_id: RXNQT-4301 - ec: - 2.7.1.49 genes: - *id372 - *id373 left: - 4-amino-2-methyl-5-pyrimidinemethanol - ATP name: ATP + 4-amino-2-methyl-5-pyrimidinemethanol -> ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + H+ pmids: - '10383756' rhea: [] right: - 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine - ADP - H+ yeastcyc_id: OHMETPYRKIN-RXN - ec: [] genes: - *id376 left: - L-histidine - pyridoxal 5'-phosphate name: pyridoxal 5'-phosphate + L-histidine -> 4-amino-2-methyl-5-pyrimidinemethanol pmids: - '12777485' - '14570482' - '18388401' - '2643995' rhea: [] right: - 4-amino-2-methyl-5-pyrimidinemethanol yeastcyc_id: RXN3O-9804 - ec: - 2.7.6.2 genes: - *id377 left: - ATP - thiamine name: thiamine + ATP -> thiamine diphosphate + AMP + H+ pmids: [] rhea: [] right: - AMP - H+ - thiamine diphosphate yeastcyc_id: THIAMIN-PYROPHOSPHOKINASE-RXN - ec: - 3.1.3.100 genes: [] left: - H2O - thiamine phosphate name: thiamine phosphate + H2O -> thiamine + phosphate pmids: [] rhea: [] right: - phosphate - thiamine yeastcyc_id: RXNQT-4191 - ec: [] genes: - *id375 left: - NAD+ - glycine - thiazole synthase name: thiazole synthase + glycine + NAD+ -> ADP-5-ethyl-4-methylthiazole-2-carboxylate + nicotinamide + thiazole synthase - dehydroalanine205 pmids: [] rhea: [] right: - ADP-5-ethyl-4-methylthiazole-2-carboxylate - nicotinamide - thiazole synthase - dehydroalanine205 yeastcyc_id: RXN3O-401 yeastcyc_id: PWY3O-17 PWY3O-1743: all_genes: - *id145 - *id146 - *id147 - *id359 comment: 'Mannose is a fermentable six-carbon monosaccharide that can be utilized for carbon and energy in S. cerevisiae. It is also required for many important mannosylation reactions in the cell, including those involved in N-linked and O-linked glycosylation of proteins and synthesis of the lipid anchor glycosylphosphatidylinositol. In S. cerevisiae, utilization of mannose begins with its phosphorylation to mannose-6-phosphate (M6P) by hexokinase (Hxk1p or Hxk2p) or glucokinase (Glk1p). Although all three proteins can phosphorylate mannose, only HXK2 is highly expressed when yeast cells are grown on mannose as a carbon source. M6P can either be converted to GDP-mannose to support mannosylation reactions in the cell, or converted to fructose-6-phosphate (F6P) to fuel glycolysis. The conversion of M6P to F6P is reversible and catalyzed in both directions by mannose-6-phosphate isomerase (Pmi40p). When yeast cells are grown on mannose as the sole carbon source, PMI40 transcription increases 12-fold, likely in order to provide sufficient levels of F6P for glycolysis. In the absence of mannose, Pmi40p activity becomes is essential for growth, as it enables S. cerevisiae to synthesize M6P from glucose or other carbon sources of F6P. References: |CITS:[9878752]||CITS: [17361015]||CITS: [8403984]||CITS: [7732723]||CITS: [1377774]|' name: mannose degradation pmids: - '1377774' - '17248750' - '17361015' - '7732723' - '8403984' - '9878752' reactions: - ec: - 5.3.1.8 genes: - *id359 left: - D-mannopyranose 6-phosphate name: D-mannopyranose 6-phosphate <-> β-D-fructofuranose 6-phosphate pmids: [] rhea: [] right: - β-D-fructofuranose 6-phosphate yeastcyc_id: MANNPISOM-RXN - ec: - 2.7.1.1 genes: - *id145 - *id146 - *id147 left: - ATP - D-mannose name: D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - D-mannopyranose 6-phosphate - H+ yeastcyc_id: RXN3O-9791 yeastcyc_id: PWY3O-1743 PWY3O-1801: all_genes: - &id378 orf: YGL055W symbol: OLE1 uniprot: UniProtKB:P21147 comment: 'Unsaturated fatty acids are essential for all eukaryotes; they are key components of cellular membranes and are used for energy storage. While most eukaryotes can synthesize polyunsaturated fatty acids, Saccharomyces cerevisiae can only form monounsaturated fatty acids, primarily |FRAME: CPD-9245| (16:l) and |FRAME: OLEATE-CPD| (18:1) (|FRAME: PWY3O-1801| and |FRAME: PWY3O-5268|). The monounsaturated fatty acids, palmitoleate (16:l) and oleate (18:1) are formed by the introduction of a single carboUnsaturated fatty acids are essential for all eukaryotes; they are key components of cellular membranes and are used for energy storage. While most eukaryotes can synthesize polyunsaturated fatty acids, Saccharomyces cerevisiae can only form monounsaturated fatty acids, primarily palmitoleate (16:l) and oleate (18:1). n - carbon double bond into the saturated fatty acyl-CoA, palmitoyl and stearoyl-CoA, respectively. OLE1 encodes the sole S. cerevisiae delta-9 fatty acid desaturase, an ER membrane-bound protein that is required for the production of monounsaturated fatty acids |CITS: [1978720]|. Ole1p catalyzes the formation of a double bond between carbons 9 and 10 (denoted by delta-9) in the cis configuration. Other fungi and eukaryotes have additional fatty acid desaturases that can produce double bonds in the delta12 and delta15 position. The Ole1p sequence is similar to homologs in rat and human (SCD1) over the majority of the protein, including a cluster of histidine residues that coordinate the binding of a diiron-oxo prosthetic group within the catalytic site (reviewed in |CITS: [16920014]|). The rat and yeast proteins are similar enough that exogenously expressed rat protein can rescue an ole1 null mutant |CITS: [1978720]|. However, Ole1p has an additional C-terminal, 113 amino acid extension (relative to the rat protein), which encodes a cytochrome b5-like domain not found in mammalian desaturases. In animal cells, cytochrome b5 is thought to be the electron donor for fatty acid desaturation. In contrast, the yeast cytochrome b5 (Cyb5) is dispensable for the synthesis of unsaturated fatty acids because Ole1p contains inherent electron donor activity. The rat protein is unable to rescue an ole1 cyb5 double mutant |CITS:[8530368]|. OLE1 is highly regulated at the levels of both transcription and mRNA stability (reviewed in |CITS: [16920014 ]| and |CITS: [17087771]|). OLE1 transcription is decreased in response to high fatty acid levels |CITS: [2687232][1556107]| and increased in response to low oxygen |CITS: [10318903]| and low temperature |CITS: [11855848]|. Much of the transcriptional regulation is mediated by two homologous ER membrane-bound transcription factors, Spt23p and Mga2p. In response to stimuli, both Spt23p and Mga2p are activated by ubiquitin-dependent processing into their soluble forms, and then targeted to the nucleus |CITS: [9927444][11007476] [11557770]|. Independent of the transcriptional regulation, OLE1 mRNA is also stabilized under fatty acid free conditions and destabilized when fatty acids are added to the growth medium |CITS: [8824209]|. Mga2p, but not Spt23p, contributes to the regulation of OLE1 mRNA stability |CITS: [15220333]|.' name: palmitoleate biosynthesis pmids: - '16920014' - '1978720' - '2674136' reactions: - ec: - 3.1.2.- genes: [] left: - H2O - palmitoleoyl-CoA name: palmitoleoyl-CoA + H2O -> palmitoleate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - palmitoleate yeastcyc_id: RXN-10662 - ec: - 1.14.19.1 genes: - *id378 left: - H+ - a ferrocytochrome b5 - oxygen - palmitoyl-CoA name: palmitoyl-CoA + 2 a ferrocytochrome b5 + oxygen + 2 H+ -> palmitoleoyl-CoA + 2 a ferricytochrome b5 + 2 H2O pmids: [] rhea: [] right: - H2O - a ferricytochrome b5 - palmitoleoyl-CoA yeastcyc_id: RXN-10664 yeastcyc_id: PWY3O-1801 PWY3O-1874: all_genes: - *id014 - *id009 name: p-aminobenzoate biosynthesis pmids: [] reactions: - ec: - 4.1.3.38 genes: - *id009 left: - 4-amino-4-deoxychorismate name: 4-amino-4-deoxychorismate -> 4-aminobenzoate + pyruvate + H+ pmids: [] rhea: [] right: - 4-aminobenzoate - H+ - pyruvate yeastcyc_id: ADCLY-RXN - ec: - 2.6.1.85 genes: - *id014 left: - L-glutamine - chorismate name: L-glutamine + chorismate <-> 4-amino-4-deoxychorismate + L-glutamate pmids: [] rhea: [] right: - 4-amino-4-deoxychorismate - L-glutamate yeastcyc_id: PABASYN-RXN yeastcyc_id: PWY3O-1874 PWY3O-188: all_genes: - &id379 orf: Q0105 symbol: COB uniprot: UniProtKB:P00163 - &id380 orf: YBL045C symbol: COR1 uniprot: UniProtKB:P07256 - &id390 orf: Q0045 symbol: COX1 uniprot: UniProtKB:P00401 - &id391 orf: YLR038C symbol: COX12 uniprot: UniProtKB:Q01519 - &id392 orf: YGL191W symbol: COX13 uniprot: UniProtKB:P32799 - &id393 orf: Q0250 symbol: COX2 uniprot: UniProtKB:P00410 - &id394 orf: Q0275 symbol: COX3 uniprot: UniProtKB:P00420 - &id395 orf: YGL187C symbol: COX4 uniprot: UniProtKB:P04037 - &id396 orf: YNL052W symbol: COX5A uniprot: UniProtKB:P00424 - &id397 orf: YHR051W symbol: COX6 uniprot: UniProtKB:P00427 - &id398 orf: YMR256C symbol: COX7 uniprot: UniProtKB:P10174 - &id399 orf: YLR395C symbol: COX8 uniprot: UniProtKB:P04039 - &id400 orf: YDL067C symbol: COX9 uniprot: UniProtKB:P07255 - &id381 orf: YOR065W symbol: CYT1 uniprot: UniProtKB:P07143 - &id389 orf: YML120C symbol: NDI1 uniprot: UniProtKB:P32340 - &id382 orf: YHR001W-A symbol: QCR10 uniprot: UniProtKB:P37299 - &id383 orf: YPR191W symbol: QCR2 uniprot: UniProtKB:P07257 - &id384 orf: YFR033C symbol: QCR6 uniprot: UniProtKB:P00127 - &id385 orf: YDR529C symbol: QCR7 uniprot: UniProtKB:P00128 - &id386 orf: YJL166W symbol: QCR8 uniprot: UniProtKB:P08525 - &id387 orf: YGR183C symbol: QCR9 uniprot: UniProtKB:P22289 - &id388 orf: YEL024W symbol: RIP1 uniprot: UniProtKB:P08067 - &id401 orf: YKL148C symbol: SDH1 uniprot: UniProtKB:Q00711 - &id402 orf: YLL041C symbol: SDH2 uniprot: UniProtKB:P21801 - &id403 orf: YKL141W symbol: SDH3 uniprot: UniProtKB:P33421 - &id404 orf: YDR178W symbol: SDH4 uniprot: UniProtKB:P37298 - &id405 orf: YJL045W symbol: null uniprot: UniProtKB:P47052 comment: 'The electron transport chain is the final step of the respiratory pathway, carried out by several large multisubunit enzyme complexes embedded in the mitochondrial inner membrane. The net effect of the electron transport chain is to transfer electrons from NADH to molecular oxygen, coupled to transport of protons across the mitochondrial inner membrane. The proton transport creates an electrochemical gradient across the membrane, which is then used to power ATP synthesis by the mitochondrial inner membrane F1F0 ATP synthase as well as transport of metabolites across the membrane |CITS: [11245784]|. NADH:ubiquinone oxidoreductase (NADH dehdrogenase) catalyzes the oxidation of NADH by ubiquinone, generating ubiquinol and NAD+ |CITS: [11245784][1900238]|. In Saccharomyces cerevisiae, Candida glabata and Schizosaccharomyces pombe, a single-subunit enzyme provides this activity (Ndi1p in S. cerevisiae). In many other fungi, mammals, insects, and plants, this activity resides in a multisubunit complex, Complex I, which transports a proton across the mitochondrial inner membrane concomitantly with NADH oxidation |CITS: [11245784]|. The succinate dehydrogenase complex (Complex II) catalyzes the oxidation of succinate by ubiquinone to fumarate, generating ubiquinol and fumarate. This reaction does not result in transfer of a proton across the mitochondrial inner membrane. In S. cerevisiae the complex is composed of the flavoprotein subunit Sdh1p, the iron-sulfur protein subunit Sdh2p, the cytochrome b subunit Sdh3p, and the membrane anchor subunit Sdh4p |CITS: [14672929]|. The ubiquinol generated by NADH dehydrogenase and Complex II is oxidized to ubiquinone by ubiquinol-cytochrome-c reductase (Complex III; cytochrome bc1 complex) in a stepwise electron transfer through the complex that results in the reduction of cytochrome c and the transfer of a proton across the mitochondrial membrane |CITS: [12788490]|. The cytochrome c that is reduced in this step is the product of the CYC1 gene. The final step in the electron transport chain is catalyzed by Complex IV, cytochrome c oxidase, which oxidizes cytochrome c while reducing oxygen to water with the concomitant transport of a proton across the mitochondrial inner membrane |CITS: [1665335][7851399]|.' name: aerobic respiration, electron transport chain pmids: [] reactions: - ec: - 1.10.2.2 genes: - *id379 - *id380 - *id381 - *id382 - *id383 - *id384 - *id385 - *id386 - *id387 - *id388 left: - oxidized cytochrome c - ubiquinol-6 name: 2 oxidized cytochrome c + ubiquinol-6 -> 2 reduced cytochrome c + ubiquinone-6 pmids: [] rhea: [] right: - reduced cytochrome c - ubiquinone-6 yeastcyc_id: RXN3O-168 - ec: - 1.6.5.3 genes: - *id389 left: - NADH - ubiquinone-6 name: NADH + ubiquinone-6 -> NAD+ + ubiquinol-6 pmids: [] rhea: [] right: - NAD+ - ubiquinol-6 yeastcyc_id: RXN3O-165 - ec: - 1.9.3.1 genes: - *id390 - *id391 - *id392 - *id393 - *id394 - *id395 - *id396 - *id397 - *id398 - *id399 - *id400 left: - oxygen - reduced cytochrome c name: reduced cytochrome c + oxygen -> oxidized cytochrome c + H2O pmids: [] rhea: [] right: - H2O - oxidized cytochrome c yeastcyc_id: RXN3O-9794 - ec: - 1.3.5.1 genes: - *id401 - *id402 - *id403 - *id404 - *id405 left: - succinate - ubiquinone-6 name: succinate + ubiquinone-6 -> fumarate + ubiquinol-6 pmids: [] rhea: [] right: - fumarate - ubiquinol-6 yeastcyc_id: SUCC-FUM-OXRED-UBI-RXN yeastcyc_id: PWY3O-188 PWY3O-19: all_genes: - &id407 orf: YOR125C symbol: CAT5 uniprot: UniProtKB:P41735 - &id410 orf: YNR041C symbol: COQ2 uniprot: UniProtKB:P32378 - &id409 orf: YOL096C symbol: COQ3 uniprot: UniProtKB:P27680 - &id408 orf: YML110C symbol: COQ5 uniprot: UniProtKB:P49017 - &id406 orf: YGR255C symbol: COQ6 uniprot: UniProtKB:P53318 name: ubiquinol-6 biosynthesis from 4-hydroxybenzoate (eukaryotic) pmids: - '11469793' - '11583838' - '13835567' - '14701817' - '15548532' - '15792955' - '16624818' - '17248750' - '17391640' - '17482885' - '2198286' - '620805' - '6369767' - '8703953' - '9083048' - '9452453' reactions: - ec: - 1.14.13.- genes: - *id406 left: - 2-hexaprenyl-6-methoxyphenol - H+ - NADPH - oxygen name: 2-hexaprenyl-6-methoxyphenol + NADPH + oxygen + H+ -> 2-methoxy-6-all trans-hexaprenyl-1,4-benzoquinol + NADP+ + H2O pmids: [] rhea: [] right: - 2-methoxy-6-all trans-hexaprenyl-1,4-benzoquinol - H2O - NADP+ yeastcyc_id: RXN3O-12 - ec: - 1.14.15.- genes: - *id406 left: - 3-hexaprenyl-4-hydroxybenzoate - H+ - a reduced ferredoxin [iron-sulfur] cluster - oxygen name: 3-hexaprenyl-4-hydroxybenzoate + 2 a reduced ferredoxin [iron-sulfur] cluster + oxygen + 2 H+ -> 3,4-dihydroxy-5-all-trans-hexaprenylbenzoate + 2 an oxidized ferredoxin [iron-sulfur] cluster + H2O pmids: [] rhea: [] right: - 3,4-dihydroxy-5-all-trans-hexaprenylbenzoate - H2O - an oxidized ferredoxin [iron-sulfur] cluster yeastcyc_id: RXN3O-58 - ec: - 4.1.1.- genes: [] left: - 3-methoxy-4-hydroxy-5-all-trans-hexaprenylbenzoate - H+ name: 3-methoxy-4-hydroxy-5-all-trans-hexaprenylbenzoate + H+ -> 2-hexaprenyl-6-methoxyphenol + CO2 pmids: [] rhea: [] right: - 2-hexaprenyl-6-methoxyphenol - CO2 yeastcyc_id: RXN3O-73 - ec: - 1.14.99.60 genes: - *id407 left: - 6-methoxy-3-methyl-2-all-trans-hexaprenyl-1,4-benzoquinol - a reduced electron acceptor - oxygen name: 6-methoxy-3-methyl-2-all-trans-hexaprenyl-1,4-benzoquinol + a reduced electron acceptor + oxygen -> 3-demethylubiquinol-6 + an oxidized electron acceptor + H2O pmids: [] rhea: [] right: - 3-demethylubiquinol-6 - H2O - an oxidized electron acceptor yeastcyc_id: RXN3O-75 - ec: - 2.1.1.201 genes: - *id408 left: - 2-methoxy-6-all trans-hexaprenyl-1,4-benzoquinol - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + 2-methoxy-6-all trans-hexaprenyl-1,4-benzoquinol -> 6-methoxy-3-methyl-2-all-trans-hexaprenyl-1,4-benzoquinol + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - 6-methoxy-3-methyl-2-all-trans-hexaprenyl-1,4-benzoquinol - H+ - S-adenosyl-L-homocysteine yeastcyc_id: RXN3O-54 - ec: - 2.1.1.114 genes: - *id409 left: - 3,4-dihydroxy-5-all-trans-hexaprenylbenzoate - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + 3,4-dihydroxy-5-all-trans-hexaprenylbenzoate -> S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-5-all-trans-hexaprenylbenzoate + H+ pmids: [] rhea: [] right: - 3-methoxy-4-hydroxy-5-all-trans-hexaprenylbenzoate - H+ - S-adenosyl-L-homocysteine yeastcyc_id: 2.1.1.114-RXN - ec: - 2.1.1.64 genes: - *id409 left: - 3-demethylubiquinol-6 - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + 3-demethylubiquinol-6 -> S-adenosyl-L-homocysteine + ubiquinol-6 + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - ubiquinol-6 yeastcyc_id: RXN3O-102 - ec: - 2.5.1.39 genes: - *id410 left: - 4-hydroxybenzoate - all-trans-hexaprenyl diphosphate name: all-trans-hexaprenyl diphosphate + 4-hydroxybenzoate -> 3-hexaprenyl-4-hydroxybenzoate + diphosphate pmids: [] rhea: [] right: - 3-hexaprenyl-4-hydroxybenzoate - diphosphate yeastcyc_id: RXN-9003 yeastcyc_id: PWY3O-19 PWY3O-2: all_genes: - *id289 - *id284 - *id292 - *id285 - *id279 - *id282 - *id293 - *id286 - *id283 - *id281 - *id291 - *id290 - *id287 - *id288 comment: 'Phospholipids are amphipathic molecules that consist of a glycerol backbone esterified to a phosphate group and two fatty acids. As a primary structural element of biological membranes, phospholipids play important roles in cell morphology and organelle function. The major phospholipids found in total cell extracts from S. cerevisiae are phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), and phosphatidylserine (PS); however, the phospholipid composition of yeast changes according to the carbon source used for growth. All major phospholipid classes in S. cerevisiae may trace their synthesis to a common precursor: cytidine diphosphate diacylglycerol (CDP-DAG). CDP-DAG is synthesized in a reaction catalyzed by CDP-DAG synthase, which converts phosphatidic acid (PA) to CDP-DAG using cytidine triphosphate (CTP) as the CDP donor. There are two distinct CDP-DAG synthases in S. cerevisiae: Cds1p, localized in the endoplasmic reticulum (ER), and Tam41p, localized in the mitochondrial matrix. In the ER, CDP-DAG generated by Cds1p can be converted to phosphatidylinositol (PI) or phosphatidylserine (PS) via PI synthase (Pis1p) or PS synthase (Cho1p), respectively. In the mitochondrion, CDP-DAG generated by Tam41p can be sequentially converted to phosphatidylglycerol (PG), which can be further converted to cardiolipin. Synthesis of PI, PG, and cardiolipin occurs through similar mechanisms in mammalian cells; however, unlike yeast, mammals primarily synthesize PS from other phospholipids and not from CDP-DAG. PS generated via Pis1p may undergo further processing in the mitochondria, where the enzyme PS decarboxylase (Psd1p) can convert it to phosphatidylethanolamine (PE). This represents the major route of PE synthesis in S. cerevisiae. The second route occurs via the CDP-ethanolamine branch of the Kennedy pathway. This pathway consists of three steps: 1) phosphorylation of ethanolamine to phosphoethanolamine by ethanolamine kinase (Eki1p) or choline kinase (Cki1p), 2) activation of phosphoethanolamine to CDP-ethanolamine by phosphoethanolamine cytidylyltransferase (Ect1p), and 3) transfer of a phosphoethanolamine moiety from CDP-ethanolamine to diacylglycerol by 1,2-diacylglycerol ethanolaminephosphotransferase (Ept1p). The other branch of the Kennedy pathway, the CDP-choline pathway, incorporates choline into phosphatidylcholine (PC) in three analogous steps. PC may also be synthesized from PE when the latter molecule undergoes three successive methylations by Cho2p and Opi3p. References: |CITS:[9885152]||CITS: [24520995]||CITS: [24866973]|' name: superpathway of phospholipid biosynthesis pmids: - '16807089' - '24520995' - '24866973' - '9885152' reactions: - ec: - 3.1.3.27 genes: [] left: - 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate - H2O name: 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate + H2O -> an L-1-phosphatidyl-sn-glycerol + phosphate pmids: [] rhea: [] right: - an L-1-phosphatidyl-sn-glycerol - phosphate yeastcyc_id: PGPPHOSPHA-RXN - ec: - 2.7.8.- genes: - *id279 left: - an L-1-phosphatidyl-sn-glycerol name: 2 an L-1-phosphatidyl-sn-glycerol -> a cardiolipin + glycerol pmids: [] rhea: [] right: - a cardiolipin - glycerol yeastcyc_id: CARDIOLIPSYN-RXN - ec: - 2.7.7.15 genes: - *id281 left: - CTP - H+ - phosphocholine name: CTP + phosphocholine + H+ -> CDP-choline + diphosphate pmids: [] rhea: [] right: - CDP-choline - diphosphate yeastcyc_id: 2.7.7.15-RXN - ec: - 2.7.7.14 genes: - *id282 left: - CTP - H+ - O-phosphoethanolamine name: O-phosphoethanolamine + CTP + H+ -> CDP-ethanolamine + diphosphate pmids: - '16807089' - '8982874' rhea: [] right: - CDP-ethanolamine - diphosphate yeastcyc_id: 2.7.7.14-RXN - ec: - 2.1.1.71 genes: - *id283 left: - S-adenosyl-L-methionine - a phosphatidyl-N-dimethylethanolamine name: S-adenosyl-L-methionine + a phosphatidyl-N-dimethylethanolamine -> a phosphatidylcholine + S-adenosyl-L-homocysteine pmids: [] rhea: [] right: - S-adenosyl-L-homocysteine - a phosphatidylcholine yeastcyc_id: RXN3O-349 - ec: - 2.1.1.71 genes: - *id283 left: - S-adenosyl-L-methionine - a phosphatidyl-N-dimethylethanolamine name: S-adenosyl-L-methionine + a phosphatidyl-N-dimethylethanolamine -> a phosphatidylcholine + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a phosphatidylcholine yeastcyc_id: RXN4FS-2 - ec: - 2.1.1.71 genes: - *id283 left: - S-adenosyl-L-methionine - a phosphatidyl-N-methylethanolamine name: S-adenosyl-L-methionine + a phosphatidyl-N-methylethanolamine -> a phosphatidyl-N-dimethylethanolamine + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a phosphatidyl-N-dimethylethanolamine yeastcyc_id: 2.1.1.71-RXN - ec: - 2.1.1.17 genes: - *id284 left: - S-adenosyl-L-methionine - an L-1-phosphatidylethanolamine name: S-adenosyl-L-methionine + an L-1-phosphatidylethanolamine -> a phosphatidyl-N-methylethanolamine + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - a phosphatidyl-N-methylethanolamine yeastcyc_id: 2.1.1.17-RXN - ec: - 2.7.8.2 genes: - *id285 left: - CDP-choline - a 1,2-diacyl-sn-glycerol name: a 1,2-diacyl-sn-glycerol + CDP-choline <-> a phosphatidylcholine + CMP + H+ pmids: [] rhea: [] right: - CMP - H+ - a phosphatidylcholine yeastcyc_id: RXN-5781 - ec: - 2.7.8.1 genes: - *id286 left: - CDP-ethanolamine - a 1,2-diacyl-sn-glycerol name: a 1,2-diacyl-sn-glycerol + CDP-ethanolamine -> an L-1-phosphatidylethanolamine + CMP + H+ pmids: - '16807089' - '2848840' rhea: [] right: - CMP - H+ - an L-1-phosphatidylethanolamine yeastcyc_id: ETHANOLAMINEPHOSPHOTRANSFERASE-RXN - ec: - 4.1.1.65 genes: - *id287 - *id288 left: - H+ - a 3-O-sn-phosphatidyl-L-serine name: a 3-O-sn-phosphatidyl-L-serine + H+ -> an L-1-phosphatidylethanolamine + CO2 pmids: [] rhea: [] right: - CO2 - an L-1-phosphatidylethanolamine yeastcyc_id: PHOSPHASERDECARB-RXN - ec: - 2.7.8.8 genes: - *id289 left: - L-serine - a CDP-diacylglycerol name: a CDP-diacylglycerol + L-serine <-> CMP + a 3-O-sn-phosphatidyl-L-serine + H+ pmids: [] rhea: [] right: - CMP - H+ - a 3-O-sn-phosphatidyl-L-serine yeastcyc_id: PHOSPHASERSYN-RXN - ec: - 2.7.8.11 genes: - *id290 left: - a CDP-diacylglycerol - myo-inositol name: a CDP-diacylglycerol + myo-inositol -> a 1-phosphatidyl-1D-myo-inositol + CMP + H+ pmids: [] rhea: [] right: - CMP - H+ - a 1-phosphatidyl-1D-myo-inositol yeastcyc_id: 2.7.8.11-RXN - ec: - 2.7.8.5 genes: - *id291 left: - a CDP-diacylglycerol - sn-glycerol 3-phosphate name: a CDP-diacylglycerol + sn-glycerol 3-phosphate -> CMP + 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate + H+ pmids: [] rhea: [] right: - 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate - CMP - H+ yeastcyc_id: PHOSPHAGLYPSYN-RXN - ec: - 2.7.1.32 genes: - *id292 left: - ATP - choline name: choline + ATP -> phosphocholine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - phosphocholine yeastcyc_id: CHOLINE-KINASE-RXN - ec: - 2.7.1.82 genes: - *id293 left: - ATP - ethanolamine name: ethanolamine + ATP -> O-phosphoethanolamine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - O-phosphoethanolamine yeastcyc_id: ETHANOLAMINE-KINASE-RXN yeastcyc_id: PWY3O-2 PWY3O-20: all_genes: - *id021 - *id027 - *id013 - *id023 - *id024 - *id265 - *id022 - *id018 - *id019 comment: 'Folates are heterocyclic compounds based on a pteroic acid skeleton conjugated to one or more glutamate molecules. The biologically active form of folate is tetrahydrofolate (THF), whose metabolic derivatives serve as cofactors that carry and chemically activate one-carbon (1C) units at different levels of oxidation (methyl-THF, methylene-THF, etc.) The 1C units carried by these folate cofactors are utilized in one-carbon metabolism for the biosynthesis of various compounds including methionine, thymidylate, and purines. S. cerevisiae and many other microorganisms are able to synthesize tetrahydrofolate de novo, unlike humans who must acquire it from the environment. In the folate biosynthesis pathway, dihydrofolate synthetase (Fol3p in S. cerevisiae) adds an initial glutamate molecule to the p-aminobenzoic acid moiety of 7,8-dihydropteroate to form 7,8-dihydrofolate. This compound is then reduced by dihydrofolate reductase (Dfr1p) to tetrahydrofolate, which can subsequently be converted to a 1C unit-carrying THF derivative. The folates produced in this pathway are subject to further glutamylation by folylpolyglutamate synthetase (Met7p), which catalyzes ATP-dependent extension of the glutamate side chain to yield folate polyglutamates. Polyglutamylation is thought to increase the affinity of intracellular folates for folate-dependent enzymes and prevent their efflux out of cells and organelles. Lending to the importance of polyglutamylation for folate coenzyme function, fol3 null mutants require folinic acid supplementation for growth and met7 null mutants are respiratory-deficient and auxotrophic for methionine. References: |CITS:[3665922]||CITS: [18804690]||CITS: [16700064]||CITS: [10799479]||CITS: [(SCOTT)]|' name: folate polyglutamylation pmids: - '10799479' - '16700064' - '18804690' - '1916088' - '3665922' reactions: - ec: - 6.3.2.17 genes: - *id265 left: - ATP - L-glutamate - a 10-formyltetrahydrofolate name: 10-formyl-tetrahydropteroyl-[γ-Glu](n) + L-glutamate + ATP -> 10-formyl-tetrahydropteroyl-[γ-Glu](n+1) + ADP + phosphate pmids: [] rhea: [] right: - ADP - a 10-formyltetrahydrofolate - phosphate yeastcyc_id: FORMYLTHFGLUSYNTH-RXN - ec: - 6.3.2.12 genes: - *id013 left: - 7,8-dihydropteroate - ATP - L-glutamate name: L-glutamate + 7,8-dihydropteroate + ATP -> ADP + 7,8-dihydrofolate monoglutamate + phosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydrofolate monoglutamate - ADP - H+ - phosphate yeastcyc_id: DIHYDROFOLATESYNTH-RXN - ec: - 6.3.2.17 genes: - *id265 left: - ATP - L-glutamate - a 7,8-dihydrofolate name: L-glutamate + ATP + tetrahydropteroyl-[γ-Glu](n) -> ADP + tetrahydropteroyl-[γ-Glu](n+1) + phosphate pmids: [] rhea: [] right: - ADP - a 7,8-dihydrofolate - phosphate yeastcyc_id: RXN3O-681 - ec: - 6.3.2.17 genes: - *id265 left: - ATP - L-glutamate - a tetrahydrofolate name: L-glutamate + tetrahydropteroyl-[γ-Glu](n) + ATP -> tetrahydropteroyl-[γ-Glu](n+1) + ADP + phosphate pmids: [] rhea: [] right: - ADP - a tetrahydrofolate - phosphate yeastcyc_id: FOLYLPOLYGLUTAMATESYNTH-RXN - ec: - 2.1.2.1 genes: - *id018 - *id019 left: - L-serine - a tetrahydrofolate name: L-serine + a tetrahydrofolate <-> glycine + a 5,10-methylenetetrahydrofolate + H2O pmids: [] rhea: [] right: - H2O - a 5,10-methylenetetrahydrofolate - glycine yeastcyc_id: GLYOHMETRANS-RXN - ec: - 6.3.2.17 genes: - *id265 left: - ATP - L-glutamate - a 5-methyltetrahydrofolate name: a 5-methyltetrahydrofolate + L-glutamate + ATP -> a 5-methyltetrahydrofolate + ADP + phosphate pmids: [] rhea: [] right: - ADP - a 5-methyltetrahydrofolate - phosphate yeastcyc_id: RXN3O-22 - ec: - 1.5.1.20 genes: - *id023 - *id024 left: - NAD+ - a 5-methyltetrahydrofolate name: a 5-methyltetrahydrofolate + NAD+ <- a 5,10-methylenetetrahydrofolate + NADH + H+ pmids: - '10600168' rhea: [] right: - H+ - NADH - a 5,10-methylenetetrahydrofolate yeastcyc_id: 1.5.1.20-RXN - ec: - 6.3.4.3 genes: - *id021 - *id022 left: - ATP - a tetrahydrofolate - formate name: a tetrahydrofolate + ATP + formate <-> a 10-formyltetrahydrofolate + ADP + phosphate pmids: - '1916088' rhea: [] right: - ADP - a 10-formyltetrahydrofolate - phosphate yeastcyc_id: FORMATETHFLIG-RXN - ec: - 1.5.1.3 genes: - *id027 left: - NADP+ - a tetrahydrofolate name: a tetrahydrofolate + NADP+ <- a 7,8-dihydrofolate + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 7,8-dihydrofolate yeastcyc_id: DIHYDROFOLATEREDUCT-RXN - ec: - 6.3.2.17 genes: - *id265 left: - ATP - L-glutamate - a 5,10-methylenetetrahydrofolate name: methylene-tetrahydropteroyl-[γ-Glu](n) + L-glutamate + ATP -> methylene-tetrahydropteroyl-[γ-Glu](n+1) + ADP + phosphate pmids: [] rhea: [] right: - ADP - a 5,10-methylenetetrahydrofolate - phosphate yeastcyc_id: RXN0-2921 yeastcyc_id: PWY3O-20 PWY3O-214: all_genes: - *id157 - *id158 - *id159 - *id160 - *id161 - &id411 orf: YDR380W symbol: ARO10 uniprot: UniProtKB:Q06408 - *id015 - *id017 - *id164 - *id165 - *id166 - *id312 comment: 'While Saccharomyces cerevisiae can use most amino acids as their sole nitrogen source, they can only use a few amino acids as a carbon source to support growth |CITS:[Large86][Cooper82]|. This is in contrast to most eukaryotes and some fungi, which can metabolize amino acids completely, utilizing them as sole sources of carbon and nitrogen |CITS:[Stryer88][Large 86]|. S. cerevisiae degrade the aromatic amino acids (tryptophan, phenylalanine, and tyrosine) and the branched-chain amino acids (valine, leucine, and iso-leucine) via the Ehrlich pathway |CITS:[Sentheshanmuganathan60][10989420]|. This pathway is comprised of the following steps: 1) deamination of the amino acid to the corresponding alpha-keto acid; 2) decarboxylation of the resulting alpha-keto acid to the respective aldehyde; and, 3) reduction of the aldehyde to form the corresponding long chain or complex alcohol, known as a fusel alcohol or fusel oil |CITS:[10989420][Large 86]|. Fusel alcohols are important flavor and aroma compounds in yeast-fermented food products and beverages (as reported in |CITS:[9546164]|. The primary aminotransferase in tryptophan degradation is postulated to be Aro9p |CITS:[6763508]|. In vitro studies demonstrated that Aro9p is active with phenylpyruvate, pyruvate, or p-hydroxyphenylpyruvate, but not 2-oxoglutarate as the amino acceptor |CITS:[6763508]|. Aro9p is induced by aromatic amino acids and is subject to nitrogen regulation |CITS:[6763508][10207060]|. The decarboxylase encoding gene ARO10 appears to be transcriptionally regulated in a similar fashion|CITS:[10207060]|. Gap1p, a general amino acid permease, and Wap1p, an inducible amino acid permease with wide substrate specificity, appear to be the main uptake systems for utilizing aromatic amino acids |CITS:[10207060]|.' name: tryptophan degradation pmids: - '12499363' - '6763508' - '9491082' - '9491083' reactions: - ec: - 4.1.1.74 genes: - *id411 - *id164 - *id165 - *id166 left: - (indol-3-yl)pyruvate - H+ name: (indol-3-yl)pyruvate + H+ -> CO2 + (indol-3-yl)acetaldehyde pmids: - '10207060' - '12499363' - '15933030' rhea: [] right: - (indol-3-yl)acetaldehyde - CO2 yeastcyc_id: 4.1.1.74-RXN - ec: - 2.6.1.27 genes: - *id015 left: - 2-oxoglutarate - L-tryptophan name: 2-oxoglutarate + L-tryptophan <-> L-glutamate + (indol-3-yl)pyruvate pmids: - '10207060' - '6763508' - '9491082' - '9491083' rhea: [] right: - (indol-3-yl)pyruvate - L-glutamate yeastcyc_id: TRYPTOPHAN-AMINOTRANSFERASE-RXN - ec: - 2.6.1.28 genes: - *id017 left: - 3-phenyl-2-oxopropanoate - L-tryptophan name: L-tryptophan + 3-phenyl-2-oxopropanoate <-> (indol-3-yl)pyruvate + L-phenylalanine pmids: - '10207060' - '6763508' - '9491082' - '9491083' rhea: [] right: - (indol-3-yl)pyruvate - L-phenylalanine yeastcyc_id: 2.6.1.28-RXN - ec: - 1.1.1.190 genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id312 left: - NAD+ - indole-3-ethanol name: indole-3-ethanol + NAD+ <- (indol-3-yl)acetaldehyde + NADH + H+ pmids: - '12499363' rhea: [] right: - (indol-3-yl)acetaldehyde - H+ - NADH yeastcyc_id: 1.1.1.190-RXN yeastcyc_id: PWY3O-214 PWY3O-2220: all_genes: - *id350 - *id351 - *id345 - *id346 - *id347 - *id348 - *id353 comment: 'In yeast and most eukaryotes, purine nucleotides levels are maintained via a combination of de novo synthesis and salvage pathways. The salvage pathways utilize purine bases and nucleosides taken up from the environment or formed from metabolism to synthesize purine nucleoside monophosphates. Compared to the de novo pathway, where 5-phosphoribosyl-1-pyrophosphate (PRPP) is converted to the adenylic/guanylic nucleotide precursor inosine 5-monophosphate (IMP) over many ATP-consuming steps, the salvage pathways synthesize IMP, GMP, and AMP directly from PRPP and a purine base via the action of purine phosphoribosyltransferases. There are three main phosphoribosyltransferases involved in purine salvage in S. cerevisiae: i) Hpt1p, which produces GMP and IMP from guanine and hypoxanthine, respectively; ii) Apt1p, which synthesizes AMP from adenine; and iii) Xpt1p, which synthesizes XMP from xanthine. XMP can be further converted to GMP via the GMP synthase Gua1p. The salvage pathways represent the preferred route of synthesis when purines are abundant in the growth medium. In S. cerevisiae, most of the ADE genes responsible for de novo synthesis of IMP and AMP are repressed by extracellular adenine, whereas extracellular guanine strongly represses the IMD genes responsible for the rate-limiting step of GMP synthesis. References: |CITS:[17052198 ]||CITS: [9864350]||CITS: [10217799]||CITS: [22419079]|' name: salvage pathways of adenine, hypoxanthine and their nucleosides pmids: - '10217799' - '11223943' - '15565584' - '1577682' - '17052198' - '22419079' - '9864350' reactions: - ec: - 3.5.4.17 - 3.5.4.6 genes: - *id345 left: - AMP - H+ - H2O name: AMP + H+ + H2O -> IMP + ammonium pmids: [] rhea: [] right: - IMP - ammonium yeastcyc_id: AMP-DEAMINASE-RXN - ec: - 2.4.2.7 genes: - *id346 - *id347 left: - AMP - diphosphate name: AMP + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + adenine pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - adenine yeastcyc_id: ADENPRIBOSYLTRAN-RXN - ec: - 2.4.2.8 genes: - *id348 left: - IMP - diphosphate name: IMP + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + hypoxanthine pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - hypoxanthine yeastcyc_id: HYPOXANPRIBOSYLTRAN-RXN - ec: - 3.5.4.2 genes: - *id350 left: - H+ - H2O - adenine name: adenine + H+ + H2O -> ammonium + hypoxanthine pmids: [] rhea: [] right: - ammonium - hypoxanthine yeastcyc_id: ADENINE-DEAMINASE-RXN - ec: - 2.7.1.20 genes: - *id351 left: - ATP - adenosine name: adenosine + ATP -> AMP + ADP + H+ pmids: [] rhea: [] right: - ADP - AMP - H+ yeastcyc_id: ADENOSINE-KINASE-RXN - ec: - 2.4.2.1 genes: - *id353 left: - inosine - phosphate name: inosine + phosphate -> α-D-ribose-1-phosphate + hypoxanthine pmids: [] rhea: [] right: - hypoxanthine - α-D-ribose-1-phosphate yeastcyc_id: INOPHOSPHOR-RXN yeastcyc_id: PWY3O-2220 PWY3O-224: all_genes: - &id412 orf: YNL129W symbol: NRK1 uniprot: UniProtKB:P53915 comment: 'Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and energy metabolism. NAD also has been shown to be an important substrate in a variety of biological processes, including transcriptional regulation, DNA repair, calcium-dependent signaling pathways, calorie-restriction-mediated life-span extension and age-associated diseases |CITS: [12736687],[12648681]|. NAD appears to affect these processes by regulating the Sir2p family of NAD-dependent deacetylases (Sirtuins) |CITS: [12648681]|. There are a number of pathways for NAD biosynthesis. In yeast and most other organisms, the two major pathways are de novo synthesis of NAD (the de novo pathway) and regeneration of NAD from its nicotinamide degradation products (the NAD salvage pathway) |CITS: [12972620], [12648681]|. NAD is synthesized de novo from tryptophan via kynurenine |CITS: [12972620]|. In this pathway tryptophan is converted to nicotinic acid mononucleotide (NAMN) in 6 enzymatic steps (catalyzed by Bna1-2p, and Bna4-7p) and one non-enzymatic step |CITS: [12972620]|. At NAMN the de novo pathway converges with the NAD salvage pathway and the last two steps to NAD are shared |CITS: [12972620], [12648681]|. In the yeast NAD salvage pathway, the vitamin precursors nicotinamide and nicotinic acid are converted to NAMN, the point of convergence with the de novo pathway |CITS: [12648681]|. The steps from nicotinic acid to NAD were elucidated by Preiss and Handler and are sometimes referred to as the Preiss-Handler pathway |CITS: [13416279], [13563526]|. Yeast can also import extracellular nicotinic acid into the cell by the permease Tna1p and then convert it into NAD via the Preiss-Handler pathway |CITS: [12648681]|. There are four additional pathways for synthesizing NAD in yeast: two salvage pathways from the vitamin precursor nicotinamide riboside (NR) and two salvage pathways from nicotinic acid riboside (NaR) |CITS: [15137942], [17482543], [17914902]|. Three of these salvage pathways converge first with the NAD salvage pathway and then with the de novo pathway, while the fourth, the NR salvage pathway I, is independent of both of these pathways. In the NR salvage pathway I, NR is phosphorylated to nicotinamide mononucleotide by the kinase Nrk1p, and then adenylated to NAD by Nma1p or Nma2p |CITS: [15137942]|. Bacteria such as Haemophilus influenza that lack the enzymes of the de novo and Preiss-Handler pathway can synthesize NAD from NR and nicotinamide mononucleotide as well |CITS: [15137942]|. Humans also appear to have this NR salvage pathway |CITS: [15137942]|. Yeast have a second NR salvage pathway (NR salvage pathway II) that is independent of Nrk1p; in NR salvage pathway II NR is split into a ribosyl product and nicotinamide, which is subsequently converted to NAD via enzymes of the NAD salvage pathway and de novo pathway |CITS: [17482543]|. The initial steps in the two NaR salvage pathways are similar to those of the NR salvage pathways and are catalyzed by the same enzymes; Nrk1p catalyzes the first step in the NR and NaR salvage pathways I and Urh1p and Pnp1p catalyze the first steps of the NR and NaR salvage pathways II |CITS: [17914902]|. ' name: nicotinate riboside salvage pathway I pmids: - '17914902' reactions: - ec: - 2.7.1.- - 2.7.1.173 genes: - *id412 left: - ATP - β-D-ribosylnicotinate name: β-D-ribosylnicotinate + ATP -> β-nicotinate D-ribonucleotide + ADP + H+ pmids: - '17914902' rhea: [] right: - ADP - H+ - β-nicotinate D-ribonucleotide yeastcyc_id: RXN-8443 yeastcyc_id: PWY3O-224 PWY3O-230: all_genes: - *id018 - *id019 comment: 'Serine is a proteinogenic amino acid and a precursor to the amino acids tryptophan, glycine, and cysteine. Serine is also the primary source of one-carbon units in folate-mediated one-carbon metabolism, a network of carbon transfer reactions required for the biosynthesis of methionine, thymidylate, and purines. S. cerevisiae possesses three major pathways for serine biosynthesis: a phosphoglycerate pathway that synthesizes serine from 3-phosphoglycerate, a threonine pathway that synthesizes serine from threonine-derived glycine, and a glyoxylate pathway that synthesizes serine from glyoxylate-derived glycine. The former two pathways operate when glucose is the carbon source while the latter pathway operates during growth on non-fermentable substrates. In the glyoxylate pathway, glyoxylate is converted to glycine via alanine:glyoxylate aminotransferase (Agx1p). Glycine is then converted to serine via serine hydroxymethyltransferase (Shm1p/Shm2p). The reaction catalyzed by serine hydroxymethyltransferase is reversible; however the cytoplasmic isoform (SHM2) is thought to contribute more to serine catabolism while the mitochondrial isoform (SHM1) contributes to serine synthesis. The roles of SHM1 and SHM2 are reported to change in accordance to the nutritional requirements of the cell, particularly to the availability of serine or glycine. Despite the proposed preference of Shm2p for glycine synthesis, expression of SHM2 but not SHM1 is increased in the presence of glycine. References: |CITS:[(JONES)]||CITS: [12525494]||CITS: [14745783]||CITS: [9398220]||CITS: [15948949]|' name: serine biosynthesis from glyoxylate pmids: - '12525494' - '14745783' - '15948949' - '7498764' - '9398220' reactions: - ec: - 2.1.2.1 genes: - *id018 - *id019 left: - L-serine - a tetrahydrofolate name: L-serine + a tetrahydrofolate <-> glycine + a 5,10-methylenetetrahydrofolate + H2O pmids: [] rhea: [] right: - H2O - a 5,10-methylenetetrahydrofolate - glycine yeastcyc_id: GLYOHMETRANS-RXN yeastcyc_id: PWY3O-230 PWY3O-236: all_genes: - *id353 - &id413 orf: YDR400W symbol: URH1 uniprot: UniProtKB:Q04179 comment: 'Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and energy metabolism. NAD also has been shown to be an important substrate in a variety of biological processes, including transcriptional regulation, DNA repair, calcium-dependent signaling pathways, calorie-restriction-mediated life-span extension and age-associated diseases |CITS: [12736687],[12648681]|. NAD appears to affect these processes by regulating the Sir2p family of NAD-dependent deacetylases (Sirtuins) |CITS: [12648681]|. There are a number of pathways for NAD biosynthesis. In yeast and most other organisms, the two major pathways are de novo synthesis of NAD (the de novo pathway) and regeneration of NAD from its nicotinamide degradation products (the NAD salvage pathway) |CITS: [12972620], [12648681]|. NAD is synthesized de novo from tryptophan via kynurenine |CITS: [12972620]|. In this pathway tryptophan is converted to nicotinic acid mononucleotide (NAMN) in 6 enzymatic steps (catalyzed by Bna1-2p, and Bna4-7p) and one non-enzymatic step |CITS: [12972620]|. At NAMN the de novo pathway converges with the NAD salvage pathway and the last two steps to NAD are shared |CITS: [12972620], [12648681]|. In the yeast NAD salvage pathway, the vitamin precursors nicotinamide and nicotinic acid are converted to NAMN, the point of convergence with the de novo pathway |CITS: [12648681]|. The steps from nicotinic acid to NAD were elucidated by Preiss and Handler and are sometimes referred to as the Preiss-Handler pathway |CITS: [13416279], [13563526]|. Yeast can also import extracellular nicotinic acid into the cell by the permease Tna1p and then convert it into NAD via the Preiss-Handler pathway |CITS: [12648681]|. There are four additional pathways for synthesizing NAD in yeast: two salvage pathways from the vitamin precursor nicotinamide riboside (NR) and two salvage pathways from nicotinic acid riboside (NaR) |CITS: [15137942], [17482543], [17914902]|. Three of these salvage pathways converge first with the NAD salvage pathway and then with the de novo pathway, while the fourth, the NR salvage pathway I, is independent of both of these pathways. In the NR salvage pathway I, NR is phosphorylated to nicotinamide mononucleotide by the kinase Nrk1p, and then adenylated to NAD by Nma1p or Nma2p |CITS: [15137942]|. Bacteria such as Haemophilus influenza that lack the enzymes of the de novo and Preiss-Handler pathway can synthesize NAD from NR and nicotinamide mononucleotide as well |CITS: [15137942]|. Humans also appear to have this NR salvage pathway |CITS: [15137942]|. Yeast have a second NR salvage pathway (NR salvage pathway II) that is independent of Nrk1p; in NR salvage pathway II NR is split into a ribosyl product and nicotinamide, which is subsequently converted to NAD via enzymes of the NAD salvage pathway and de novo pathway |CITS: [17482543]|. The initial steps in the two NaR salvage pathways are similar to those of the NR salvage pathways and are catalyzed by the same enzymes; Nrk1p catalyzes the first step in the NR and NaR salvage pathways I and Urh1p and Pnp1p catalyze the first steps of the NR and NaR salvage pathways II |CITS: [17914902]|. ' name: nicotinate riboside salvage pathway II pmids: - '17914902' reactions: - ec: [] genes: - *id413 left: - H2O - β-D-ribosylnicotinate name: β-D-ribosylnicotinate + H2O -> D-ribose + nicotinate pmids: - '17914902' rhea: [] right: - D-ribose - nicotinate yeastcyc_id: RXN3O-214 - ec: [] genes: - *id353 left: - phosphate - β-D-ribosylnicotinate name: β-D-ribosylnicotinate + phosphate -> nicotinate + α-D-ribose-1-phosphate pmids: - '17914902' rhea: [] right: - nicotinate - α-D-ribose-1-phosphate yeastcyc_id: RXN3O-205 yeastcyc_id: PWY3O-236 PWY3O-238: all_genes: - *id262 - *id265 comment: 'S. cerevisiae synthesizes methionine via the methylation of homocysteine. In this reaction, the cobalamin-independent methionine synthase Met6p catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5-methyl-THF) to the thiol of homocysteine, forming methionine. 5-methyl-THF is a folate coenzyme that carries a single-carbon unit originating from one-carbon metabolism. It exists in both monoglutamated and polyglutamated forms, however only the latter can be used by Met6p as the methyl donor for this reaction. Yeast cells defective in polyglutamylation of folate coenzymes (MET7 null mutants) are auxotrophic for methionine. The other component of this reaction, homocysteine, is derived from aspartate and sulfur. In S. cerevisiae, aspartate can be utilized for homocysteine biosynthesis by undergoing a three-step conversion to homoserine followed by acetylation to O-acetylhomoserine. O-acetylhomoserine can then react with sulfide to produce homocysteine directly, or it can react with cysteine (a sulfur amino acid) to produce cystathionine via the transsulfuration pathway. The subsequent cleavage of cystathionine produces homocysteine. References: |CITS:[9409150]||CITS: [16700064]||CITS: [10799479]|' name: methionine biosynthesis pmids: - '10799479' - '16700064' - '1789001' - '9409150' reactions: - ec: - 2.1.1.14 genes: - *id262 left: - 5-methyltetrahydropteroyl tri-L-glutamate - L-homocysteine name: L-homocysteine + 5-methyltetrahydropteroyl tri-L-glutamate <-> L-methionine + tetrahydropteroyl tri-L-glutamate pmids: [] rhea: [] right: - L-methionine - tetrahydropteroyl tri-L-glutamate yeastcyc_id: HOMOCYSMET-RXN - ec: - 6.3.2.17 genes: - *id265 left: - ATP - L-glutamate - a 5-methyltetrahydrofolate name: a 5-methyltetrahydrofolate + L-glutamate + ATP -> a 5-methyltetrahydrofolate + ADP + phosphate pmids: [] rhea: [] right: - ADP - a 5-methyltetrahydrofolate - phosphate yeastcyc_id: RXN3O-22 yeastcyc_id: PWY3O-238 PWY3O-242: all_genes: - &id422 orf: YFR019W symbol: FAB1 uniprot: UniProtKB:P34756 - &id414 orf: YNL325C symbol: FIG4 uniprot: UniProtKB:P42837 - &id424 orf: YIL002C symbol: INP51 uniprot: UniProtKB:P40559 - &id415 orf: YNL106C symbol: INP52 uniprot: UniProtKB:P50942 - &id416 orf: YOR109W symbol: INP53 uniprot: UniProtKB:Q12271 - &id425 orf: YOL065C symbol: INP54 uniprot: UniProtKB:Q08227 - &id419 orf: YJL100W symbol: LSB6 uniprot: UniProtKB:P42951 - &id426 orf: YDR208W symbol: MSS4 uniprot: UniProtKB:P38994 - &id420 orf: YNL267W symbol: PIK1 uniprot: UniProtKB:P39104 - &id417 orf: YKL212W symbol: SAC1 uniprot: UniProtKB:P32368 - &id421 orf: YLR305C symbol: STT4 uniprot: UniProtKB:P37297 - &id418 orf: YLR240W symbol: VPS34 uniprot: UniProtKB:P22543 - &id423 orf: YJR110W symbol: YMR1 uniprot: UniProtKB:P47147 comment: The phosphorylated products of phosphatidylinositol (PtdIns, PI), collectively referred to as phosphoinositides or phosphatidylinositol phosphates (PtdInsPs, PIPs), are membrane-bound lipids that function as structural components of membranes, as well as regulators of many cellular processes in eukaryotes, including vesicle-mediated membrane trafficking, cell wall integrity, and actin cytoskeleton organization (reviewed in |CITS:[17382260]| and |CITS:[8599109]|). PtdInsPs are also precursors of the water-soluble inositol phosphates (IPs), an important class of intracellular signaling molecules (reviewed in |CITS:[16781889], [16429326], [17488633]|). The inositol ring of the membrane phospholipids and the water-soluble IPs are readily phosphorylated and dephosphorylated at a number of positions making them well suited as key regulators. PtdIns can be phosphorylated at one or a combination of positions (3', 4', or 5') on the inositol headgroup, generating a set of unique stereoisomers that have specific biological functions (reviewed in |CITS:[17382260]|). These stereoisomers have been shown to be restricted to certain membranes (reviewed in |CITS:[17382260]|). Phosphatidylinositol 4-phosphate (PtdIns4P) is the major PtdInsP species of the Golgi apparatus, where it plays a role in the vesicular trafficking of secretory proteins from the Golgi to the plasma membrane (reviewed in |CITS:[17382260]|). Phosphatidylinositol 4,5-bisphosphate (PtdIns[4,5]P2) is the major species found at the plasma membrane and is involved in the regulation of actin cytoskeleton organization, as well as cell wall integrity, and heat shock response pathways (reviewed in |CITS:[17382260]|). Phosphatidylinositol 3-phosphate (PtdIns3P) is found predominantly at endosomal membranes and in multivesicular bodies (MVB), where it plays a role in endosomal and vacuolar membrane trafficking. Phosphatidylinositol 3,5-bisphosphate (PtdIns[3,5]P2) is found on vacuolar membranes where it plays an important role in the MVB sorting pathway (reviewed in |CITS:[17382260]|). Phosphorylation and dephosphorylation of the inositol headgroups of PtdInsPs at specific membrane locations signals the recruitment of certain proteins essential for vesicular transport (|CITS:[8599109]|, and reviewed in |CITS:[17382260]|). PtdInsPs recruit proteins that contain PtdInsP-specific binding domains, such as the well-studied pleckstrin homology (PH) domain that recognizes the phosphorylation pattern of specific PtdInsP inositol headgroups (reviewed in |CITS:[17382260]|). A number of kinases and phosphatases are involved in the generation and interconversions of PtdInsPs, the majority of which have been well conserved during evolution (reviewed in |CITS:[17382260]|). The PtdInsP kinases, in contrast to the lipid phosphatases, have a higher degree of specificity. While each kinase appears to phosphorylate only one substrate, many of the lipid phosphatases can dephosphorylate a number of substrates. name: phosphatidylinositol phosphate biosynthesis pmids: - '17382260' reactions: - ec: - 3.1.3.- genes: - *id414 - *id415 - *id416 - *id417 left: - 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate - H2O name: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H2O -> a 1-phosphatidyl-1D-myo-inositol 3-phosphate + phosphate pmids: - '10224048' - '11950935' - '16492811' rhea: [] right: - a 1-phosphatidyl-1D-myo-inositol 3-phosphate - phosphate yeastcyc_id: RXN-10938 - ec: - 2.7.1.137 genes: - *id418 left: - ATP - a 1-phosphatidyl-1D-myo-inositol name: a 1-phosphatidyl-1D-myo-inositol + ATP -> a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + H+ pmids: - '7989323' rhea: [] right: - ADP - H+ - a 1-phosphatidyl-1D-myo-inositol 3-phosphate yeastcyc_id: 1-PHOSPHATIDYLINOSITOL-3-KINASE-RXN - ec: - 2.7.1.67 genes: - *id419 - *id420 - *id421 left: - ATP - a 1-phosphatidyl-1D-myo-inositol name: a 1-phosphatidyl-1D-myo-inositol + ATP -> a 1-phosphatidyl-1D-myo-inositol 4-phosphate + ADP + H+ pmids: - '12361950' - '8194527' - '8288577' rhea: [] right: - ADP - H+ - a 1-phosphatidyl-1D-myo-inositol 4-phosphate yeastcyc_id: 1-PHOSPHATIDYLINOSITOL-KINASE-RXN - ec: - 2.7.1.150 genes: - *id422 left: - ATP - a 1-phosphatidyl-1D-myo-inositol 3-phosphate name: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP -> 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + ADP + H+ pmids: - '9763421' rhea: [] right: - 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate - ADP - H+ yeastcyc_id: 2.7.1.150-RXN - ec: - 3.1.3.64 genes: - *id415 - *id416 - *id417 - *id423 left: - H2O - a 1-phosphatidyl-1D-myo-inositol 3-phosphate name: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + H2O -> a 1-phosphatidyl-1D-myo-inositol + phosphate pmids: - '10224048' - '10900271' - '15169871' rhea: [] right: - a 1-phosphatidyl-1D-myo-inositol - phosphate yeastcyc_id: RXN3O-364 - ec: - 3.1.3.36 genes: - *id424 - *id415 - *id416 - *id425 left: - H2O - a 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate name: a 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O -> a 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate pmids: - '10224048' - '10660045' - '9565610' rhea: [] right: - a 1-phosphatidyl-1D-myo-inositol 4-phosphate - phosphate yeastcyc_id: PHOSPHATIDYLINOSITOL-BISPHOSPHATASE-RXN - ec: - 2.7.1.68 genes: - *id426 left: - ATP - a 1-phosphatidyl-1D-myo-inositol 4-phosphate name: a 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP -> a 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ADP + H+ pmids: - '9624177' rhea: [] right: - ADP - H+ - a 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate yeastcyc_id: 2.7.1.68-RXN - ec: - 3.1.3.- genes: - *id415 - *id416 - *id417 left: - H2O - a 1-phosphatidyl-1D-myo-inositol 4-phosphate name: a 1-phosphatidyl-1D-myo-inositol 4-phosphate + H2O -> a 1-phosphatidyl-1D-myo-inositol + phosphate pmids: [] rhea: [] right: - a 1-phosphatidyl-1D-myo-inositol - phosphate yeastcyc_id: RXN-10961 yeastcyc_id: PWY3O-242 PWY3O-246: all_genes: - &id427 orf: YAL060W symbol: BDH1 uniprot: UniProtKB:P39714 comment: 'Saccharomyces cerevisiae can grow on acetoin and 2,3-butanediol as the sole carbon and energy sources, indicating S. cerevisiae''s ability to degrade these metabolites |CITS: [10938079]|. Acetoin and 2,3-butanediol are both by-products of alcoholic fermentation by S. cerevisiae and other wine yeasts. Various lines of evidence suggest that Bdh1p catalyzes the first step in 2,3-butanediol degradation, the oxidation of 2,3-butanediol to acetoin |CITS: [10938079]|. However, S. cerevisiae mutants with a disrupted BDH1 gene can still grow on 2,3-butanediol as the sole carbon and energy source, indicating that there are other enzymes that can metabolize 2,3-butanediol |CITS: [10938079]|). How acetoin is further degraded in S. cerevisiae is not yet known. Many prokaryotes have a multienzyme complex, acetoin dehydrogenase , that is similar to pyruvate dehdrogenase and transforms acetoin into acetaldehyde and acetyl-CoA, which can enter the glyoxylate and TCA cycle (as reported in |CITS: [11306064]|).' name: (R,R)-butanediol degradation pmids: - '10938079' - '11306064' reactions: - ec: - 1.1.1.4 genes: - *id427 left: - (R,R)-2,3-butanediol - NAD+ name: (R,R)-2,3-butanediol + NAD+ <-> (R)-acetoin + NADH + H+ pmids: [] rhea: [] right: - (R)-acetoin - H+ - NADH yeastcyc_id: RR-BUTANEDIOL-DEHYDROGENASE-RXN yeastcyc_id: PWY3O-246 PWY3O-259: all_genes: - *id282 - *id293 - *id286 comment: 'Phosphatidylethanolamine (PE) is a major structural component of cellular membranes and one of the most abundant phospholipids in eukaryotes. The roles of PE in the cell are many: it contributes to membrane architecture, influences the structure and activity of integral and peripheral membrane proteins, is required for mitochondrial function in yeast, and plays important roles in cell division and autophagy. In addition, PE donates the phosphoethanolamine required for the biosynthesis of glycosylphosphatidylinositol, a lipid anchor involved in attaching proteins to the cell surface. In S. cerevisiae, the major route of PE synthesis involves the production and decarboxylation of phosphatidylserine. Alternatively, S. cerevisiae can synthesize PE from free ethanolamine via the CDP-ethanolamine branch of the Kennedy pathway. This route consists of three steps: 1) phosphorylation of ethanolamine to phosphoethanolamine by ethanolamine kinase (Eki1p) or choline kinase (Cki1p), 2) activation of phosphoethanolamine to CDP-ethanolamine by phosphoethanolamine cytidylyltransferase (Ect1p), and 3) transfer of a phosphoethanolamine moiety from CDP-ethanolamine to diacylglycerol by 1,2-diacylglycerol ethanolaminephosphotransferase (Ept1p). The other branch of the Kennedy pathway, the CDP-choline pathway, analogously incorporates choline into phosphatidylcholine (PC). The Kennedy pathway is not essential in yeast. Nevertheless, it plays an important role in PE and PC synthesis when the preferred de novo pathways are disrupted or repressed. This stands in contrast to mammalian cells, where the Kennedy pathway represents the major route of synthesis and is essential for mammalian development. References: |CITS:[20503434]||CITS: [17428789]||CITS: [11294902]||CITS: [21275641]||CITS: [9370323]||CITS: [17612623]|' name: phospholipid biosynthesis II (Kennedy pathway) pmids: - '11294902' - '16807089' - '17428789' - '17612623' - '20503434' - '21275641' - '9370323' reactions: - ec: - 2.7.7.14 genes: - *id282 left: - CTP - H+ - O-phosphoethanolamine name: O-phosphoethanolamine + CTP + H+ -> CDP-ethanolamine + diphosphate pmids: - '16807089' - '8982874' rhea: [] right: - CDP-ethanolamine - diphosphate yeastcyc_id: 2.7.7.14-RXN - ec: - 2.7.8.1 genes: - *id286 left: - CDP-ethanolamine - a 1,2-diacyl-sn-glycerol name: a 1,2-diacyl-sn-glycerol + CDP-ethanolamine -> an L-1-phosphatidylethanolamine + CMP + H+ pmids: - '16807089' - '2848840' rhea: [] right: - CMP - H+ - an L-1-phosphatidylethanolamine yeastcyc_id: ETHANOLAMINEPHOSPHOTRANSFERASE-RXN - ec: - 2.7.1.82 genes: - *id293 left: - ATP - ethanolamine name: ethanolamine + ATP -> O-phosphoethanolamine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - O-phosphoethanolamine yeastcyc_id: ETHANOLAMINE-KINASE-RXN yeastcyc_id: PWY3O-259 PWY3O-261: all_genes: - *id213 - *id214 - &id428 orf: YOR184W symbol: SER1 uniprot: UniProtKB:P33330 - &id431 orf: YGR208W symbol: SER2 uniprot: UniProtKB:P42941 - &id429 orf: YER081W symbol: SER3 uniprot: UniProtKB:P40054 - &id430 orf: YIL074C symbol: SER33 uniprot: UniProtKB:P40510 - *id018 - *id019 comment: 'There are several pathways for serine and glycine biosynthesis in S. cerevisiae. When glucose is used as the carbon source, glycine can be synthesized from threonine via threonine aldolase (Gly1p) in the threonine pathway, while serine can be synthesized from the glycolytic intermediate 3-phosphoglycerate in the phosphoglycerate pathway. Expression of the genes involved in the latter pathway decreases upon depletion of glucose. When ethanol or other non-fermentable substrates are used as the carbon source, S. cerevisiae can alternatively synthesize glycine from glyoxylate via alanine glyoxylate aminotransferase (Agx1p). Glycine and serine produced in these pathways can be interconverted to one another via the tetrahydrofolate-dependent serine hydroxymethyltransferases Shm1p and Shm2p. Between these, the cytoplasmic isoform Shm2p serves as the major source of glycine (via serine breakdown) in serine-rich conditions. The mitochondrial isoform Shm1p may also contribute to glycine synthesis, however it preferentially catalyzes serine synthesis from glycine under conditions of serine starvation. References: |CITS:[(JONES)]||CITS: [12525494]||CITS: [9163906]||CITS: [14745783]||CITS: [9398220]|' name: superpathway of serine and glycine biosynthesis pmids: - '12525494' - '14745783' - '9163906' - '9398220' reactions: - ec: - 2.6.1.52 genes: - *id428 left: - 2-oxoglutarate - 3-phospho-L-serine name: 2-oxoglutarate + 3-phospho-L-serine <- 3-phosphooxypyruvate + L-glutamate pmids: [] rhea: [] right: - 3-phosphooxypyruvate - L-glutamate yeastcyc_id: PSERTRANSAM-RXN - ec: - 1.1.1.95 genes: - *id429 - *id430 left: - 3-phospho-D-glycerate - NAD+ name: 3-phospho-D-glycerate + NAD+ <-> 3-phosphooxypyruvate + NADH + H+ pmids: [] rhea: [] right: - 3-phosphooxypyruvate - H+ - NADH yeastcyc_id: PGLYCDEHYDROG-RXN - ec: - 3.1.3.3 genes: - *id431 left: - 3-phospho-L-serine - H2O name: 3-phospho-L-serine + H2O -> L-serine + phosphate pmids: [] rhea: [] right: - L-serine - phosphate yeastcyc_id: RXN0-5114 - ec: - 2.1.2.1 genes: - *id018 - *id019 left: - L-serine - a tetrahydrofolate name: L-serine + a tetrahydrofolate <-> glycine + a 5,10-methylenetetrahydrofolate + H2O pmids: [] rhea: [] right: - H2O - a 5,10-methylenetetrahydrofolate - glycine yeastcyc_id: GLYOHMETRANS-RXN - ec: - 4.1.2.48 - 4.1.2.5 genes: - *id214 left: - L-threonine name: L-threonine -> acetaldehyde + glycine pmids: [] rhea: [] right: - acetaldehyde - glycine yeastcyc_id: THREONINE-ALDOLASE-RXN - ec: - 2.6.1.44 genes: - *id213 left: - L-alanine - glyoxylate name: glyoxylate + L-alanine -> glycine + pyruvate pmids: [] rhea: [] right: - glycine - pyruvate yeastcyc_id: ALANINE--GLYOXYLATE-AMINOTRANSFERASE-RXN yeastcyc_id: PWY3O-261 PWY3O-285: all_genes: - *id350 - *id092 - *id101 - *id086 - *id096 - *id097 - *id087 - *id088 - *id091 - *id093 - *id103 - *id089 - *id090 - *id351 - *id345 - *id346 - *id347 - *id102 - *id352 - *id095 - *id348 - *id098 - *id099 - *id100 - &id432 orf: YOR155C symbol: ISN1 uniprot: UniProtKB:Q99312 - *id353 - *id104 - *id105 - *id106 - *id107 - *id349 - *id094 comment: 'Purine and pyrimidine nucleotides serve many diverse and essential roles in the cell. They are precursors to DNA, RNA, and many important metabolites (e.g. CDP-diacylglycerol). In addition, nucleotides can be used as an energy source (primarily as ATP), signaling molecules, and cofactor components (e.g. coenzyme A). In yeast and most eukaryotes, purine nucleotides levels are maintained via a combination of de novo synthesis and salvage pathways. The salvage pathways utilize purine bases and nucleosides taken up from the environment or formed from metabolism to synthesize purine nucleoside monophosphates. Compared to the de novo pathway, where 5-phosphoribosyl-1-pyrophosphate (PRPP) is converted to the adenylic/guanylic nucleotide precursor inosine 5-monophosphate (IMP) over many ATP-consuming steps, the salvage pathways synthesize IMP, GMP, and AMP directly from PRPP and a purine base via the action of purine phosphoribosyltransferases. When purines are abundant in the growth medium, the salvage pathways are the preferred routes of purine nucleotide synthesis. In S. cerevisiae, most of the ADE genes responsible for de novo synthesis of IMP and AMP are repressed in response to extracellular adenine, whereas extracellular guanine strongly represses the IMD genes responsible for the rate-limiting step of GMP synthesis. Adenine limitation, on the other hand, results in derepression of ADE genes and active de novo purine biosynthesis. Adenine-repressible transcriptional activation of ADE genes is mediated by the transcription factors Bas1p and Pho2p. References: |CITS:[22419079]||CITS: [17052198]||CITS: [(JONES)]||CITS: [1495962]||CITS: [9822821]|' name: superpathway of purine biosynthesis and salvage pathways pmids: - '1495962' - '17052198' - '22419079' - '9822821' reactions: - ec: - 4.3.2.2 genes: - *id086 left: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole name: 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <-> fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - fumarate yeastcyc_id: AICARSYN-RXN - ec: - 4.1.1.21 genes: - *id087 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - H+ name: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H+ <-> 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + CO2 pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - CO2 yeastcyc_id: AIRCARBOXY-RXN - ec: - 2.4.2.14 genes: - *id088 left: - 5-phospho-β-D-ribosylamine - L-glutamate - diphosphate name: 5-phospho-β-D-ribosylamine + L-glutamate + diphosphate <-> 5-phospho-α-D-ribose 1-diphosphate + L-glutamine + H2O pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - H2O - L-glutamine yeastcyc_id: PRPPAMIDOTRANS-RXN - ec: - 2.7.4.3 genes: - *id089 - *id090 left: - AMP - ATP name: AMP + ATP <-> 2 ADP pmids: [] rhea: [] right: - ADP yeastcyc_id: ADENYL-KIN-RXN - ec: - 3.5.4.17 - 3.5.4.6 genes: - *id345 left: - AMP - H+ - H2O name: AMP + H+ + H2O -> IMP + ammonium pmids: [] rhea: [] right: - IMP - ammonium yeastcyc_id: AMP-DEAMINASE-RXN - ec: - 2.4.2.7 genes: - *id346 - *id347 left: - AMP - diphosphate name: AMP + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + adenine pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - adenine yeastcyc_id: ADENPRIBOSYLTRAN-RXN - ec: - 6.3.3.1 genes: - *id091 left: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ATP name: ATP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine -> ADP + 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + phosphate + H+ pmids: [] rhea: [] right: - 5-amino-1-(5-phospho-β-D-ribosyl)imidazole - ADP - H+ - phosphate yeastcyc_id: AIRS-RXN - ec: - 6.3.2.6 genes: - *id092 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate - ATP - L-aspartate name: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate -> ADP + 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole + phosphate + H+ pmids: [] rhea: [] right: - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole - ADP - H+ - phosphate yeastcyc_id: SAICARSYN-RXN - ec: - 6.3.4.13 genes: - *id091 left: - 5-phospho-β-D-ribosylamine - ATP - glycine name: ATP + 5-phospho-β-D-ribosylamine + glycine -> ADP + N1-(5-phospho-β-D-ribosyl)glycinamide + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - N1-(5-phospho-β-D-ribosyl)glycinamide - phosphate yeastcyc_id: GLYRIBONUCSYN-RXN - ec: - 6.3.5.3 genes: - *id093 left: - ATP - H2O - L-glutamine - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide name: ATP + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + L-glutamine + H2O -> L-glutamate + ADP + 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine + phosphate + H+ pmids: [] rhea: [] right: - 2-(formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine - ADP - H+ - L-glutamate - phosphate yeastcyc_id: FGAMSYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - GDP name: GDP + ATP -> GTP + ADP pmids: [] rhea: [] right: - ADP - GTP yeastcyc_id: GDPKIN-RXN - ec: - 2.7.4.8 genes: - *id095 left: - ATP - GMP name: GMP + ATP <-> GDP + ADP pmids: [] rhea: [] right: - ADP - GDP yeastcyc_id: GUANYL-KIN-RXN - ec: - 2.4.2.8 genes: - *id348 left: - GMP - diphosphate name: GMP + diphosphate <- guanine + 5-phospho-α-D-ribose 1-diphosphate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - guanine yeastcyc_id: GUANPRIBOSYLTRAN-RXN - ec: - 3.1.3.5 - 3.1.3.99 genes: - *id432 left: - H2O - IMP name: IMP + H2O -> inosine + phosphate pmids: - '12735798' - '8141771' rhea: [] right: - inosine - phosphate yeastcyc_id: RXN-7607 - ec: - 3.5.4.10 genes: - *id096 - *id097 left: - H2O - IMP name: IMP + H2O <-> 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide yeastcyc_id: IMPCYCLOHYDROLASE-RXN - ec: - 1.1.1.205 genes: - *id098 - *id099 - *id100 left: - H2O - IMP - NAD+ name: IMP + NAD+ + H2O <-> XMP + NADH + H+ pmids: - '12746440' rhea: [] right: - H+ - NADH - XMP yeastcyc_id: IMP-DEHYDROG-RXN - ec: - 2.4.2.8 genes: - *id348 left: - IMP - diphosphate name: IMP + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + hypoxanthine pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - hypoxanthine yeastcyc_id: HYPOXANPRIBOSYLTRAN-RXN - ec: - 6.3.4.4 genes: - *id101 left: - GTP - IMP - L-aspartate name: L-aspartate + IMP + GTP -> adenylo-succinate + GDP + phosphate + 2 H+ pmids: [] rhea: [] right: - GDP - H+ - adenylo-succinate - phosphate yeastcyc_id: ADENYLOSUCCINATE-SYNTHASE-RXN - ec: - 6.3.5.2 genes: - *id102 left: - ATP - H2O - L-glutamine - XMP name: XMP + L-glutamine + ATP + H2O -> L-glutamate + GMP + AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - AMP - GMP - H+ - L-glutamate - diphosphate yeastcyc_id: GMP-SYN-GLUT-RXN - ec: [] genes: [] left: - ATP - XMP - ammonium name: XMP + ammonium + ATP -> GMP + AMP + diphosphate + 2 H+ pmids: [] rhea: [] right: - AMP - GMP - H+ - diphosphate yeastcyc_id: GMP-SYN-NH3-RXN - ec: - 2.4.2.22 genes: - *id349 left: - XMP - diphosphate name: XMP + diphosphate <- xanthine + 5-phospho-α-D-ribose 1-diphosphate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - xanthine yeastcyc_id: XANPRIBOSYLTRAN-RXN - ec: - 2.1.2.3 genes: - *id096 - *id097 left: - 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide <-> a tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide pmids: [] rhea: [] right: - 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide - a tetrahydrofolate yeastcyc_id: AICARTRANSFORM-RXN - ec: - 2.1.2.2 genes: - *id103 left: - N1-(5-phospho-β-D-ribosyl)glycinamide - a 10-formyltetrahydrofolate name: a 10-formyltetrahydrofolate + N1-(5-phospho-β-D-ribosyl)glycinamide <-> a tetrahydrofolate + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide + H+ pmids: [] rhea: [] right: - H+ - N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide - a tetrahydrofolate yeastcyc_id: GART-RXN - ec: - 3.5.4.2 genes: - *id350 left: - H+ - H2O - adenine name: adenine + H+ + H2O -> ammonium + hypoxanthine pmids: [] rhea: [] right: - ammonium - hypoxanthine yeastcyc_id: ADENINE-DEAMINASE-RXN - ec: - 2.7.1.20 genes: - *id351 left: - ATP - adenosine name: adenosine + ATP -> AMP + ADP + H+ pmids: [] rhea: [] right: - ADP - AMP - H+ yeastcyc_id: ADENOSINE-KINASE-RXN - ec: - 4.3.2.2 genes: - *id086 left: - adenylo-succinate name: adenylo-succinate <-> fumarate + AMP pmids: [] rhea: [] right: - AMP - fumarate yeastcyc_id: AMPSYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dADP name: dADP + ATP -> dATP + ADP pmids: [] rhea: [] right: - ADP - dATP yeastcyc_id: DADPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dADP name: dADP + an oxidized thioredoxin + H2O <- ADP + a reduced thioredoxin pmids: [] rhea: [] right: - ADP - a reduced thioredoxin yeastcyc_id: ADPREDUCT-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dGDP name: dGDP + ATP -> dGTP + ADP pmids: [] rhea: [] right: - ADP - dGTP yeastcyc_id: DGDPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dGDP name: dGDP + an oxidized thioredoxin + H2O <- GDP + a reduced thioredoxin pmids: [] rhea: [] right: - GDP - a reduced thioredoxin yeastcyc_id: GDPREDUCT-RXN - ec: - 1.1.98.6 genes: [] left: - ATP - H+ - formate name: formate + ATP + H+ -> CO2 + dATP + H2O pmids: [] rhea: [] right: - CO2 - H2O - dATP yeastcyc_id: RXN0-745 - ec: - 1.1.98.6 genes: [] left: - GTP - H+ - formate name: formate + GTP + H+ -> dGTP + CO2 + H2O pmids: [] rhea: [] right: - CO2 - H2O - dGTP yeastcyc_id: RXN0-746 - ec: - 3.5.4.3 genes: - *id352 left: - H+ - H2O - guanine name: guanine + H+ + H2O -> ammonium + xanthine pmids: [] rhea: [] right: - ammonium - xanthine yeastcyc_id: GUANINE-DEAMINASE-RXN - ec: - 2.4.2.1 genes: - *id353 left: - inosine - phosphate name: inosine + phosphate -> α-D-ribose-1-phosphate + hypoxanthine pmids: [] rhea: [] right: - hypoxanthine - α-D-ribose-1-phosphate yeastcyc_id: INOPHOSPHOR-RXN yeastcyc_id: PWY3O-285 PWY3O-3: all_genes: - *id290 comment: 'Phosphatidylinositol (PI) is an essential myo-inositol-containing phospholipid in all eukaryotes. It is the third most abundant phospholipid found in the membranes of S. cerevisiae and a precursor to phosphoinositides, inositol polyphosphates, and complex sphingolipids. PI and its metabolites are involved in a variety of biological processes including signal transduction, nuclear mRNA export, vesicle trafficking, and synthesis of the lipid anchor glycosylphosphatidylinositol. PI is synthesized at the endoplasmic reticulum from cytidine diphosphate diacylglycerol (CDP-DAG) and inositol in a reaction catalyzed by PI synthase (Pis1p). Synthesis of PI is increased by exogenously supplied inositol or zinc depletion. When cells are grown in inositol, PI synthase activity is greatly stimulated while phosphatidylserine synthase (Cho1p), which competes with Pis1p for their common substrate, CDP-DAG, is inhibited. Under conditions of zinc depletion, the transcription factor Zap1p binds to a zinc-responsive cis-acting element (UAS-ZRE) in the PIS1 promoter and increases PI synthase expression. Increased PI synthesis through zinc depletion or inositol supplementation leads to reduced CDP-DAG levels as well as its precursor, phosphatidic acid (PA). This PA level drop causes the Opi1p repressor to translocate to the nucleus, where it subsequently represses the transcription of many UAS-INO-containing phospholipid biosynthetic genes. Thus, in addition to its role in the biosynthesis of many important metabolites, PI synthesis indirectly contributes to the transcriptional regulation of phospholipid metabolism through its effect on intracellular PA level. References: |CITS:[15967713]||CITS: [2002005]||CITS: [9885152]||CITS: [22345606]|' name: phosphatidylinositol biosynthesis pmids: - '15967713' - '2002005' - '22345606' - '3031032' - '6088233' - '9370330' - '9885152' reactions: - ec: - 2.7.8.11 genes: - *id290 left: - a CDP-diacylglycerol - myo-inositol name: a CDP-diacylglycerol + myo-inositol -> a 1-phosphatidyl-1D-myo-inositol + CMP + H+ pmids: [] rhea: [] right: - CMP - H+ - a 1-phosphatidyl-1D-myo-inositol yeastcyc_id: 2.7.8.11-RXN yeastcyc_id: PWY3O-3 PWY3O-31704: all_genes: - *id133 - *id132 - *id130 - *id126 - *id121 - *id120 - *id122 - *id123 - *id127 - *id129 - *id128 - *id124 - *id112 - *id118 comment: 'The ergosterol biosynthesis pathway is required for generation of a major constituent of the fungal plasma membrane, ergosterol |CITS: [Paltauf]||CITS: [8561481]|. This pathway is fungal-specific; plasma membranes of other organisms are composed predominantly of other types of sterol. However, the pathway is not universally present in fungi; for example, Pneumocystis carinii plasma membranes lack ergosterol |CITS: [12531182]|. In S. cerevisiae, some steps in the pathway are dispensible while others are essential for viability |CITS: [8277826]|. The ergosterol biosynthesis pathway has been the subject of intensive investigation as a target of antifungal drugs |CITS: [11815273]|. The major target of azole antifungal drugs is lanosterol 14-alpha demethylase, a member of the cytochrome P450 family known as Erg11 protein in many fungal species. Squalene epoxidase (Erg1p in S. cerevisiae) is the specific target of allylamine drugs such as terbinafine |CITS: [14638499]|. Mutations in the genes encoding these enzymes and others in the pathway, as well as alterations in the expression levels of the pathway constituents, can lead to antifungal drug resistance |CITS: [11815273]|.' name: ergosterol biosynthesis pmids: - '12119386' - '8552601' - '8561481' reactions: - ec: - 5.4.99.7 genes: - *id112 left: - (3S)-2,3-epoxy-2,3-dihydrosqualene name: (3S)-2,3-epoxy-2,3-dihydrosqualene -> lanosterol pmids: [] rhea: [] right: - lanosterol yeastcyc_id: LANOSTEROL-SYNTHASE-RXN - ec: - 2.5.1.103 genes: - *id118 left: - (2E,6E)-farnesyl diphosphate name: 2 (2E,6E)-farnesyl diphosphate -> presqualene diphosphate + diphosphate pmids: - '2068081' - '3277535' rhea: [] right: - diphosphate - presqualene diphosphate yeastcyc_id: RXN-12263 - ec: [] genes: - *id120 left: - 4,4-dimethylzymosterol - H+ - a ferrocytochrome b5 - oxygen name: 4,4-dimethylzymosterol + 2 a ferrocytochrome b5 + oxygen + 2 H+ -> 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + 2 a ferricytochrome b5 + H2O pmids: [] rhea: [] right: - 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H2O - a ferricytochrome b5 yeastcyc_id: RXN66-310 - ec: - 1.3.1.70 genes: - *id121 left: - 4,4-dimethylzymosterol - NADP+ name: 4,4-dimethylzymosterol + NADP+ <- 4,4-dimethyl-cholesta-8,14,24-trienol + NADPH + H+ pmids: [] rhea: [] right: - 4,4-dimethyl-cholesta-8,14,24-trienol - H+ - NADPH yeastcyc_id: RXN66-306 - ec: - 1.1.1.170 genes: - *id122 left: - 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol - NAD(P)+ name: 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ -> 3-dehydro-4-methylzymosterol + CO2 + NAD(P)H pmids: [] rhea: [] right: - 3-dehydro-4-methylzymosterol - CO2 - NAD(P)H yeastcyc_id: RXN66-313 - ec: - 1.1.1.170 genes: - *id122 left: - 4α-carboxy-5α-cholesta-8,24-dien-3β-ol - NAD(P)+ name: 4α-carboxy-5α-cholesta-8,24-dien-3β-ol + NAD(P)+ -> zymosterone + CO2 + NAD(P)H pmids: [] rhea: [] right: - CO2 - NAD(P)H - zymosterone yeastcyc_id: RXN66-318 - ec: [] genes: - *id120 left: - 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H+ - a ferrocytochrome b5 - oxygen name: 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + 2 a ferrocytochrome b5 + oxygen + H+ -> 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol + 2 a ferricytochrome b5 + H2O pmids: [] rhea: [] right: - 4α-carboxy-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H2O - a ferricytochrome b5 yeastcyc_id: RXN66-312 - ec: [] genes: - *id120 left: - 4α-formyl-5α-cholesta-8,24-dien-3β-ol - H+ - a ferrocytochrome b5 - oxygen name: 4α-formyl-5α-cholesta-8,24-dien-3β-ol + 2 a ferrocytochrome b5 + oxygen + H+ -> 4α-carboxy-5α-cholesta-8,24-dien-3β-ol + 2 a ferricytochrome b5 + H2O pmids: [] rhea: [] right: - 4α-carboxy-5α-cholesta-8,24-dien-3β-ol - H2O - a ferricytochrome b5 yeastcyc_id: RXN66-317 - ec: [] genes: - *id120 left: - 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H+ - a ferrocytochrome b5 - oxygen name: 4α-hydroxymethyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + 2 a ferrocytochrome b5 + oxygen + 2 H+ -> 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol + 2 a ferricytochrome b5 + 2 H2O pmids: [] rhea: [] right: - 4α-formyl-4β-methyl-5α-cholesta-8,24-dien-3β-ol - H2O - a ferricytochrome b5 yeastcyc_id: RXN66-311 - ec: [] genes: - *id120 left: - 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol - H+ - a ferrocytochrome b5 - oxygen name: 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol + 2 a ferrocytochrome b5 + oxygen + 2 H+ -> 4α-formyl-5α-cholesta-8,24-dien-3β-ol + 2 a ferricytochrome b5 + 2 H2O pmids: [] rhea: [] right: - 4α-formyl-5α-cholesta-8,24-dien-3β-ol - H2O - a ferricytochrome b5 yeastcyc_id: RXN66-316 - ec: [] genes: - *id120 left: - 4α-methyl-zymosterol - H+ - a ferrocytochrome b5 - oxygen name: 4α-methyl-zymosterol + 2 a ferrocytochrome b5 + oxygen + 2 H+ -> 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol + 2 a ferricytochrome b5 + H2O pmids: [] rhea: [] right: - 4α-hydroxymethyl-5α-cholesta-8,24-dien-3β-ol - H2O - a ferricytochrome b5 yeastcyc_id: RXN66-315 - ec: - 1.1.1.270 genes: - *id123 left: - 4α-methyl-zymosterol - NADP+ name: 4α-methyl-zymosterol + NADP+ <- 3-dehydro-4-methylzymosterol + NADPH + H+ pmids: [] rhea: [] right: - 3-dehydro-4-methylzymosterol - H+ - NADPH yeastcyc_id: RXN66-314 - ec: - 2.1.1.41 genes: - *id124 left: - S-adenosyl-L-methionine - zymosterol name: S-adenosyl-L-methionine + zymosterol -> S-adenosyl-L-homocysteine + fecosterol + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - fecosterol yeastcyc_id: RXN3O-178 - ec: - 2.5.1.1 genes: - *id126 left: - dimethylallyl diphosphate - isopentenyl diphosphate name: dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - geranyl diphosphate yeastcyc_id: GPPSYN-RXN - ec: - 1.14.19.20 genes: - *id127 left: - H+ - a ferrocytochrome b5 - episterol - oxygen name: episterol + 2 a ferrocytochrome b5 + oxygen + 2 H+ -> ergosta-5,7,24(28)-trien-3β-ol + 2 a ferricytochrome b5 + 2 H2O pmids: [] rhea: [] right: - H2O - a ferricytochrome b5 - ergosta-5,7,24(28)-trien-3β-ol yeastcyc_id: RXN3O-218 - ec: - 1.14.19.41 genes: - *id128 left: - a reduced [NADPH-hemoprotein reductase] - ergosta-5,7,24(28)-trien-3β-ol - oxygen name: ergosta-5,7,24(28)-trien-3β-ol + a reduced [NADPH-hemoprotein reductase] + oxygen -> ergosta-5,7,22,24(28)-tetraen-3-β-ol + an oxidized [NADPH-hemoprotein reductase] + 2 H2O pmids: [] rhea: [] right: - H2O - an oxidized [NADPH-hemoprotein reductase] - ergosta-5,7,22,24(28)-tetraen-3-β-ol yeastcyc_id: RXN3O-227 - ec: - 1.3.1.71 genes: - *id129 left: - NADP+ - ergosterol name: ergosterol + NADP+ <- ergosta-5,7,22,24(28)-tetraen-3-β-ol + NADPH + H+ pmids: - '10722850' rhea: [] right: - H+ - NADPH - ergosta-5,7,22,24(28)-tetraen-3-β-ol yeastcyc_id: 1.3.1.71-RXN - ec: [] genes: - *id130 left: - fecosterol name: fecosterol -> episterol pmids: [] rhea: [] right: - episterol yeastcyc_id: RXN3O-203 - ec: - 2.5.1.10 genes: - *id126 left: - geranyl diphosphate - isopentenyl diphosphate name: geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate pmids: [] rhea: [] right: - (2E,6E)-farnesyl diphosphate - diphosphate yeastcyc_id: FPPSYN-RXN - ec: - 1.14.14.154 genes: - *id132 left: - a reduced [NADPH-hemoprotein reductase] - lanosterol - oxygen name: lanosterol + 3 a reduced [NADPH-hemoprotein reductase] + 3 oxygen -> 4,4-dimethyl-cholesta-8,14,24-trienol + formate + 3 an oxidized [NADPH-hemoprotein reductase] + 4 H2O + H+ pmids: [] rhea: [] right: - 4,4-dimethyl-cholesta-8,14,24-trienol - H+ - H2O - an oxidized [NADPH-hemoprotein reductase] - formate yeastcyc_id: RXN3O-130 - ec: [] genes: - *id118 left: - H+ - NAD(P)H - presqualene diphosphate name: presqualene diphosphate + NAD(P)H + H+ -> squalene + NAD(P)+ + diphosphate pmids: [] rhea: [] right: - NAD(P)+ - diphosphate - squalene yeastcyc_id: RXN66-281 - ec: - 1.14.14.17 genes: - *id133 left: - a reduced [NADPH-hemoprotein reductase] - oxygen - squalene name: squalene + a reduced [NADPH-hemoprotein reductase] + oxygen -> (3S)-2,3-epoxy-2,3-dihydrosqualene + an oxidized [NADPH-hemoprotein reductase] + H2O pmids: [] rhea: [] right: - (3S)-2,3-epoxy-2,3-dihydrosqualene - H2O - an oxidized [NADPH-hemoprotein reductase] yeastcyc_id: SQUALENE-MONOOXYGENASE-RXN - ec: - 1.1.1.270 genes: - *id123 left: - NADP+ - zymosterol name: zymosterol + NADP+ <- zymosterone + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - zymosterone yeastcyc_id: RXN66-319 yeastcyc_id: PWY3O-31704 PWY3O-31723: all_genes: - *id134 - *id135 name: fatty acids biosynthesis (yeast) pmids: [] reactions: - ec: - 2.3.1.86 genes: - *id134 - *id135 left: - H+ - NADPH - acetyl-CoA - malonyl-CoA name: acetyl-CoA + n malonyl-CoA + 2n NADPH + 4n H+ -> a long-chain acyl-CoA + n CO2 + n coenzyme A + 2n NADP+ pmids: [] rhea: [] right: - CO2 - NADP+ - a long-chain acyl-CoA - coenzyme A yeastcyc_id: FATTY-ACYL-COA-SYNTHASE-RXN yeastcyc_id: PWY3O-31723 PWY3O-335: all_genes: - *id427 - *id076 - *id077 comment: 'Many yeast and bacterial species ferment pyruvate to 2,3-butanediol via the intermediate, acetoin. Although acetoin is a flavorless compound, it is a precursor to some off-odor compounds, such as diacetyl, which can be unfavorable in beer and wine. Acetoin and 2,3-butanediol are both by-products of alcoholic fermentation by S. cerevisiae and other wine yeasts. Acetoin production during alcoholic fermentation depends on the yeast strain and other variables such as substrate and temperature (as reported in |CITS: [16535224]|). Wine yeasts with high fermentation power generally produce low acetoin levels and large amounts of ethanol and higher alcohols (alcohols with more than 2 carbons) (as reported in |CITS: [16535224]|).' name: acetoin biosynthesis pmids: - '10938079' - '16535224' reactions: - ec: [] genes: [] left: - (S)-2-acetolactate - H+ - an oxidized electron acceptor name: (S)-2-acetolactate + an oxidized electron acceptor + H+ -> diacetyl + CO2 + a reduced electron acceptor pmids: [] rhea: [] right: - CO2 - a reduced electron acceptor - diacetyl yeastcyc_id: RXN-6081 - ec: - 2.2.1.6 genes: - *id076 - *id077 left: - H+ - pyruvate name: 2 pyruvate + H+ -> (S)-2-acetolactate + CO2 pmids: [] rhea: [] right: - (S)-2-acetolactate - CO2 yeastcyc_id: ACETOLACTSYN-RXN - ec: - 1.1.1.- genes: - *id427 left: - NAD+ - acetoin name: acetoin + NAD+ <- diacetyl + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - diacetyl yeastcyc_id: ACETOINDEHYDROG-RXN yeastcyc_id: PWY3O-335 PWY3O-351: all_genes: - &id433 orf: YMR009W symbol: ADI1 uniprot: UniProtKB:Q03677 - *id015 - *id017 - *id080 - *id081 - &id435 orf: YJR024C symbol: MDE1 uniprot: UniProtKB:P47095 - &id436 orf: YLR017W symbol: MEU1 uniprot: UniProtKB:Q07938 - &id437 orf: YPR118W symbol: MRI1 uniprot: UniProtKB:Q06489 - *id320 - *id321 - *id047 - *id083 - *id048 - &id434 orf: YEL038W symbol: UTR4 uniprot: UniProtKB:P32626 comment: 'Many organisms possess sulfur salvage pathways that enable recovery of the reduced sulfur atom in metabolites of S-adenosylmethionine (AdoMet) after AdoMet is consumed in a metabolic reaction. The methionine salvage pathway, also known as the 5-methylthioadenosine (MTA) cycle, is one such example. The MTA cycle regenerates methionine from the AdoMet metabolite 5-methylthioadenosine/MTA, which is formed predominantly as a byproduct of polyamine biosynthesis. The methionine salvage pathway is present in all types of organisms, and may have evolved to reuse sulfur after its costly assimilation into the cell. In S. cerevisiae, biosynthesis of the polyamines spermidine and spermine account for over 98% of MTA produced by the cell. In the polyamine pathway, decarboxylated AdoMet (derived from methionine) is converted to MTA after losing an aminopropyl group to putrescine via spermidine synthase (Spe3p). This converts putrescine to spermidine, which can likewise react with decarboxylated AdoMet via spermine synthase (Spe4p) to form spermine and another molecule of MTA. The MTA produced by these two reactions can then enter the MTA cycle to be converted back to methionine. References: |CITS:[9409150]||CITS: [19946895]||CITS: [16530730]||CITS: [9073064]||CITS: [9573363]|' name: superpathway of methionine salvage pathway pmids: - '16530730' - '18625006' - '19946895' - '9073064' - '9409150' - '9573363' reactions: - ec: - 1.13.11.54 genes: - *id433 left: - 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one - oxygen name: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + oxygen -> 4-(methylsulfanyl)-2-oxobutanoate + formate + H+ pmids: - '15938715' - '18625006' rhea: [] right: - 4-(methylsulfanyl)-2-oxobutanoate - H+ - formate yeastcyc_id: R147-RXN - ec: - 3.1.3.77 genes: - *id434 left: - 5-(methylsulfanyl)-2,3-dioxopentyl 1-phosphate - H2O name: 5-(methylsulfanyl)-2,3-dioxopentyl 1-phosphate + H2O -> 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate + H+ pmids: - '18625006' rhea: [] right: - 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one - H+ - phosphate yeastcyc_id: 3.1.3.77-RXN - ec: - 4.2.1.109 genes: - *id435 left: - 5-(methylsulfanyl)-ribulose 1-phosphate name: 5-(methylsulfanyl)-ribulose 1-phosphate -> 5-(methylsulfanyl)-2,3-dioxopentyl 1-phosphate + H2O pmids: - '18625006' rhea: [] right: - 5-(methylsulfanyl)-2,3-dioxopentyl 1-phosphate - H2O yeastcyc_id: R145-RXN - ec: - 2.5.1.6 genes: - *id320 - *id321 left: - ATP - H2O - L-methionine name: ATP + L-methionine + H2O -> S-adenosyl-L-methionine + phosphate + diphosphate pmids: [] rhea: [] right: - S-adenosyl-L-methionine - diphosphate - phosphate yeastcyc_id: S-ADENMETSYN-RXN - ec: - 2.6.1.88 genes: - *id015 - *id017 - *id080 - *id081 left: - L-methionine - a 2-oxo carboxylate name: L-methionine + a 2-oxo carboxylate <- 4-(methylsulfanyl)-2-oxobutanoate + a proteinogenic amino acid pmids: - '18625006' rhea: [] right: - 4-(methylsulfanyl)-2-oxobutanoate - a proteinogenic amino acid yeastcyc_id: R15-RXN - ec: - 4.1.1.50 genes: - *id047 left: - H+ - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + H+ -> CO2 + S-adenosyl 3-(methylsulfanyl)propylamine pmids: [] rhea: [] right: - CO2 - S-adenosyl 3-(methylsulfanyl)propylamine yeastcyc_id: SAMDECARB-RXN - ec: - 2.4.2.28 genes: - *id436 left: - S-methyl-5'-thioadenosine - phosphate name: S-methyl-5'-thioadenosine + phosphate -> adenine + S-methyl-5-thio-α-D-ribose 1-phosphate pmids: [] rhea: [] right: - S-methyl-5-thio-α-D-ribose 1-phosphate - adenine yeastcyc_id: 5-METHYLTHIOADENOSINE-PHOSPHORYLASE-RXN - ec: - 5.3.1.23 genes: - *id437 left: - S-methyl-5-thio-α-D-ribose 1-phosphate name: S-methyl-5-thio-α-D-ribose 1-phosphate -> 5-(methylsulfanyl)-ribulose 1-phosphate pmids: - '15215245' - '18625006' rhea: [] right: - 5-(methylsulfanyl)-ribulose 1-phosphate yeastcyc_id: 5.3.1.23-RXN - ec: - 2.5.1.16 genes: - *id083 left: - S-adenosyl 3-(methylsulfanyl)propylamine - putrescine name: putrescine + S-adenosyl 3-(methylsulfanyl)propylamine -> spermidine + S-methyl-5'-thioadenosine + H+ pmids: [] rhea: [] right: - H+ - S-methyl-5'-thioadenosine - spermidine yeastcyc_id: SPERMIDINESYN-RXN - ec: - 2.5.1.22 genes: - *id048 left: - S-adenosyl 3-(methylsulfanyl)propylamine - spermidine name: spermidine + S-adenosyl 3-(methylsulfanyl)propylamine -> spermine + S-methyl-5'-thioadenosine + H+ pmids: [] rhea: [] right: - H+ - S-methyl-5'-thioadenosine - spermine yeastcyc_id: SPERMINE-SYNTHASE-RXN yeastcyc_id: PWY3O-351 PWY3O-355: all_genes: - *id137 - *id134 - *id135 comment: 'Fatty acids are essential to all organisms except for archaea; they are major constituents of cellular membranes, and are used for energy storage and for posttranslational protein modifications. Most organisms are capable of synthesizing long chain (C12:0-C16:0) saturated fatty acids de novo. Although the initiation and termination reactions may vary, the cyclic series of chain-lengthening reactions are essentially the same across all organisms. The fatty acid chain, which starts as a 2-carbon chain from acetyl-CoA, is extended two carbons at a time by the addition of an acetyl group from malonyl-CoA. When the final length of the fatty acid is achieved, fatty acid synthesis is terminated. Each cycle of chain elongation involves 5 reactions with the following enzymatic activities: malonyl transferase (EC: 2.3.1.39), ketoacyl synthase (EC: 2.3.1.41), ketoacyl reductase (EC: 1.1.1.100), 3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61), and enoyl-acyl reductase (EC: 1.3.1.10). In yeast, fatty acid biosynthesis is terminated with the release of fatty acyl-CoAs from fatty acid synthase (FAS), the enzyme complex that carries out de novo fatty acid biosynthesis. Palmitoyl- (C16) and stearoyl-CoA (C18) are the main products in yeast, while myristoyl-CoA (C14) is only produced in small amounts |CITS: [Lynen69]|. To synthesize palmitoyl-CoA (C16) one acetyl-CoA and 7 malonyl-CoA molecules are required. The elongation substrate, malonyl-CoA is synthesized from the carboxylation of acetyl-CoA (EC 6.4.1.2) by the biotin-containing enzyme, acetyl-CoA carboxylase (Acc1p) |CITS: [1350093]|). Acetyl-CoA carboxylase is activated by the biotin:apoprotein ligase (Bpl1p) |CITS: [7649444]|). There are two types of FAS systems based on the organization of the catalytic sites. Fungi, animals, and some bacteria have type I FASs, which are large multi-functional proteins that contain all of the requisite catalytic active sites for fatty acid biosynthesis within domains on a single polypeptide (alpha) or on two polypeptides (alpha and beta). Fungal FASs are alpha6beta6 heterododecamers, animal FASs are alpha2 homodimers, and some type I bacterial FASs are alpha6 |CITS: [17448991]|. Bacteria, plants and mitochondria, on the other hand, have type II FAS systems, which are comprised of independent proteins, whereby each protein catalyzes a single step in the cyclic series of reactions |CITS: [15952903]|. The yeast FAS complex catalyzes a total of 8 reactions. The alpha subunit(Fas2p) catalyzes 3 reactions, ketoacyl synthase (EC: 2.3.1.41),ketoacyl reductase (EC: 1.1.1.100) and self pantetheinylation and the yeast beta subunit (Fas1p) catalyzes 5 reactions, acetyltransferase (EC 2.3.1.38), malonyl transferase (EC: 2.3.1.39),3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61),enoyl-acyl reductase (EC: 1.3.1.10), and palmitoyl transferase (EC:2.3.1.-) |CITS: [365179], [1100391], [10785388], [3528750], [374077]|. FASs are regulated at the transcriptional and translational level as well as posttranslationally. In yeast, FAS is a housekeeping enzyme that is expressed constitutively at a low level, but its expression is also activated by the general yeast transcription factors Rap1, Abf1 and Reb1 |CITS: [7925441]| and theinositol/choline-responsive transcription factor heterodimer, Ino2p-Ino4p |CITS: [1461729][7862526]|. The coordinate expression of the two subunits also appears to be regulated by Fas1p controlling the expression of FAS2 |CITS: [11713312]|. The FAS subunits are further regulated by proteolytic degradation of excess subunits. While the intact FAS multimeric complex (alpha6beta6 ) is stable, its individual subunits are rapidly degraded |CITS: [1735446][8262967]|.' name: stearate biosynthesis III (fungi) pmids: [] reactions: - ec: - 4.2.1.- genes: - *id134 left: - a (3R)-3-hydroxyoctadecanoyl-[acp] name: a (3R)-3-hydroxyoctadecanoyl-[acp] -> a (2E)-octadec-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-octadec-2-enoyl-[acp] yeastcyc_id: RXN-9634 - ec: - 2.3.1.86 genes: [] left: - NADP+ - a (3R)-3-hydroxyoctadecanoyl-[acp] name: a (3R)-3-hydroxyoctadecanoyl-[acp] + NADP+ <- a 3-oxooctadecanoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxooctadecanoyl-[acp] yeastcyc_id: RXN-9633 - ec: - 2.3.1.179 genes: - *id137 - *id135 left: - H+ - a malonyl-[acp] - a palmitoyl-[acp] name: a palmitoyl-[acp] + a malonyl-[acp] + H+ -> a 3-oxooctadecanoyl-[acp] + CO2 + acyl-carrier protein pmids: [] rhea: [] right: - CO2 - a 3-oxooctadecanoyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: RXN3O-1803 - ec: - 2.3.1.86 genes: - *id134 left: - NADP+ - a stearoyl-[acp] name: a stearoyl-[acp] + NADP+ <- a (2E)-octadec-2-enoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a (2E)-octadec-2-enoyl-[acp] yeastcyc_id: RXN3O-5293 - ec: - 2.3.1.- genes: - *id134 left: - a stearoyl-[acp] - coenzyme A name: a stearoyl-[acp] + coenzyme A -> stearoyl-CoA + acyl-carrier protein pmids: [] rhea: [] right: - a soluble [acyl-carrier protein] - stearoyl-CoA yeastcyc_id: RXN3O-5304 - ec: - 3.1.2.2 genes: [] left: - H2O - stearoyl-CoA name: stearoyl-CoA + H2O -> stearate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - stearate yeastcyc_id: RXN-9624 yeastcyc_id: PWY3O-355 PWY3O-3827: all_genes: - *id145 - *id146 - *id147 comment: 'The first step of glycolysis is the irreversible phosphorylation of glucose at C6. In S. cerevisiae, this reaction is catalyzed by the hexokinases Hxk1p and Hxk2p and the glucokinase Glk1p. Any single one of these enzymes is sufficient for growth on glucose, however Hxk2p appears to be the main glucose-phosphorylating isoenzyme. While HXK2 is expressed in glucose, both HXK1 and GLK1 are glucose-repressed, and expression of GLK1 and HXK1 occurs at significant levels only in the presence of non-fermentable carbon sources or galactose. Hxk2p is thought to have dual functions depending on localization: cytosolic Hxk2p is a glycolytic enzyme, whereas nuclear Hxk2p is a transcriptional regulator involved in glucose-induced repression of HXK1 and GLK1 and glucose-induced expression of HXK2. In addition to glucose-mediated transcriptional regulation, the hexokinase step of glycolysis is also subject to allosteric control. Yeast hexokinase is strongly inhibited by high ATP concentrations and competitively inhibited by trehalose-6-phosphate. Enzyme regulation of hexokinase is thought to play an important role in the control of glycolytic flux in S. cerevisiae. References: |CITS:[12007644]||CITS: [7732723]||CITS: [3882419]||CITS: [8354408]|' name: glucose-6-phosphate biosynthesis pmids: - '12007644' - '3882419' - '7732723' - '8354408' reactions: - ec: - 2.7.1.1 - 2.7.1.2 genes: - *id145 - *id146 - *id147 left: - ATP - D-glucopyranose name: D-glucopyranose + ATP -> D-glucopyranose 6-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - D-glucopyranose 6-phosphate - H+ yeastcyc_id: GLUCOKIN-RXN yeastcyc_id: PWY3O-3827 PWY3O-4: all_genes: - &id438 orf: YML042W symbol: CAT2 uniprot: UniProtKB:P32796 - &id439 orf: YAR035W symbol: YAT1 uniprot: UniProtKB:P80235 - &id440 orf: YER024W symbol: YAT2 uniprot: UniProtKB:P40017 comment: 'In eukaryotes, metabolism is compartmented and does not occur homogenously throughout the cell. As a consequence, membrane-impermeable metabolites produced in one cellular compartment often cannot support biochemical pathways in another compartment unless they are transferred to the site of action. Several mechanisms exist in eukaryotes for the translocation of acetyl-coenzyme A (acetyl-CoA) between cellular compartments. The carnitine shuttle, which uses carnitine to carry activated acetyl from coenzyme A across intracellular membranes, is one such example. In S. cerevisiae, acetyl-CoA can be generated in the peroxisome via fatty acid -oxidation and in the cytoplasm via degradation of non-fermentable carbon sources. The carnitine shuttle plays an important role in transporting the activated acetyl generated from these processes into mitochondria for further metabolism in the TCA cycle. The carnitine shuttle begins with the transfer of an acetyl group from acetyl-CoA to carnitine via carnitine acetyltransferase (CAT), forming acetyl-carnitine. There are several CATs in S. cerevisiae: Cat2p, localized in peroxisomes and mitochondria; Yat1p, localized on the outer mitochondrial membrane; and Yat2p, localized in the cytosol. After its formation, acetyl-carnitine is transported into the mitochondrion via carnitine acylcarnitine translocase (Crc1p). Mitochondrial CAT (Cat2p) then catalyzes the reverse transfer of the acetyl group from acetyl-carnitine to coenzyme A, regenerating acetyl-CoA and carnitine inside the mitochondrion. References: |CITS:[20889721]||CITS: [18427809]||CITS: [11329169]|' name: carnitine shuttle pmids: - '11329169' - '18427809' - '20889721' reactions: - ec: - 2.3.1.7 genes: - *id438 - *id439 - *id440 left: - L-carnitine - acetyl-CoA name: L-carnitine + acetyl-CoA <-> O-acetyl-L-carnitine + coenzyme A pmids: - '11329169' - '18427809' - '8262985' rhea: [] right: - O-acetyl-L-carnitine - coenzyme A yeastcyc_id: CARNITINE-O-ACETYLTRANSFERASE-RXN - ec: - 2.3.1.7 genes: - *id438 left: - L-carnitine - acetyl-CoA name: L-carnitine[mitochondrial lumen] + acetyl-CoA[mitochondrial lumen] <- O-acetyl-L-carnitine[mitochondrial lumen] + coenzyme A[mitochondrial lumen] pmids: [] rhea: [] right: - O-acetyl-L-carnitine - coenzyme A yeastcyc_id: RXN3O-37 yeastcyc_id: PWY3O-4 PWY3O-402: all_genes: - &id442 orf: YDR173C symbol: ARG82 uniprot: UniProtKB:P07250 - &id445 orf: YOR163W symbol: DDP1 uniprot: UniProtKB:Q99321 - &id444 orf: YDR315C symbol: IPK1 uniprot: UniProtKB:Q06667 - &id443 orf: YDR017C symbol: KCS1 uniprot: UniProtKB:Q12494 - *id234 - &id441 orf: YLR410W symbol: VIP1 uniprot: UniProtKB:Q06685 comment: Inositol phosphates (IPs) are an important class of signaling molecules that regulate cellular processes such as transcription, mRNA export, DNA repair, chromatin remodeling, glucose-induced calcium signaling, telomere elongation, vacuolar biogenesis, the stress response, cell wall synthesis and phosphate homeostasis (reviewed in |CITS:[16781889]| and |CITS:[16429326]|). The water-soluble IPs are derived from the lipid, phosphatidylinositol 4,5-bisphosphate (PIP2, PI(4,5)P2, PtdIns 4,5-P2). Plc1p hydrolyses PIP2 to inositol 1,4,5-trisphosphate (IP3) and diacylglycerol, releasing IP3 from the membrane |CITS:[8395015]|. IP3 is then sequentially phosphorylated to inositol tetrakisphosphate (IP4) and inositol pentakisphosphate (IP5) by the inositol polyphosphate multikinase (IPMK) Arg82p |CITS:[10720331][11311242][10683435]| and reviewed in |CITS:[16781889]|. IP5 is further phosphorylated to inositol hexakisphosphate (IP6, phytate) by Ipk1p or to the inositol pyrophosphate diphosphoinositol tetrakisphosphate (PP-IP4) by Arg82p or Kcs1p |CITS:[10960485][10827188][11311242]| and reviewed in |CITS:[16781889]|. The fully phosphorylated ring of IP6 is further phosphorylated to the inositol pyrophosphates diphosphoinositol pentakisphosphate (PP-IP5, IP7) and bis-diphosphoinositol tetrakisphosphate (2[PP]-IP4, [PP]2-IP4, IP8) |CITS:[17412958][11956213][10574768]| reviewed in |CITS:[16781889]| and |CITS:[16429326]|. Two different forms of PP-IP5 have been identified, 5-PP-IP7 synthesized by Kcs1p and 4- or 6-PP-IP7 synthesized by Vip1p (the exact phosphorylation position has yet to be determined) |CITS:[17412958]|. Kcs1p and Vip1p are believed to work in concert to form [PP]2-IP4; the PP-IP5 product produced by one enzyme is converted to [PP]2-IP4 by the other enzyme |CITS:[17412958]|. [PP]2-IP4 was shown to be dephosphorylated to PP-IP5 and PP-IP5 to IP6 by the phosphatase Ddp1p, but the particular isomer(s) are not yet known |CITS:[10419486]|. name: inositol phosphate biosynthesis pmids: - '11956213' reactions: - ec: [] genes: [] left: - 4- or 6-diphosphoinositol pentakisphosphate - ATP name: 4- or 6-diphosphoinositol pentakisphosphate + ATP -> [PP]2-IP4 + ADP pmids: [] rhea: [] right: - ADP - '[PP]2-IP4' yeastcyc_id: RXN3O-9819 - ec: - 2.7.4.24 genes: - *id441 left: - 1D-myoinositol 5-diphosphate 1,2,3,4,6-pentakisphosphate - ATP name: ATP + 1D-myoinositol 5-diphosphate 1,2,3,4,6-pentakisphosphate -> ADP + [PP]2-IP4 pmids: - '17412958' rhea: [] right: - ADP - '[PP]2-IP4' yeastcyc_id: RXN3O-143 - ec: - 2.7.1.- genes: - *id442 - *id443 left: - ATP - D-myo-inositol 1,3,4,5,6-pentakisphosphate name: ATP + D-myo-inositol 1,3,4,5,6-pentakisphosphate -> a diphospho-1D-myo-inositol tetrakisphosphate + ADP pmids: - '10827188' - '11311242' rhea: [] right: - ADP - a diphospho-1D-myo-inositol tetrakisphosphate yeastcyc_id: RXN-4941 - ec: - 2.7.4.- genes: - *id441 left: - ATP - phytate name: ATP + phytate -> ADP + 4- or 6-diphosphoinositol pentakisphosphate pmids: - '17412958' rhea: [] right: - 4- or 6-diphosphoinositol pentakisphosphate - ADP yeastcyc_id: RXN3O-258 - ec: - 2.7.1.151 genes: - *id442 left: - ATP - D-myo-inositol (1,3,4,5)-tetrakisphosphate name: D-myo-inositol (1,3,4,5)-tetrakisphosphate + ATP -> D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+ pmids: - '11311242' rhea: [] right: - ADP - D-myo-inositol 1,3,4,5,6-pentakisphosphate - H+ yeastcyc_id: RXN-7184 - ec: - 2.7.1.127 genes: - *id442 left: - ATP - D-myo-inositol (1,4,5)-trisphosphate name: D-myo-inositol (1,4,5)-trisphosphate + ATP -> D-myo-inositol (1,3,4,5)-tetrakisphosphate + ADP + H+ pmids: - '10683435' - '11311242' rhea: [] right: - ADP - D-myo-inositol (1,3,4,5)-tetrakisphosphate - H+ yeastcyc_id: 2.7.1.127-RXN - ec: - 2.7.1.151 genes: - *id442 left: - ATP - D-myo-inositol (1,4,5)-trisphosphate name: D-myo-inositol (1,4,5)-trisphosphate + ATP -> D-myo-inositol (1,4,5,6)-tetrakisphosphate + ADP + H+ pmids: - '10574768' - '10683435' - '10720331' rhea: [] right: - ADP - D-myo-inositol (1,4,5,6)-tetrakisphosphate - H+ yeastcyc_id: 2.7.1.151-RXN - ec: - 2.7.1.151 genes: - *id442 left: - ATP - D-myo-inositol (1,4,5,6)-tetrakisphosphate name: D-myo-inositol (1,4,5,6)-tetrakisphosphate + ATP -> D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+ pmids: - '10574768' - '10720331' rhea: [] right: - ADP - D-myo-inositol 1,3,4,5,6-pentakisphosphate - H+ yeastcyc_id: RXN-7162 - ec: - 2.7.1.158 genes: - *id444 left: - ATP - D-myo-inositol 1,3,4,5,6-pentakisphosphate name: D-myo-inositol 1,3,4,5,6-pentakisphosphate + ATP -> phytate + ADP + H+ pmids: - '10390371' - '10960485' rhea: [] right: - ADP - H+ - phytate yeastcyc_id: RXN-7163 - ec: - 3.6.-.- genes: - *id445 left: - H2O - '[PP]2-IP4' name: '[PP]2-IP4 + H2O -> diphosphoinositol pentakisphosphate + phosphate' pmids: - '10419486' rhea: [] right: - diphosphoinositol pentakisphosphate - phosphate yeastcyc_id: RXN3O-786 - ec: - 3.1.4.11 genes: - *id234 left: - H2O - a 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate name: a 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O -> a 1,2-diacyl-sn-glycerol + D-myo-inositol (1,4,5)-trisphosphate + H+ pmids: - '8395015' rhea: [] right: - D-myo-inositol (1,4,5)-trisphosphate - H+ - a 1,2-diacyl-sn-glycerol yeastcyc_id: 3.1.4.11-RXN - ec: - 3.6.1.52 genes: - *id445 left: - H2O - diphosphoinositol pentakisphosphate name: diphosphoinositol pentakisphosphate + H2O -> phytate + phosphate pmids: - '10419486' rhea: [] right: - phosphate - phytate yeastcyc_id: RXN3O-785 - ec: - 2.7.4.21 genes: - *id443 left: - ATP - H+ - phytate name: phytate + ATP + H+ -> 1D-myoinositol 5-diphosphate 1,2,3,4,6-pentakisphosphate + ADP + H+ pmids: - '10574768' - '11956213' rhea: [] right: - 1D-myoinositol 5-diphosphate 1,2,3,4,6-pentakisphosphate - ADP - H+ yeastcyc_id: 2.7.1.152-RXN yeastcyc_id: PWY3O-402 PWY3O-4031: all_genes: - &id450 orf: YEL011W symbol: GLC3 uniprot: UniProtKB:P32775 - &id448 orf: YKR058W symbol: GLG1 uniprot: UniProtKB:P36143 - &id449 orf: YJL137C symbol: GLG2 uniprot: UniProtKB:P47011 - &id446 orf: YFR015C symbol: GSY1 uniprot: UniProtKB:P23337 - &id447 orf: YLR258W symbol: GSY2 uniprot: UniProtKB:P27472 - *id203 - *id204 - *id370 - *id371 comment: 'Glycogen, a branched polymer of glucose, is a storage molecule whose accumulation is under rigorous control in many cells |CITS:11152943|. Glycogen metabolism increases in response to a wide variety of environmental stresses, including heat stress or exposure to sodium chloride, hydrogen peroxide, copper sulfate, high levels of ethanol, or weak organic acids, such as sorbate or benzoate |CITS:11152943|. Glycogen metabolism also increases in response to conditions of nutrient starvation, such as limited nitrogen, carbon, phosphorous, or sulfur, and during diauxic growth on glucose |CITS:11152943|. In Saccharomyces cerevisiae, glycogen biosynthesis involves three processes: nucleation, elongation, and branching (also known as ramification) |CITS:11152943|. The formation of glycogen begins when either Glg1p or Glg2p uses UDP-glucose to self-glucosylate to produce a short alpha (1,4)-glucosyl chain covalently attached to one of their internal tyrosine residues |CITS:8900126|. After the self-glucosylation of Glg1p or Glg2p, glycogen synthase is able to extend the linear alpha (1,4)-glucosyl chains of glycogen by catalyzing the formation of alpha (1,4)-glucosidic bonds from UDP- glucose at the non-reducing ends |CITS:1908457|. Branches can be added into the glycogen molecule by Glc3p, which is the glycogen branching enzyme (EC:2.4.1.18) in S. cerevisiae |CITS:1634552|. No enzyme that releases the glycogen chain from Glg1p or Glg2p has been identified |CITS:11152943|. Thus far, none of the phenotypes seen in S. cerevisiae glycogen catabolism mutants correspond to the mammalian glycogen storage diseases associated with mutations in human genes involved in glycogen metabolism |CITS:11152943|.' name: glycogen biosynthesis pmids: - '11152943' reactions: - ec: - 2.4.1.11 genes: - *id446 - *id447 left: - UDP-α-D-glucose - a glucosylated glycogenin name: UDP-α-D-glucose + (1,4-α-D-glucosyl)(n) glycogenin -> (1,4-α-D-glucosyl)(n+1) glycogenin + UDP pmids: [] rhea: [] right: - UDP - a glucosylated glycogenin yeastcyc_id: RXN-7668 - ec: - 2.4.1.186 genes: - *id448 - *id449 left: - UDP-α-D-glucose - a [glycogenin] name: UDP-α-D-glucose + a [glycogenin] -> an α-D-glucosyl-[glycogenin] + UDP + H+ pmids: [] rhea: [] right: - H+ - UDP - an α-D-glucosyl-[glycogenin] yeastcyc_id: GLYCOGENIN-GLUCOSYLTRANSFERASE-RXN - ec: - 2.4.1.186 genes: - *id448 - *id449 left: - UDP-α-D-glucose - an α-D-glucosyl-[glycogenin] name: UDP-α-D-glucose + an α-D-glucosyl-[glycogenin] -> (1,4-α-D-glucosyl)n-glucosyl glucogenin + UDP + H+ pmids: [] rhea: [] right: - (1,4-α-D-glucosyl)n-glucosyl glucogenin - H+ - UDP yeastcyc_id: RXN-7667 - ec: - 2.4.1.18 genes: - *id450 left: - a glucosylated glycogenin name: a glucosylated glycogenin -> a glycogen pmids: [] rhea: [] right: - a glycogen yeastcyc_id: RXN-7669 - ec: - 5.4.2.2 genes: - *id203 - *id204 left: - α-D-glucopyranose 1-phosphate name: α-D-glucopyranose 1-phosphate <-> D-glucopyranose 6-phosphate pmids: [] rhea: [] right: - D-glucopyranose 6-phosphate yeastcyc_id: PHOSPHOGLUCMUT-RXN - ec: - 2.7.7.64 - 2.7.7.9 genes: - *id370 - *id371 left: - H+ - UTP - α-D-glucopyranose 1-phosphate name: α-D-glucopyranose 1-phosphate + UTP + H+ -> UDP-α-D-glucose + diphosphate pmids: [] rhea: [] right: - UDP-α-D-glucose - diphosphate yeastcyc_id: GLUC1PURIDYLTRANS-RXN yeastcyc_id: PWY3O-4031 PWY3O-4105: all_genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id080 - *id081 - *id164 - *id165 - *id166 - *id312 comment: 'While Saccharomyces cerevisiae can use most amino acids as their sole nitrogen source, they can only use a few amino acids as a carbon source to support growth |CITS:[Large86][Cooper82]|. This is in contrast to most eukaryotes and some fungi, which can metabolize amino acids completely, utilizing them as sole sources of carbon and nitrogen |CITS:[Stryer88][Large 86]|. S. cerevisiae degrade the branched-chain amino acids (valine, leucine, and iso-leucine) and the aromatic amino acids (tryptophan, phenylalanine, and tyrosine) via the Ehrlich pathway |CITS:[Sentheshanmuganathan60][10989420]|. This pathway is comprised of the following steps: 1) deamination of the amino acid to the corresponding alpha-keto acid; 2) decarboxylation of the resulting alpha-keto acid to the respective aldehyde; and, 3) reduction of the aldehyde to form the corresponding long chain or complex alcohol, known as a fusel alcohol or fusel oil |CITS:[10989420][Large 86]|. Fusel alcohols are important flavor and aroma compounds in yeast-fermented food products and beverages (as reported in |CITS:[9546164]|. Each of the three steps in branched-chain amino acid degradation can be catalyzed by more than one isozyme; which enzyme is used appears to depend on the amino acid, the carbon source and the stage of growth of the culture |CITS: [12499363]|. In valine degradation, the major pyruvate decarboxylases used under most cultivation conditions are Pdc1p and Pdc5p |CITS: [9748245][9546164]|, while Pdc6p is used under low sulfur conditions (as reported in |CITS: [15933030]|).' name: valine degradation pmids: - '10989420' - '10989445' - '8702755' - '8798704' - '9748245' reactions: - ec: - 4.1.1.1 genes: - *id164 - *id165 - *id166 left: - 3-methyl-2-oxobutanoate name: 3-methyl-2-oxobutanoate -> isobutanal + CO2 pmids: - '9546164' - '9748245' rhea: [] right: - CO2 - isobutanal yeastcyc_id: RXN3O-4133 - ec: - 2.6.1.42 genes: - *id080 - *id081 left: - 2-oxoglutarate - L-valine name: L-valine + 2-oxoglutarate <-> L-glutamate + 3-methyl-2-oxobutanoate pmids: - '10989445' - '8702755' - '8798704' rhea: [] right: - 3-methyl-2-oxobutanoate - L-glutamate yeastcyc_id: BRANCHED-CHAINAMINOTRANSFERVAL-RXN - ec: - 1.1.1.1 genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id312 left: - NADH - isobutanal name: isobutanal + NADH -> isobutanol + NAD+ pmids: - '12499363' rhea: [] right: - NAD+ - isobutanol yeastcyc_id: RXN3O-4141 yeastcyc_id: PWY3O-4105 PWY3O-4106: all_genes: - *id252 - *id253 - *id412 comment: 'Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and energy metabolism. NAD also has been shown to be an important substrate in a variety of biological processes, including transcriptional regulation, DNA repair, calcium-dependent signaling pathways, calorie-restriction-mediated life-span extension and age-associated diseases |CITS: [12736687],[12648681]|. NAD appears to affect these processes by regulating the Sir2p family of NAD-dependent deacetylases (Sirtuins) |CITS: [12648681]|. There are a number of pathways for NAD biosynthesis. In yeast and most other organisms, the two major pathways are de novo synthesis of NAD (the de novo pathway) and regeneration of NAD from its nicotinamide degradation products (the NAD salvage pathway) |CITS: [12972620], [12648681]|. NAD is synthesized de novo from tryptophan via kynurenine |CITS: [12972620]|. In this pathway tryptophan is converted to nicotinic acid mononucleotide (NAMN) in 6 enzymatic steps (catalyzed by Bna1-2p, and Bna4-7p) and one non-enzymatic step |CITS: [12972620]|. At NAMN the de novo pathway converges with the NAD salvage pathway and the last two steps to NAD are shared |CITS: [12972620], [12648681]|. In the yeast NAD salvage pathway, the vitamin precursors nicotinamide and nicotinic acid are converted to NAMN, the point of convergence with the de novo pathway |CITS: [12648681]|. The steps from nicotinic acid to NAD were elucidated by Preiss and Handler and are sometimes referred to as the Preiss-Handler pathway |CITS: [13416279], [13563526]|. Yeast can also import extracellular nicotinic acid into the cell by the permease Tna1p and then convert it into NAD via the Preiss-Handler pathway |CITS: [12648681]|. There are four additional pathways for synthesizing NAD in yeast: two salvage pathways from the vitamin precursor nicotinamide riboside (NR) and two salvage pathways from nicotinic acid riboside (NaR) |CITS: [15137942], [17482543], [17914902]|. Three of these salvage pathways converge first with the NAD salvage pathway and then with the de novo pathway, while the fourth, the NR salvage pathway I, is independent of both of these pathways. In the NR salvage pathway I, NR is phosphorylated to nicotinamide mononucleotide by the kinase Nrk1p, and then adenylated to NAD by Nma1p or Nma2p |CITS: [15137942]|. Bacteria such as Haemophilus influenza that lack the enzymes of the de novo and Preiss-Handler pathway can synthesize NAD from NR and nicotinamide mononucleotide as well |CITS: [15137942]|. Humans also appear to have this NR salvage pathway |CITS: [15137942]|. Yeast have a second NR salvage pathway (NR salvage pathway II) that is independent of Nrk1p; in NR salvage pathway II NR is split into a ribosyl product and nicotinamide, which is subsequently converted to NAD via enzymes of the NAD salvage pathway and de novo pathway |CITS: [17482543]|. The initial steps in the two NaR salvage pathways are similar to those of the NR salvage pathways and are catalyzed by the same enzymes; Nrk1p catalyzes the first step in the NR and NaR salvage pathways I and Urh1p and Pnp1p catalyze the first steps of the NR and NaR salvage pathways II |CITS: [17914902]|. ' name: NAD salvage pathway IV (from nicotinamide riboside) pmids: - '15137942' reactions: - ec: - 2.7.1.22 genes: - *id412 left: - 1-(β-D ribofuranosyl)nicotinamide - ATP name: 1-(β-D ribofuranosyl)nicotinamide + ATP -> β-nicotinamide D-ribonucleotide + ADP + H+ pmids: - '15137942' rhea: [] right: - ADP - H+ - β-nicotinamide D-ribonucleotide yeastcyc_id: RIBOSYLNICOTINAMIDE-KINASE-RXN - ec: - 2.7.7.1 genes: - *id252 - *id253 left: - ATP - H+ - β-nicotinamide D-ribonucleotide name: β-nicotinamide D-ribonucleotide + ATP + H+ -> NAD+ + diphosphate pmids: [] rhea: [] right: - NAD+ - diphosphate yeastcyc_id: 2.7.7.1-RXN yeastcyc_id: PWY3O-4106 PWY3O-4107: all_genes: - *id252 - *id253 - &id453 orf: YOR209C symbol: NPT1 uniprot: UniProtKB:P39683 - &id452 orf: YGL037C symbol: PNC1 uniprot: UniProtKB:P53184 - *id246 - &id451 orf: YDL042C symbol: SIR2 uniprot: UniProtKB:P06700 comment: 'Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and energy metabolism. NAD also has been shown to be an important substrate in a variety of biological processes, including transcriptional regulation, DNA repair, calcium-dependent signaling pathways, calorie-restriction-mediated life-span extension and age-associated diseases |CITS: [12736687],[12648681]|. NAD appears to affect these processes by regulating the Sir2p family of NAD-dependent deacetylases (Sirtuins) |CITS: [12648681]|. There are a number of pathways for NAD biosynthesis. In yeast and most other organisms, the two major pathways are de novo synthesis of NAD (the de novo pathway) and regeneration of NAD from its nicotinamide degradation products (the NAD salvage pathway) |CITS: [12972620], [12648681]|. NAD is synthesized de novo from tryptophan via kynurenine |CITS: [12972620]|. In this pathway tryptophan is converted to nicotinic acid mononucleotide (NAMN) in 6 enzymatic steps (catalyzed by Bna1-2p, and Bna4-7p) and one non-enzymatic step |CITS: [12972620]|. At NAMN the de novo pathway converges with the NAD salvage pathway and the last two steps to NAD are shared |CITS: [12972620], [12648681]|. In the yeast NAD salvage pathway, the vitamin precursors nicotinamide and nicotinic acid are converted to NAMN, the point of convergence with the de novo pathway |CITS: [12648681]|. The steps from nicotinic acid to NAD were elucidated by Preiss and Handler and are sometimes referred to as the Preiss-Handler pathway |CITS: [13416279], [13563526]|. Yeast can also import extracellular nicotinic acid into the cell by the permease Tna1p and then convert it into NAD via the Preiss-Handler pathway |CITS: [12648681]|. There are four additional pathways for synthesizing NAD in yeast: two salvage pathways from the vitamin precursor nicotinamide riboside (NR) and two salvage pathways from nicotinic acid riboside (NaR) |CITS: [15137942], [17482543], [17914902]|. Three of these salvage pathways converge first with the NAD salvage pathway and then with the de novo pathway, while the fourth, the NR salvage pathway I, is independent of both of these pathways. In the NR salvage pathway I, NR is phosphorylated to nicotinamide mononucleotide by the kinase Nrk1p, and then adenylated to NAD by Nma1p or Nma2p |CITS: [15137942]|. Bacteria such as Haemophilus influenza that lack the enzymes of the de novo and Preiss-Handler pathway can synthesize NAD from NR and nicotinamide mononucleotide as well |CITS: [15137942]|. Humans also appear to have this NR salvage pathway |CITS: [15137942]|. Yeast have a second NR salvage pathway (NR salvage pathway II) that is independent of Nrk1p; in NR salvage pathway II NR is split into a ribosyl product and nicotinamide, which is subsequently converted to NAD via enzymes of the NAD salvage pathway and de novo pathway |CITS: [17482543]|. The initial steps in the two NaR salvage pathways are similar to those of the NR salvage pathways and are catalyzed by the same enzymes; Nrk1p catalyzes the first step in the NR and NaR salvage pathways I and Urh1p and Pnp1p catalyze the first steps of the NR and NaR salvage pathways II |CITS: [17914902]|.' name: NAD salvage pathway V (PNC V cycle) pmids: - '11884393' reactions: - ec: - 6.3.5.1 genes: - *id246 left: - ATP - H2O - L-glutamine - nicotinate adenine dinucleotide name: ATP + nicotinate adenine dinucleotide + L-glutamine + H2O -> L-glutamate + AMP + NAD+ + diphosphate + H+ pmids: [] rhea: [] right: - AMP - H+ - L-glutamate - NAD+ - diphosphate yeastcyc_id: NAD-SYNTH-GLN-RXN - ec: - 2.3.1.- genes: - *id451 left: - H2O - NAD+ - a [histone]-N6-acetyl-L-lysine name: a [histone]-N6-acetyl-L-lysine + NAD+ + H2O -> a [histone]-L-lysine + 2''-O-acetyl-ADP-ribose + nicotinamide pmids: [] rhea: [] right: - 2''-O-acetyl-ADP-ribose - a [histone]-L-lysine - nicotinamide yeastcyc_id: RXN-15025 - ec: - 3.5.1.19 genes: - *id452 left: - H2O - nicotinamide name: nicotinamide + H2O -> ammonium + nicotinate pmids: [] rhea: [] right: - ammonium - nicotinate yeastcyc_id: NICOTINAMID-RXN - ec: - 6.3.4.21 genes: - *id453 left: - 5-phospho-α-D-ribose 1-diphosphate - ATP - H2O - nicotinate name: nicotinate + 5-phospho-α-D-ribose 1-diphosphate + ATP + H2O -> β-nicotinate D-ribonucleotide + ADP + diphosphate + phosphate pmids: [] rhea: [] right: - ADP - diphosphate - phosphate - β-nicotinate D-ribonucleotide yeastcyc_id: NICOTINATEPRIBOSYLTRANS-RXN - ec: - 2.7.7.18 genes: - *id252 - *id253 left: - ATP - H+ - β-nicotinate D-ribonucleotide name: β-nicotinate D-ribonucleotide + ATP + H+ -> nicotinate adenine dinucleotide + diphosphate pmids: [] rhea: [] right: - diphosphate - nicotinate adenine dinucleotide yeastcyc_id: NICONUCADENYLYLTRAN-RXN yeastcyc_id: PWY3O-4107 PWY3O-4108: all_genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id015 - *id017 comment: 'While Saccharomyces cerevisiae can use most amino acids as their sole nitrogen source, they can only use a few amino acids as a carbon source to support growth |CITS:[Large86][Cooper82]|. This is in contrast to most eukaryotes and some fungi, which can metabolize amino acids completely, utilizing them as sole sources of carbon and nitrogen |CITS:[Stryer88][Large 86]|. S. cerevisiae degrade the aromatic amino acids (tyrosine, phenylalanine, and tryptophan) and branched-chain amino acids (valine, leucine, and iso-leucine) via the Ehrlich pathway |CITS:[Sentheshanmuganathan60][10989420]|. This pathway is comprised of the following steps: 1) deamination of the amino acid to the corresponding alpha-keto acid; 2) decarboxylation of the resulting alpha-keto acid to the respective aldehyde; and, 3) reduction of the aldehyde to form the corresponding long chain or complex alcohol, known as a fusel alcohol or fusel oil |CITS:[10989420][Large 86]|. Fusel alcohols are important flavor and aroma compounds in yeast-fermented food products and beverages (as reported in |CITS:[9546164]|. Both the constitutive aromatic aminotransferase I (ARO8p) and the inducible aromatic aminotransferase II (ARO9p) can catalyze the initial reaction in tyrosine degradation |CITS:[ 6763508]|. In vitro studies demonstrated that Aro9p is active with phenylpyruvate, pyruvate, or p-hydroxyphenylpyruvate, but not 2-oxoglutarate as the amino acceptor, while Aro8p is active with phenylpyruvate, pyruvate, or 2-oxoglutarate |CITS:[6763508]|. Aro9p is induced by aromatic amino acids and is subject to nitrogen regulation |CITS:[6763508][10207060]|. ' name: L-tyrosine degradation III pmids: - '13546168' - '13750129' - '9491082' - '9491083' reactions: - ec: - 4.1.1.80 genes: [] left: - 3-(4-hydroxyphenyl)pyruvate - H+ name: 3-(4-hydroxyphenyl)pyruvate + H+ -> CO2 + (4-hydroxyphenyl)acetaldehyde pmids: [] rhea: [] right: - (4-hydroxyphenyl)acetaldehyde - CO2 yeastcyc_id: 4.1.1.80-RXN - ec: - 1.1.1.1 genes: - *id157 - *id158 - *id159 - *id160 - *id161 left: - 4-tyrosol - NAD+ name: 4-tyrosol + NAD+ <- (4-hydroxyphenyl)acetaldehyde + NADH + H+ pmids: [] rhea: [] right: - (4-hydroxyphenyl)acetaldehyde - H+ - NADH yeastcyc_id: RXN3O-4113 - ec: - 2.6.1.27 - 2.6.1.5 - 2.6.1.57 genes: - *id015 left: - 2-oxoglutarate - L-tyrosine name: L-tyrosine + 2-oxoglutarate <-> 3-(4-hydroxyphenyl)pyruvate + L-glutamate pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - L-glutamate yeastcyc_id: TYROSINE-AMINOTRANSFERASE-RXN - ec: - 2.6.1.58 genes: - *id017 left: - L-tyrosine - pyruvate name: L-tyrosine + pyruvate <-> 3-(4-hydroxyphenyl)pyruvate + L-alanine pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - L-alanine yeastcyc_id: RXN3O-4157 yeastcyc_id: PWY3O-4108 PWY3O-4109: all_genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id411 - *id080 - *id081 - *id164 - *id165 - *id166 - *id312 - &id454 orf: YDL080C symbol: THI3 uniprot: UniProtKB:Q07471 comment: 'While Saccharomyces cerevisiae can use most amino acids as their sole nitrogen source, they can only use a few amino acids as a carbon source to support growth |CITS:[Large86][Cooper82]|. This is in contrast to most eukaryotes and some fungi, which can metabolize amino acids completely, utilizing them as sole sources of carbon and nitrogen |CITS:[Stryer88][Large 86]|. S. cerevisiae degrade the branched-chain amino acids (iso-leucine, leucine, and valine) and the aromatic amino acids (tryptophan, phenylalanine, and tyrosine) via the Ehrlich pathway |CITS:[Sentheshanmuganathan60][10989420]|. This pathway is comprised of the following steps: 1) deamination of the amino acid to the corresponding alpha-keto acid; 2) decarboxylation of the resulting alpha-keto acid to the respective aldehyde; and, 3) reduction of the aldehyde to form the corresponding long chain or complex alcohol, known as a fusel alcohol or fusel oil |CITS:[10989420][Large 86]|. Fusel alcohols are important flavor and aroma compounds in yeast-fermented food products and beverages (as reported in |CITS:[9546164]| Each of the three steps in branched-chain amino acid degradation can be catalyzed by more than one isozyme; which enzyme is used appears to depend on the amino acid, the carbon source and the stage of growth of the culture |CITS:[12499363]|. The initial transamination step in iso-leucine degradation can be catalyzed by either of the branched-chain amino acid transaminases BAT1 (mitochondrial) or BAT2 (cytosolic) |CITS:[10989445][8798704][8702755]|. The subsequent decarboxylation step can be catalyzed by any one of the five decarboxylases (Pdc1p, Pdc5p, Pdc6p, Thi3p, and Aro10p) |CITS:[9546164][10753893]| and the final step can be catalyzed by any one of six alcohol dehydrogenases (Adh1p, Adh2p, Adh3p, Adh4p, Adh5p, and Sfa1p) |CITS:[12499363]|.' name: isoleucine degradation pmids: - '10753893' - '10989445' - '8702755' - '8798704' reactions: - ec: - 4.1.1.72 genes: - *id411 - *id164 - *id165 - *id166 - *id454 left: - (S)-3-methyl-2-oxopentanoate - H+ name: (S)-3-methyl-2-oxopentanoate + H+ -> 2-methylbutanal + CO2 pmids: - '10753893' - '9546164' rhea: [] right: - 2-methylbutanal - CO2 yeastcyc_id: 4.1.1.72-RXN - ec: - 1.1.1.1 genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id312 left: - 2-methylbutanal - NADH name: 2-methylbutanal + NADH -> 2-methylbutanol + NAD+ pmids: - '12499363' rhea: [] right: - 2-methylbutanol - NAD+ yeastcyc_id: RXN3O-4117 - ec: - 2.6.1.42 genes: - *id080 - *id081 left: - 2-oxoglutarate - L-isoleucine name: L-isoleucine + 2-oxoglutarate <-> L-glutamate + (S)-3-methyl-2-oxopentanoate pmids: - '10989445' - '8702755' - '8798704' rhea: [] right: - (S)-3-methyl-2-oxopentanoate - L-glutamate yeastcyc_id: BRANCHED-CHAINAMINOTRANSFERILEU-RXN yeastcyc_id: PWY3O-4109 PWY3O-4112: all_genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id411 - *id080 - *id081 - *id312 - *id454 comment: 'While Saccharomyces cerevisiae can use most amino acids as their sole nitrogen source, they can only use a few amino acids as a carbon source to support growth |CITS:[Large86][Cooper82]|. This is in contrast to most eukaryotes and some fungi, which can metabolize amino acids completely, utilizing them as sole sources of carbon and nitrogen |CITS:[Stryer88][Large 86]|. S. cerevisiae degrade the branched-chain amino acids (leucine, iso-leucine, and valine) and the aromatic amino acids (tryptophan, phenylalanine, and tyrosine) via the Ehrlich pathway |CITS:[Sentheshanmuganathan60][10989420]|. This pathway is comprised of the following steps: 1) deamination of the amino acid to the corresponding alpha-keto acid; 2) decarboxylation of the resulting alpha-keto acid to the respective aldehyde; and, 3) reduction of the aldehyde to form the corresponding long chain or complex alcohol, known as a fusel alcohol or fusel oil |CITS:[10989420][Large 86]|. Fusel alcohols are important flavor and aroma compounds in yeast-fermented food products and beverages (as reported in |CITS:[9546164]|. Each of the three steps in branched-chain amino acid degradation can be catalyzed by more than one isozyme; which enzyme is used appears to depend on the amino acid, the carbon source and the stage of growth of the culture |CITS:[12499363]|. In leucine degradation, Thi3p is believed to be the major decarboxylase |CITS: [12499363]|.' name: leucine degradation pmids: - '10989420' - '10989445' - '12499363' - '15933030' - '8702755' - '8798704' - '9341119' - '9546164' - '9748245' reactions: - ec: - 1.1.1.1 genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id312 left: - 3-methylbutanal - NADH name: 3-methylbutanal + NADH -> 3-methylbutanol + NAD+ pmids: - '12499363' rhea: [] right: - 3-methylbutanol - NAD+ yeastcyc_id: RXN3O-4109 - ec: - 4.1.1.1 genes: - *id411 - *id454 left: - 4-methyl-2-oxopentanoate name: 4-methyl-2-oxopentanoate -> 3-methylbutanal + CO2 pmids: - '15933030' - '9341119' rhea: [] right: - 3-methylbutanal - CO2 yeastcyc_id: RXN3O-4108 - ec: - 2.6.1.42 - 2.6.1.6 genes: - *id080 - *id081 left: - 2-oxoglutarate - L-leucine name: L-leucine + 2-oxoglutarate <-> L-glutamate + 4-methyl-2-oxopentanoate pmids: - '10989445' - '8702755' - '8798704' rhea: [] right: - 4-methyl-2-oxopentanoate - L-glutamate yeastcyc_id: BRANCHED-CHAINAMINOTRANSFERLEU-RXN yeastcyc_id: PWY3O-4112 PWY3O-4115: all_genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id411 - *id015 - *id017 - *id016 - *id164 - *id165 - *id166 - *id312 comment: 'While Saccharomyces cerevisiae can use most amino acids as their sole nitrogen source, they can only use a few amino acids as a carbon source to support growth |CITS:[Large86][Cooper82]|. This is in contrast to most eukaryotes and some fungi, which can metabolize amino acids completely, utilizing them as sole sources of carbon and nitrogen |CITS:[Stryer88][Large 86]|. S. cerevisiae degrade the aromatic amino acids (phenylalanine, tyrosine, and tryptophan) and the branched-chain amino acids (valine, leucine, and iso-leucine) via the Ehrlich pathway |CITS:[Sentheshanmuganathan60][10989420]|. This pathway is comprised of the following steps: 1) deamination of the amino acid to the corresponding alpha-keto acid; 2) decarboxylation of the resulting alpha-keto acid to the respective aldehyde; and, 3) reduction of the aldehyde to form the corresponding long chain or complex alcohol, known as a fusel alcohol or fusel oil |CITS:[10989420][Large 86]|. Fusel alcohols are important flavor and aroma compounds in yeast-fermented food products and beverages (as reported in |CITS:[9546164]|. Aro10p appears to be the primary decarboxylase catalyzing the second step in phenylalanine degradation |CITS:[12902239][15933030]|. Although Vulrahan et. al. (2003) |CITS:[12902239]| found that THI3 does not encode an active phenylpyruvate decarboxylase, they found Thi3p was required in conjunction with one of the pyruvate decarboxylases Pdc1p, Pdc5p or Pdc6p for the ARO10-independent decarboxylase activity. The main uptake systems for utilizing aromatic amino acids appear to be Gap1p, a general amino acid permease, and Wap1p, an inducible amino acid permease with wide substrate specificity |CITS:[10207060]|' name: phenylalanine degradation pmids: - '12499363' - '12902239' - '15933030' - '9491082' - '9491083' reactions: - ec: - 4.1.1.- - 4.1.1.43 genes: - *id411 - *id164 - *id165 - *id166 left: - 3-phenyl-2-oxopropanoate - H+ name: 3-phenyl-2-oxopropanoate + H+ -> phenylacetaldehyde + CO2 pmids: - '12499363' - '12902239' - '15933030' rhea: [] right: - CO2 - phenylacetaldehyde yeastcyc_id: PHENYLPYRUVATE-DECARBOXYLASE-RXN - ec: - 2.6.1.1 - 2.6.1.27 - 2.6.1.57 - 2.6.1.9 genes: - *id015 - *id016 left: - 2-oxoglutarate - L-phenylalanine name: L-phenylalanine + 2-oxoglutarate <-> 3-phenyl-2-oxopropanoate + L-glutamate pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-phenyl-2-oxopropanoate - L-glutamate yeastcyc_id: RXN-10814 - ec: - 2.6.1.58 genes: - *id017 left: - L-phenylalanine - pyruvate name: L-phenylalanine + pyruvate <-> 3-phenyl-2-oxopropanoate + L-alanine pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-phenyl-2-oxopropanoate - L-alanine yeastcyc_id: 2.6.1.58-RXN - ec: - 1.1.1.1 genes: - *id157 - *id158 - *id159 - *id160 - *id161 - *id312 left: - NADH - phenylacetaldehyde name: phenylacetaldehyde + NADH -> 2-phenylethanol + NAD+ pmids: - '12499363' rhea: [] right: - 2-phenylethanol - NAD+ yeastcyc_id: RXN3O-163 yeastcyc_id: PWY3O-4115 PWY3O-4120: all_genes: - *id029 - *id015 - *id017 - *id038 comment: Biosynthesis of the aromatic amino acids tyrosine, phenylalanine, and tryptophan proceeds via a common pathway to chorismate, at which point the pathway branches|CITS:[Jones][1943992]|. One branch proceeds to tyrosine and phenylalanine, and the other to tryptophan |CITS:[Jones]|. The series of reactions to chorismate, called the shikimate pathway, and the series of reactions from chorismate to tryptophan have been found to be common to all eukaryotes and prokaryotes studied thus far (as reported in |CITS:[1943992]|). In contrast, there appears to be two separate routes for tyrosine and phenylalanine biosynthesis from chorismate, only one of which has been found in S. cerevisiae |CITS:[1943992]|. S. cerevisiae, similar to E. coli, synthesize tyrosine and phenylalanine via the intermediate 4-hydroxyphenylpyruvate and phenylpyruvate, respectively, whereas some other organisms synthesize them via arogenate |CITS:[1943992]|. Aromatic amino acid biosynthesis in S. cerevisiae is controlled by a combination of feedback inhibition, activation of enzyme activity, and regulation of enzyme synthesis |CITS:[Jones][1943992]|. The carbon flow through the pathways is regulated primarily at the initial step and the branching points by the terminal end-products. The initial step of chorismate biosynthesis can be catalyzed by two isoenzymes Aro3p or Aro4p, whereby Aro3p is inhibited by phenylalanine, and Aro4p by tyrosine |CITS:[Jones][1943992]|. The first step in the phenylalanine-tyrosine branch is feedback inhibited by tyrosine and activated by tryptophan, and the first step in the tryptophan branch is feedback inhibited by tryptophan |CITS:[1943992]|. The transcriptional activator GCN4 regulates most of the genes encoding for the aromatic amino acid biosynthetic enzymes; however, no GCN4 regulation was found for TYR1 of the tyrosine branch, ARO7 of the tyrosine and phenylalanine branch or TRP1 of the tryptophan branch, |CITS:[1943992]|. name: tyrosine biosynthesis pmids: - '1943992' - '9491082' reactions: - ec: - 2.6.1.27 - 2.6.1.5 - 2.6.1.57 genes: - *id015 left: - 2-oxoglutarate - L-tyrosine name: L-tyrosine + 2-oxoglutarate <-> 3-(4-hydroxyphenyl)pyruvate + L-glutamate pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - L-glutamate yeastcyc_id: TYROSINE-AMINOTRANSFERASE-RXN - ec: - 2.6.1.58 genes: - *id017 left: - L-tyrosine - pyruvate name: L-tyrosine + pyruvate <-> 3-(4-hydroxyphenyl)pyruvate + L-alanine pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - L-alanine yeastcyc_id: RXN3O-4157 - ec: - 5.4.99.5 genes: - *id029 left: - chorismate name: chorismate <-> prephenate pmids: [] rhea: [] right: - prephenate yeastcyc_id: CHORISMATEMUT-RXN - ec: - 1.3.1.13 genes: - *id038 left: - NADP+ - prephenate name: prephenate + NADP+ -> CO2 + 3-(4-hydroxyphenyl)pyruvate + NADPH pmids: [] rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - CO2 - NADPH yeastcyc_id: PREPHENATE-DEHYDROGENASE-NADP+-RXN yeastcyc_id: PWY3O-4120 PWY3O-4153: all_genes: - *id029 - *id015 - *id017 - *id016 - *id037 comment: Biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan proceeds via a common pathway to chorismate, at which point the pathway branches |CITS:[Jones][1943992]|. One branch proceeds to phenylalanine and tyrosine, and the other to tryptophan |CITS:[Jones]|. The phenylalanine and tyrosine branch has one reaction in common, rearrangement of chorismate to prephenate, at which point, the pathway branches again to either phenylalanine or tyrosine |CITS:[1943992]|). S. cerevisiae, similar to E. coli, synthesize phenylalanine and tyrosine via the intermediate 4-hydroxyphenylpyruvate and phenylpyruvate, respectively, while some other organisms synthesize them via arogenate |CITS:[1943992]|. Aromatic amino acid biosynthesis in S. cerevisiae is controlled by a combination of feedback inhibition, activation of enzyme activity, and regulation of enzyme synthesis |CITS:[Jones][1943992]|. The carbon flow through the pathways is regulated primarily at the initial step and the branching points by the terminal end-products. The initial step of chorismate biosynthesis can be catalyzed by two isoenzymes Aro3p or Aro4p, whereby Aro3p is inhibited by phenylalanine, and Aro4p by tyrosine |CITS:[Jones][1943992]|. The first step in the phenylalanine-tyrosine branch is feedback inhibited by tyrosine and activated by tryptophan |CITS:[1943992]|. The transcriptional activator GCN4 regulates most of the genes encoding for the aromatic amino acid biosynthetic enzymes; however, no GCN4 regulation was found for ARO7 of the phenylalanine and tyrosine and branch, TYR1 of the tyrosine branch, or TRP1 of the tryptophan branch |CITS:[1943992]|. name: phenylalanine biosynthesis pmids: - '1943992' - '9491082' - '9491083' - '9642265' reactions: - ec: - 2.6.1.1 - 2.6.1.27 - 2.6.1.57 - 2.6.1.9 genes: - *id015 - *id016 left: - 2-oxoglutarate - L-phenylalanine name: L-phenylalanine + 2-oxoglutarate <-> 3-phenyl-2-oxopropanoate + L-glutamate pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-phenyl-2-oxopropanoate - L-glutamate yeastcyc_id: RXN-10814 - ec: - 2.6.1.58 genes: - *id017 left: - L-phenylalanine - pyruvate name: L-phenylalanine + pyruvate <-> 3-phenyl-2-oxopropanoate + L-alanine pmids: - '6763508' - '9491082' - '9491083' rhea: [] right: - 3-phenyl-2-oxopropanoate - L-alanine yeastcyc_id: 2.6.1.58-RXN - ec: - 5.4.99.5 genes: - *id029 left: - chorismate name: chorismate <-> prephenate pmids: [] rhea: [] right: - prephenate yeastcyc_id: CHORISMATEMUT-RXN - ec: - 4.2.1.51 genes: - *id037 left: - H+ - prephenate name: prephenate + H+ <-> 3-phenyl-2-oxopropanoate + CO2 + H2O pmids: [] rhea: [] right: - 3-phenyl-2-oxopropanoate - CO2 - H2O yeastcyc_id: PREPHENATEDEHYDRAT-RXN yeastcyc_id: PWY3O-4153 PWY3O-4158: all_genes: - *id245 - *id249 - *id250 - *id248 - *id244 - *id247 - *id251 - *id252 - *id253 - *id453 - *id412 - *id452 - *id353 - *id246 - *id451 - *id413 comment: 'Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and energy metabolism. NAD also has been shown to be an important substrate in a variety of biological processes, including transcriptional regulation, DNA repair, calcium-dependent signaling pathways, calorie-restriction-mediated life-span extension and age-associated diseases |CITS: [12736687],[12648681]|. NAD appears to affect these processes by regulating the Sir2p family of NAD-dependent deacetylases (Sirtuins) |CITS: [12648681]|. There are a number of pathways for NAD biosynthesis. In yeast and most other organisms, the two major pathways are de novo synthesis of NAD (the de novo pathway) and regeneration of NAD from its nicotinamide degradation products (the NAD salvage pathway) |CITS: [12972620], [12648681]|. NAD is synthesized de novo from tryptophan via kynurenine |CITS: [12972620]|. In this pathway tryptophan is converted to nicotinic acid mononucleotide (NAMN) in 6 enzymatic steps (catalyzed by Bna1-2p, and Bna4-7p) and one non-enzymatic step |CITS: [12972620]|. At NAMN the de novo pathway converges with the NAD salvage pathway and the last two steps to NAD are shared |CITS: [12972620], [12648681]|. In the yeast NAD salvage pathway, the vitamin precursors nicotinamide and nicotinic acid are converted to NAMN, the point of convergence with the de novo pathway |CITS: [12648681]|. The steps from nicotinic acid to NAD were elucidated by Preiss and Handler and are sometimes referred to as the Preiss-Handler pathway |CITS: [13416279], [13563526]|. Yeast can also import extracellular nicotinic acid into the cell by the permease Tna1p and then convert it into NAD via the Preiss-Handler pathway |CITS: [12648681]|. There are four additional pathways for synthesizing NAD in yeast: two salvage pathways from the vitamin precursor nicotinamide riboside (NR) and two salvage pathways from nicotinic acid riboside (NaR) |CITS: [15137942], [17482543], [17914902]|. Three of these salvage pathways converge first with the NAD salvage pathway and then with the de novo pathway, while the fourth, the NR salvage pathway I, is independent of both of these pathways. In the NR salvage pathway I, NR is phosphorylated to nicotinamide mononucleotide by the kinase Nrk1p, and then adenylated to NAD by Nma1p or Nma2p |CITS: [15137942]|. Bacteria such as Haemophilus influenza that lack the enzymes of the de novo and Preiss-Handler pathway can synthesize NAD from NR and nicotinamide mononucleotide as well |CITS: [15137942]|. Humans also appear to have this NR salvage pathway |CITS: [15137942]|. Yeast have a second NR salvage pathway (NR salvage pathway II) that is independent of Nrk1p; in NR salvage pathway II NR is split into a ribosyl product and nicotinamide, which is subsequently converted to NAD via enzymes of the NAD salvage pathway and de novo pathway |CITS: [17482543]|. The initial steps in the two NaR salvage pathways are similar to those of the NR salvage pathways and are catalyzed by the same enzymes; Nrk1p catalyzes the first step in the NR and NaR salvage pathways I and Urh1p and Pnp1p catalyze the first steps of the NR and NaR salvage pathways II |CITS: [17914902]|. ' name: superpathway of NAD biosynthesis pmids: - '15137942' reactions: - ec: - 2.7.1.22 genes: - *id412 left: - 1-(β-D ribofuranosyl)nicotinamide - ATP name: 1-(β-D ribofuranosyl)nicotinamide + ATP -> β-nicotinamide D-ribonucleotide + ADP + H+ pmids: - '15137942' rhea: [] right: - ADP - H+ - β-nicotinamide D-ribonucleotide yeastcyc_id: RIBOSYLNICOTINAMIDE-KINASE-RXN - ec: - 3.2.2.3 genes: - *id413 left: - 1-(β-D ribofuranosyl)nicotinamide - H2O name: 1-(β-D ribofuranosyl)nicotinamide + H2O -> D-ribofuranose + nicotinamide + H+ pmids: - '17482543' rhea: [] right: - D-ribofuranose - H+ - nicotinamide yeastcyc_id: RXN-8441 - ec: - 2.4.2.- genes: - *id353 left: - H+ - nicotinamide - α-D-ribose-1-phosphate name: 1-(β-D ribofuranosyl)nicotinamide + phosphate -> nicotinamide + α-D-ribose-1-phosphate + H+ pmids: - '17482543' rhea: [] right: - 1-(β-D ribofuranosyl)nicotinamide - phosphate yeastcyc_id: RXN0-7092 - ec: [] genes: [] left: - 2-amino-3-carboxymuconate-6-semialdehyde name: 2-amino-3-carboxymuconate-6-semialdehyde -> quinolinate + H2O pmids: [] rhea: [] right: - H2O - quinolinate yeastcyc_id: RXN-5721 - ec: - 3.7.1.3 genes: - *id244 left: - 3-hydroxy-L-kynurenine - H2O name: 3-hydroxy-L-kynurenine + H2O -> 3-hydroxyanthranilate + L-alanine + H+ pmids: [] rhea: [] right: - 3-hydroxyanthranilate - H+ - L-alanine yeastcyc_id: 3-HYDROXY-KYNURENINASE-RXN - ec: - 1.13.11.6 genes: - *id245 left: - 3-hydroxyanthranilate - oxygen name: 3-hydroxyanthranilate + oxygen -> 2-amino-3-carboxymuconate-6-semialdehyde + H+ pmids: [] rhea: [] right: - 2-amino-3-carboxymuconate-6-semialdehyde - H+ yeastcyc_id: 1.13.11.6-RXN - ec: - 6.3.5.1 genes: - *id246 left: - ATP - H2O - L-glutamine - nicotinate adenine dinucleotide name: ATP + nicotinate adenine dinucleotide + L-glutamine + H2O -> L-glutamate + AMP + NAD+ + diphosphate + H+ pmids: [] rhea: [] right: - AMP - H+ - L-glutamate - NAD+ - diphosphate yeastcyc_id: NAD-SYNTH-GLN-RXN - ec: - 2.4.2.19 genes: - *id247 left: - CO2 - diphosphate - β-nicotinate D-ribonucleotide name: CO2 + β-nicotinate D-ribonucleotide + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + quinolinate + 2 H+ pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - H+ - quinolinate yeastcyc_id: QUINOPRIBOTRANS-RXN - ec: - 1.14.13.9 genes: - *id248 left: - H+ - L-kynurenine - NADPH - oxygen name: L-kynurenine + NADPH + oxygen + H+ -> 3-hydroxy-L-kynurenine + NADP+ + H2O pmids: [] rhea: [] right: - 3-hydroxy-L-kynurenine - H2O - NADP+ yeastcyc_id: KYNURENINE-3-MONOOXYGENASE-RXN - ec: - 1.13.11.11 - 1.13.11.52 genes: - *id249 left: - L-tryptophan - oxygen name: L-tryptophan + oxygen -> N-Formyl-L-kynurenine pmids: [] rhea: [] right: - N-Formyl-L-kynurenine yeastcyc_id: RXN-8665 - ec: - 3.5.1.9 genes: - *id250 - *id251 left: - H2O - N-Formyl-L-kynurenine name: N-Formyl-L-kynurenine + H2O -> L-kynurenine + formate + H+ pmids: [] rhea: [] right: - H+ - L-kynurenine - formate yeastcyc_id: ARYLFORMAMIDASE-RXN - ec: - 2.3.1.- genes: - *id451 left: - H2O - NAD+ - a [histone]-N6-acetyl-L-lysine name: a [histone]-N6-acetyl-L-lysine + NAD+ + H2O -> a [histone]-L-lysine + 2''-O-acetyl-ADP-ribose + nicotinamide pmids: [] rhea: [] right: - 2''-O-acetyl-ADP-ribose - a [histone]-L-lysine - nicotinamide yeastcyc_id: RXN-15025 - ec: - 3.5.1.19 genes: - *id452 left: - H2O - nicotinamide name: nicotinamide + H2O -> ammonium + nicotinate pmids: [] rhea: [] right: - ammonium - nicotinate yeastcyc_id: NICOTINAMID-RXN - ec: - 6.3.4.21 genes: - *id453 left: - 5-phospho-α-D-ribose 1-diphosphate - ATP - H2O - nicotinate name: nicotinate + 5-phospho-α-D-ribose 1-diphosphate + ATP + H2O -> β-nicotinate D-ribonucleotide + ADP + diphosphate + phosphate pmids: [] rhea: [] right: - ADP - diphosphate - phosphate - β-nicotinate D-ribonucleotide yeastcyc_id: NICOTINATEPRIBOSYLTRANS-RXN - ec: - 2.7.1.- - 2.7.1.173 genes: - *id412 left: - ATP - β-D-ribosylnicotinate name: β-D-ribosylnicotinate + ATP -> β-nicotinate D-ribonucleotide + ADP + H+ pmids: - '17914902' rhea: [] right: - ADP - H+ - β-nicotinate D-ribonucleotide yeastcyc_id: RXN-8443 - ec: [] genes: - *id413 left: - H2O - β-D-ribosylnicotinate name: β-D-ribosylnicotinate + H2O -> D-ribose + nicotinate pmids: - '17914902' rhea: [] right: - D-ribose - nicotinate yeastcyc_id: RXN3O-214 - ec: [] genes: - *id353 left: - phosphate - β-D-ribosylnicotinate name: β-D-ribosylnicotinate + phosphate -> nicotinate + α-D-ribose-1-phosphate pmids: - '17914902' rhea: [] right: - nicotinate - α-D-ribose-1-phosphate yeastcyc_id: RXN3O-205 - ec: - 2.7.7.1 genes: - *id252 - *id253 left: - ATP - H+ - β-nicotinamide D-ribonucleotide name: β-nicotinamide D-ribonucleotide + ATP + H+ -> NAD+ + diphosphate pmids: [] rhea: [] right: - NAD+ - diphosphate yeastcyc_id: 2.7.7.1-RXN - ec: - 2.7.7.18 genes: - *id252 - *id253 left: - ATP - H+ - β-nicotinate D-ribonucleotide name: β-nicotinate D-ribonucleotide + ATP + H+ -> nicotinate adenine dinucleotide + diphosphate pmids: [] rhea: [] right: - diphosphate - nicotinate adenine dinucleotide yeastcyc_id: NICONUCADENYLYLTRAN-RXN yeastcyc_id: PWY3O-4158 PWY3O-4300: all_genes: - *id001 - *id002 - *id157 - *id158 - *id159 - *id160 - *id161 comment: 'S. cerevisiae, as a Crabtree-positive yeast, predominantly ferments pyruvate to ethanol in high glucose conditions. When glucose or other preferred carbon sources are depleted, S. cerevisiae switches to aerobic respiration and utilizes ethanol as carbon source instead, a phenomenon known as diauxic shift. Ethanol degradation is a three-step pathway that begins with the oxidation of ethanol to acetaldehyde by alcohol dehydrogenase (ADH). Aldehyde dehydrogenase (ALD) then converts acetaldehyde to acetate, which acetyl-CoA synthetase (ACS) subsequently ligates with coenzyme A to produce acetyl-CoA. Alcohol and aldehyde dehydrogenase each have several isozymes in S. cerevisiae. Of the alcohol dehydrogenases involved in catalyzing interconversion between ethanol and acetaldehyde, the cytosolic enzyme Adh2p is thought to preferentially catalyze ethanol oxidation to acetaldehyde due to its relatively low Km for ethanol. ADH2 is glucose-repressed and activated by Cat8p and Adr1p. The oxidation of acetaldehyde to acetate is catalyzed by both cytosolic and mitochondrial aldehyde dehydrogenase, of which the main isoforms (Ald6p and Ald4p, respectively) are important for growth on ethanol. References: |CITS:[9123965]||CITS: [20863251]||CITS: [25326522]||CITS: [18479436]||CITS: [15864308]||CITS: [11495982]||CITS: [9392076]||CITS: [9675847]|' name: ethanol degradation pmids: - '11024040' - '11495982' - '15864308' - '18479436' - '20863251' - '2171877' - '25326522' - '9123965' - '9392076' - '9675847' reactions: - ec: - 1.2.1.3 genes: [] left: - H2O - NAD+ - acetaldehyde name: acetaldehyde + NAD+ + H2O -> acetate + NADH + 2 H+ pmids: [] rhea: [] right: - H+ - NADH - acetate yeastcyc_id: RXN66-3 - ec: - 6.2.1.1 genes: - *id001 - *id002 left: - ATP - acetate - coenzyme A name: acetate + ATP + coenzyme A -> acetyl-CoA + AMP + diphosphate pmids: [] rhea: [] right: - AMP - acetyl-CoA - diphosphate yeastcyc_id: ACETATE--COA-LIGASE-RXN - ec: - 1.1.1.1 genes: - *id157 - *id158 - *id159 - *id160 - *id161 left: - NAD+ - ethanol name: ethanol + NAD+ <-> acetaldehyde + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - acetaldehyde yeastcyc_id: ALCOHOL-DEHYDROG-RXN yeastcyc_id: PWY3O-4300 PWY3O-440: all_genes: - *id164 - *id165 - *id166 comment: 'Many yeast and bacterial species ferment pyruvate to 2,3-butanediol via the intermediate, acetoin. Although acetoin is a flavorless compound, it is a precursor to some off-odor compounds, such as diacetyl, which can be unfavorable in beer and wine. Acetoin and 2,3-butanediol are both by-products of alcoholic fermentation by S. cerevisiae and other wine yeasts. Acetoin production during alcoholic fermentation depends on the yeast strain and other variables such as substrate and temperature (as reported in |CITS: [16535224]|). Wine yeasts with high fermentation power generally produce low acetoin levels and large amounts of ethanol and higher alcohols (alcohols with more than 2 carbons) (as reported in |CITS: [16535224]|).' name: pyruvate fermentation to acetoin III pmids: - '16535224' - '2404950' - '6383467' reactions: - ec: [] genes: - *id164 - *id165 - *id166 left: - acetaldehyde name: 2 acetaldehyde -> acetoin pmids: - '6383467' rhea: [] right: - acetoin yeastcyc_id: RXN3O-470 - ec: - 4.1.1.1 genes: - *id164 - *id165 - *id166 left: - H+ - pyruvate name: pyruvate + H+ -> acetaldehyde + CO2 pmids: - '9123965' rhea: [] right: - CO2 - acetaldehyde yeastcyc_id: RXN-6161 - ec: [] genes: - *id164 - *id165 - *id166 left: - H+ - acetaldehyde - pyruvate name: pyruvate + acetaldehyde + H+ -> acetoin + CO2 pmids: - '6383467' rhea: [] right: - CO2 - acetoin yeastcyc_id: RXN0-2022 yeastcyc_id: PWY3O-440 PWY3O-45: all_genes: - *id014 - *id009 - *id027 - *id010 - *id012 - *id013 comment: 'reference for curation: (1) Cherest, H., et al J Biol Chem (2000) 275:14056-14063. (2) [for FOL2] Mancini, R., et al. Biochem Biophys Res Commun (1999) 255:521-527. (3) [sequence similarity for EC:2.7.6.3] Sen-Gupta, M, et al. Yeast (1997) 13:849-860. (4) Bayly, A.M. and I.G. Macreadie. FEMS Microbiol Lett (2002) 213:189-192. (5) [for EC:2.5.1.15] Bayly, A.M., et al. FEMS Microbiol Lett (2001) 204:387-390. (6) [for ABZ1] Castelli, L.A., et al. FEMS Microbiol Lett (2001) 199:181-184.' name: folate biosynthesis II pmids: - '10871621' - '1916088' - '2836393' - '8852837' reactions: - ec: - 4.1.3.38 genes: - *id009 left: - 4-amino-4-deoxychorismate name: 4-amino-4-deoxychorismate -> 4-aminobenzoate + pyruvate + H+ pmids: [] rhea: [] right: - 4-aminobenzoate - H+ - pyruvate yeastcyc_id: ADCLY-RXN - ec: - 2.5.1.15 genes: - *id010 left: - (7,8-dihydropterin-6-yl)methyl diphosphate - 4-aminobenzoate name: 4-aminobenzoate + (7,8-dihydropterin-6-yl)methyl diphosphate -> 7,8-dihydropteroate + diphosphate pmids: [] rhea: [] right: - 7,8-dihydropteroate - diphosphate yeastcyc_id: H2PTEROATESYNTH-RXN - ec: - 2.7.6.3 genes: - *id010 left: - 6-(hydroxymethyl)-7,8-dihydropterin - ATP name: 6-(hydroxymethyl)-7,8-dihydropterin + ATP -> (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H+ pmids: [] rhea: [] right: - (7,8-dihydropterin-6-yl)methyl diphosphate - AMP - H+ yeastcyc_id: H2PTERIDINEPYROPHOSPHOKIN-RXN - ec: - 4.1.2.25 genes: - *id010 left: - 7,8-dihydroneopterin name: 7,8-dihydroneopterin -> glycolaldehyde + 6-(hydroxymethyl)-7,8-dihydropterin pmids: [] rhea: [] right: - 6-(hydroxymethyl)-7,8-dihydropterin - glycolaldehyde yeastcyc_id: H2NEOPTERINALDOL-RXN - ec: - 3.6.1.- genes: [] left: - 7,8-dihydroneopterin 3'-phosphate - H2O name: 7,8-dihydroneopterin 3'-phosphate + H2O -> 7,8-dihydroneopterin + phosphate pmids: [] rhea: [] right: - 7,8-dihydroneopterin - phosphate yeastcyc_id: DIHYDRONEOPTERIN-MONO-P-DEPHOS-RXN - ec: - 3.6.1.67 genes: [] left: - 7,8-dihydroneopterin 3'-triphosphate - H2O name: 7,8-dihydroneopterin 3'-triphosphate + H2O -> 7,8-dihydroneopterin 3'-phosphate + diphosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydroneopterin 3'-phosphate - H+ - diphosphate yeastcyc_id: H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN - ec: - 3.5.4.16 genes: - *id012 left: - GTP - H2O name: GTP + H2O -> formate + 7,8-dihydroneopterin 3'-triphosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydroneopterin 3'-triphosphate - H+ - formate yeastcyc_id: GTP-CYCLOHYDRO-I-RXN - ec: - 6.3.2.12 genes: - *id013 left: - 7,8-dihydropteroate - ATP - L-glutamate name: L-glutamate + 7,8-dihydropteroate + ATP -> ADP + 7,8-dihydrofolate monoglutamate + phosphate + H+ pmids: [] rhea: [] right: - 7,8-dihydrofolate monoglutamate - ADP - H+ - phosphate yeastcyc_id: DIHYDROFOLATESYNTH-RXN - ec: - 2.6.1.85 genes: - *id014 left: - L-glutamine - chorismate name: L-glutamine + chorismate <-> 4-amino-4-deoxychorismate + L-glutamate pmids: [] rhea: [] right: - 4-amino-4-deoxychorismate - L-glutamate yeastcyc_id: PABASYN-RXN - ec: - 1.5.1.3 genes: - *id027 left: - NADP+ - a tetrahydrofolate name: a tetrahydrofolate + NADP+ <- a 7,8-dihydrofolate + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 7,8-dihydrofolate yeastcyc_id: DIHYDROFOLATEREDUCT-RXN yeastcyc_id: PWY3O-45 PWY3O-450: all_genes: - *id292 - *id285 - *id281 name: phosphatidylcholine biosynthesis I pmids: - '16807089' reactions: - ec: - 2.7.7.15 genes: - *id281 left: - CTP - H+ - phosphocholine name: CTP + phosphocholine + H+ -> CDP-choline + diphosphate pmids: [] rhea: [] right: - CDP-choline - diphosphate yeastcyc_id: 2.7.7.15-RXN - ec: - 2.7.8.2 genes: - *id285 left: - CDP-choline - a 1,2-diacyl-sn-glycerol name: a 1,2-diacyl-sn-glycerol + CDP-choline <-> a phosphatidylcholine + CMP + H+ pmids: [] rhea: [] right: - CMP - H+ - a phosphatidylcholine yeastcyc_id: RXN-5781 - ec: - 2.7.1.32 genes: - *id292 left: - ATP - choline name: choline + ATP -> phosphocholine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - phosphocholine yeastcyc_id: CHOLINE-KINASE-RXN yeastcyc_id: PWY3O-450 PWY3O-48: all_genes: - &id457 orf: YDL022W symbol: GPD1 uniprot: UniProtKB:Q00055 - &id458 orf: YOL059W symbol: GPD2 uniprot: UniProtKB:P41911 - &id455 orf: YIL053W symbol: GPP1 uniprot: UniProtKB:P41277 - &id456 orf: YER062C symbol: GPP2 uniprot: UniProtKB:P40106 comment: 'The polyol glycerol has several biological roles in yeast. In carbon metabolism, glycerol is a major byproduct of ethanol fermentation and can be used as a sole source of carbon under aerobic conditions. In osmoregulation, glycerol acts as a key osmolyte during hyperosmotic stress and is the primary compatible solute in S. cerevisiae. Biosynthesis of glycerol, as a NADH-consuming process, also plays an important role in maintaining cytosolic redox balance during anaerobic conditions by oxidizing excess NADH to NAD. Consistent with these functions, S. cerevisiae cells defective in glycerol biosynthesis are sensitive to osmotic stress and do not exhibit anaerobic growth. Glycerol is produced from the reduction of dihydroxyacetone phosphate via glycerol-3-phosphate dehydrogenase, consuming NADH and forming glycerol-3-phosphate. In S. cerevisiae, glycerol-3-phosphate dehydrogenase is encoded by both GPD1 and GPD2. GPD1 is induced by osmotic stress and is thought to play a role in osmoregulation, while GPD2 is induced under anaerobic conditions and may be involved in redox balancing. Glycerol-3-phosphate is subsequently dephosphorylated by glycerol-3-phosphatase, producing glycerol. There are two genes encoding for glycerol-3-phosphatase in S. cerevisiae: GPP1, which is constitutively expressed, and GPP2, which is induced during hyperosmotic stress. References: |CITS:[9451815]||CITS: [10978547]||CITS:[8196651]||CITS: [9171333]||CITS: [8662716]|' name: glycerol biosynthesis pmids: - '10705374' - '10978547' - '11058591' - '12200299' - '14618562' - '8196651' - '8662716' - '8979347' - '9171333' - '9451815' reactions: - ec: - 3.1.3.21 genes: - *id455 - *id456 left: - H2O - glycerol 1-phosphate name: glycerol 1-phosphate + H2O -> glycerol + phosphate pmids: - '11058591' rhea: [] right: - glycerol - phosphate yeastcyc_id: GLYCEROL-1-PHOSPHATASE-RXN - ec: - 1.1.1.8 genes: - *id457 - *id458 left: - NAD+ - sn-glycerol 3-phosphate name: sn-glycerol 3-phosphate + NAD+ <- glycerone phosphate + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - glycerone phosphate yeastcyc_id: 1.1.1.8-RXN yeastcyc_id: PWY3O-48 PWY3O-5: all_genes: - &id459 orf: YGR194C symbol: XKS1 uniprot: UniProtKB:P42826 comment: 'Xylulose is a pentose sugar and a fermentable carbon source in S. cerevisiae. While xylulose is not abundant in nature, many organisms produce it as an intermediate in metabolism of xylose, the most naturally abundant sugar after glucose. In many xylose-utilizing species of yeast, degradation of xylose proceeds through its conversion to xylulose, phosphorylation to xylulose-5-phosphate, and subsequent metabolism in the pentose phosphate pathway. Although enzyme activities for all necessary steps in xylose utilization have been detected in S. cerevisiae, the conversion of xylose to xylulose does not occur at a rate sufficient for growth on xylose in this species. As a consequence, S. cerevisiae can utilize xylulose but not xylose for growth and carbon in vivo. S. cerevisiae ferments xylulose at a rate ten times lower than for glucose. The rate-limiting step of xylulose utilization is catalyzed by xylulokinase (Xks1p), which phosphorylates xylulose for subsequent incorporation into the pentose phosphate pathway. XKS1 expression in S. cerevisiae is generally low and is not induced in the presence of xylose or xylulose. While some studies show that overexpressing XKS1 improves growth on xylulose, others report that XKS1 overexpression is toxic when cells are grown on xylulose as the sole carbon source. References: |CITS:[20171088]||CITS: [18555359]||CITS: [16348083]||CITS: [15184173]||CITS: [10981687]||CITS: [9595677]|' name: xylulose degradation pmids: - '10981687' - '15184173' - '16345828' - '16348083' - '18555359' - '20171088' - '9595677' reactions: - ec: - 2.7.1.17 genes: - *id459 left: - ATP - D-xylulose name: D-xylulose + ATP -> D-xylulose 5-phosphate + ADP + H+ pmids: - '10981687' - '9595677' rhea: [] right: - ADP - D-xylulose 5-phosphate - H+ yeastcyc_id: XYLULOKIN-RXN yeastcyc_id: PWY3O-5 PWY3O-50: all_genes: - &id462 orf: YDR232W symbol: HEM1 uniprot: UniProtKB:P09950 - &id460 orf: YGL040C symbol: HEM2 uniprot: UniProtKB:P05373 - &id461 orf: YDL205C symbol: HEM3 uniprot: UniProtKB:P28789 - &id463 orf: YOR278W symbol: HEM4 uniprot: UniProtKB:P06174 comment: 'Tetrapyrroles, such as heme, siroheme, chlorophyll, and cobalamin (vitamin B12) function as cofactors in a variety of essential biological processes. Tetrapyrroles are comprised of four pyrrole rings linked together by single-carbon bridges in a linear or cyclic fashion. The cyclic tetrapyrroles heme and siroheme contain an iron-atom coordinated in their central cavity and function in respiration and sulfur assimilation, respectively. Saccharomyces cerevisiae synthesize heme and siroheme de novo via a common pathway up to the intermediate uroporphyrinogen III; oxidative decarboxylation of uroporphyrinogen III leads to the synthesis of heme while its methylation leads to siroheme synthesis. The first committed precursor in the biosynthesis of tetrapyrroles is the 5-carbon compound 5-aminolevulinic acid (ALA) |CITS: [2077690]|. Animals, fungi, apicomplexan protozoa (such as the malaria parasite Plasmodium falciparum) and photosynthetic bacteria, synthesize ALA from succinyl CoA and glycine |CITS: [2789025][15144063]|, while higher plants and other bacteria (including Escherichia coli) synthesize ALA from glutamate |CITS: [2789025][2077690]|. In Saccharomyces cerevisiae, HEM1 encodes for ALA synthase, the enzyme catalyzing the first committed step in the biosynthesis of tetrapyrroles |CITS: [6381051]|. Pyridoxal 5''-phosphate is an essential factor for Hem1p |CITS: [6381051]|. The second step, the condensation of ALA to form the pyrrole porphobilinogen, is catalyzed by ALA dehydratase (also known as porphobilinogen synthase; EC 4.2.1.24), a homo-octameric enzyme encoded by HEM2 |CITS: [2204246]|. Hem3p and Hem4p catalyze the third and fourth steps, respectively. HEM3 encodes for porphobilinogen deaminase (also known as hydroxymethylbilane synthase; EC 2.5.1.61), the enzyme catalyzing the condensation of four molecules of 4-porphobilinogen to form the linear tetrapyrrole hydroxymethylbilane |CITS: [1508149]|, and HEM4 encodes for uroporphyrinogen III synthase (UROS; EC 4.2.1.75), the enzyme catalyzing the cyclization of hydroxymethylbilane and rearrangement of the fourth pyrrole to form the important intermediate uroporphyrinogen III |CITS: [7597845]|. In the absence of UROS, the linear tetrapyrrole hydroxymethylbilane undergoes non-enzymatic cyclization without rearrangement of the fourth pyrrole ring to form uroporphyrinogen I, which is not an intermediate in the synthesis of biological tetrapyrroles. Uroporphyrinogen III is a major branch point intermediate leading to biosynthesis of different tetrapyrrole-derived compounds, such as siroheme, heme, cobalamin (vitamin B12), and the methanogenic coenzyme F430 |CITS: [2077690]|. S. cerevisiae is not believed to synthesize cobalamin de novo |CITS: [9003798][10051442]|. ' name: tetrapyrrole biosynthesis pmids: - '14559249' reactions: - ec: - 4.2.1.24 genes: - *id460 left: - 5-aminolevulinate name: 2 5-aminolevulinate -> porphobilinogen + H+ + 2 H2O pmids: [] rhea: [] right: - H+ - H2O - porphobilinogen yeastcyc_id: PORPHOBILSYNTH-RXN - ec: - 2.5.1.61 genes: - *id461 left: - H2O - porphobilinogen name: 4 porphobilinogen + H2O -> 4 ammonium + preuroporphyrinogen pmids: - '1508149' rhea: [] right: - ammonium - preuroporphyrinogen yeastcyc_id: OHMETHYLBILANESYN-RXN - ec: - 2.3.1.37 genes: - *id462 left: - H+ - glycine - succinyl-CoA name: glycine + succinyl-CoA + H+ -> CO2 + 5-aminolevulinate + coenzyme A pmids: [] rhea: [] right: - 5-aminolevulinate - CO2 - coenzyme A yeastcyc_id: 5-AMINOLEVULINIC-ACID-SYNTHASE-RXN - ec: - 4.2.1.75 genes: - *id463 left: - preuroporphyrinogen name: preuroporphyrinogen -> uroporphyrinogen-III + H2O pmids: [] rhea: [] right: - H2O - uroporphyrinogen-III yeastcyc_id: UROGENIIISYN-RXN yeastcyc_id: PWY3O-50 PWY3O-5268: all_genes: - *id378 comment: 'Unsaturated fatty acids are essential for all eukaryotes; they are key components of cellular membranes and are used for energy storage. While most eukaryotes can synthesize polyunsaturated fatty acids, Saccharomyces cerevisiae can only form monounsaturated fatty acids, primarily |FRAME: CPD-9245| (16:l) and |FRAME: OLEATE-CPD| (18:1) (|FRAME: PWY3O-1801| and |FRAME: PWY3O-5268|). The monounsaturated fatty acids, palmitoleate (16:l) and oleate (18:1) are formed by the introduction of a single carbon - carbon double bond into the saturated fatty acyl-CoA, palmitoyl and stearoyl-CoA, respectively. OLE1 encodes the sole S. cerevisiae delta-9 fatty acid desaturase, an ER membrane-bound protein that is required for the production of monounsaturated fatty acids |CITS: [1978720]|. Ole1p catalyzes the formation of a double bond between carbons 9 and 10 (denoted by delta-9) in the cis configuration. Other fungi and eukaryotes have additional fatty acid desaturases that can produce double bonds in the delta12 and delta15 position. The Ole1p sequence is similar to homologs in rat and human (SCD1) over the majority of the protein, including a cluster of histidine residues that coordinate the binding of a diiron-oxo prosthetic group within the catalytic site (reviewed in |CITS: [16920014]|). The rat and yeast proteins are similar enough that exogenously expressed rat protein can rescue an ole1 null mutant |CITS: [1978720]|. However, Ole1p has an additional C-terminal, 113 amino acid extension (relative to the rat protein), which encodes a cytochrome b5-like domain not found in mammalian desaturases. In animal cells, cytochrome b5 is thought to be the electron donor for fatty acid desaturation. In contrast, the yeast cytochrome b5 (Cyb5) is dispensable for the synthesis of unsaturated fatty acids because Ole1p contains inherent electron donor activity. The rat protein is unable to rescue an ole1 cyb5 double mutant |CITS:[8530368]|. OLE1 is highly regulated at the levels of both transcription and mRNA stability (reviewed in |CITS: [16920014 ]| and |CITS: [17087771]|). OLE1 transcription is decreased in response to high fatty acid levels |CITS: [2687232][1556107]| and increased in response to low oxygen |CITS: [10318903]| and low temperature |CITS: [11855848]|. Much of the transcriptional regulation is mediated by two homologous ER membrane-bound transcription factors, Spt23p and Mga2p. In response to stimuli, both Spt23p and Mga2p are activated by ubiquitin-dependent processing into their soluble forms, and then targeted to the nucleus |CITS: [9927444][11007476] [11557770]|. Independent of the transcriptional regulation, OLE1 mRNA is also stabilized under fatty acid free conditions and destabilized when fatty acids are added to the growth medium |CITS: [8824209]|. Mga2p, but not Spt23p, contributes to the regulation of OLE1 mRNA stability |CITS: [15220333]|.' name: oleate biosynthesis pmids: - '16920014' - '1978720' - '2674136' reactions: - ec: - 1.14.19.1 genes: - *id378 left: - H+ - a ferrocytochrome b5 - oxygen - stearoyl-CoA name: 2 a ferrocytochrome b5 + stearoyl-CoA + oxygen + 2 H+ -> 2 a ferricytochrome b5 + oleoyl-CoA + 2 H2O pmids: [] rhea: [] right: - H2O - a ferricytochrome b5 - oleoyl-CoA yeastcyc_id: 1.14.19.1-RXN - ec: - 3.1.2.2 genes: [] left: - H2O - oleoyl-CoA name: oleoyl-CoA + H2O -> oleate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - oleate yeastcyc_id: RXN-9666 yeastcyc_id: PWY3O-5268 PWY3O-592: all_genes: - *id192 comment: The glutathione/glutaredoxin and thioredoxin systems help maintain the reduced environment of the cell and play a significant role in defending the cell against oxidative stress. They also have been proposed to play a role in DNA synthesis, protein folding and regulation, and sulfur metabolism |CITS:[11169096],[2668278]|. Glutaredoxins and thioredoxins are small heat-stable proteins that can reduce disulfides by way of conserved cysteines. Glutaredoxins catalyze reductions of intracellular disulfides or glutathione-mixed disulfides in a coupled system with glutathione, NADPH and glutathione reductase. Unlike the thioredoxin system where oxidized thioredoxin disulfide is reduced directly by thioredoxin reductase with electrons from NADPH, oxidized glutaredoxin is reduced by glutathione with electrons donated by NADPH |CITS:[2668278]|. Yeast, similar to bacteria, plants, and humans have monothiol and dithiol glutaredoxins with the conserved active site motif Cys-Pro-Tyr-Cys and Cys-Gly-Phe-Ser, respectively |CITS:[11898418]|. Monothiol glutaredoxins (Grx-SH) catalyze the reduction of thiol-glutathione mixed disulfides (Protein-S-S-G) only, while dithiol glutaredoxins (Grx-(SH)2) reduce both protein disulfides (Protein-S2) and GSH-mixed disulfides (Protein-S-S-G) |CITS:[11898418]|. Five glutaredoxins have been identified in S. cerevisiae, two dithiol glutaredoxins, Grx1p and Grx2p, and three monothiol glutaredoxins, Grx3p, Grx4p, and Grx5p |CITS:[11898418]|. All five glutaredoxins participate in the response against oxidative stress |CITS:[9571241][10567543]|. GRX1 and GRX2 mutants are sensitive to the oxidants superoxide anions and hydrogen peroxide respectively, suggesting that they have different roles in protecting the cells |CITS:[9571241]|. The defensive roles of Grx1p and Grx2p may overlap with those of the cytosolic thioredoxins, Trx1p and Trx2p as at least one Grx1p/Grx2p glutaredoxin or one Trx1p/Trx2p thioredoxin is required for yeast cell viability |CITS:[10844700]|. Although GRX3 and GRX4 mutants do not have strong sensitivity to oxidants, mutants lacking GRX5 do. GRX5 mutants also have increased protein oxidative damage, growth defects in minimal medium, and inability for respiratory growth |CITS:[10567543]|. Grx5p has also been found to be a mitochondrial glutaredoxin required for the activity of iron/sulfur enzymes |CITS:[11950925]|. name: glutathione-glutaredoxin system pmids: - '11169096' - '2668278' reactions: - ec: - 1.8.1.7 genes: - *id192 left: - NADP+ - glutathione name: 2 glutathione + NADP+ <- glutathione disulfide + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - glutathione disulfide yeastcyc_id: GLUTATHIONE-REDUCT-NADPH-RXN - ec: [] genes: [] left: - an oxidized glutaredoxin - glutathione name: 2 glutathione + an oxidized glutaredoxin -> glutathione disulfide + a reduced glutaredoxin pmids: [] rhea: [] right: - a reduced glutaredoxin - glutathione disulfide yeastcyc_id: PRODISULFREDUCT-A-RXN - ec: [] genes: [] left: - an oxidized glutaredoxin - e- name: an oxidized glutaredoxin + 2 e- = a reduced glutaredoxin pmids: [] rhea: [] right: - a reduced glutaredoxin yeastcyc_id: RXN3O-547 yeastcyc_id: PWY3O-592 PWY3O-5962: all_genes: - *id354 - *id137 - *id134 - *id135 - *id355 - *id356 - *id136 - *id378 comment: 'Fatty acids are essential to all organisms except for archaea; they are major constituents of cellular membranes, and are used for energy storage and for posttranslational protein modifications. Most organisms are capable of synthesizing long chain (C12:0-C16:0) saturated fatty acids de novo. Although the initiation and termination reactions may vary, the cyclic series of chain-lengthening reactions are essentially the same across all organisms. The fatty acid chain, which starts as a 2-carbon chain from acetyl-CoA, is extended two carbons at a time by the addition of an acetyl group from malonyl-CoA. When the final length of the fatty acid is achieved, fatty acid synthesis is terminated. Each cycle of chain elongation involves 5 reactions with the following enzymatic activities: malonyl transferase (EC: 2.3.1.39), ketoacyl synthase (EC: 2.3.1.41), ketoacyl reductase (EC: 1.1.1.100), 3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61), and enoyl-acyl reductase (EC: 1.3.1.10). In yeast, fatty acid biosynthesis is terminated with the release of fatty acyl-CoAs from fatty acid synthase (FAS), the enzyme complex that carries out de novo fatty acid biosynthesis. Palmitoyl- (C16) and stearoyl-CoA (C18) are the main products in yeast, while myristoyl-CoA (C14) is only produced in small amounts |CITS: [Lynen69]|. To synthesize palmitoyl-CoA (C16) one acetyl-CoA and 7 malonyl-CoA molecules are required. The elongation substrate, malonyl-CoA is synthesized from the carboxylation of acetyl-CoA (EC 6.4.1.2) by the biotin-containing enzyme, acetyl-CoA carboxylase (Acc1p) |CITS: [1350093]|). Acetyl-CoA carboxylase is activated by the biotin:apoprotein ligase (Bpl1p) |CITS: [7649444]|). There are two types of FAS systems based on the organization of the catalytic sites. Fungi, animals, and some bacteria have type I FASs, which are large multi-functional proteins that contain all of the requisite catalytic active sites for fatty acid biosynthesis within domains on a single polypeptide (alpha) or on two polypeptides (alpha and beta). Fungal FASs are alpha6beta6 heterododecamers, animal FASs are alpha2 homodimers, and some type I bacterial FASs are alpha6 |CITS: [17448991]|. Bacteria, plants and mitochondria, on the other hand, have type II FAS systems, which are comprised of independent proteins, whereby each protein catalyzes a single step in the cyclic series of reactions |CITS: [15952903]|. The yeast FAS complex catalyzes a total of 8 reactions. The alpha subunit(Fas2p) catalyzes 3 reactions, ketoacyl synthase (EC: 2.3.1.41),ketoacyl reductase (EC: 1.1.1.100) and self pantetheinylation and the yeast beta subunit (Fas1p) catalyzes 5 reactions, acetyltransferase (EC 2.3.1.38), malonyl transferase (EC: 2.3.1.39),3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61),enoyl-acyl reductase (EC: 1.3.1.10), and palmitoyl transferase (EC:2.3.1.-) |CITS: [365179], [1100391], [10785388], [3528750], [374077]|. FASs are regulated at the transcriptional and translational level as well as posttranslationally. In yeast, FAS is a housekeeping enzyme that is expressed constitutively at a low level, but its expression is also activated by the general yeast transcription factors Rap1, Abf1 and Reb1 |CITS: [7925441]| and theinositol/choline-responsive transcription factor heterodimer, Ino2p-Ino4p |CITS: [1461729][7862526]|. The coordinate expression of the two subunits also appears to be regulated by Fas1p controlling the expression of FAS2 |CITS: [11713312]|. The FAS subunits are further regulated by proteolytic degradation of excess subunits. While the intact FAS multimeric complex (alpha6beta6 ) is stable, its individual subunits are rapidly degraded |CITS: [1735446][8262967]|.' name: superpathway of fatty acid biosynthesis, saturated and unsaturated pmids: [] reactions: - ec: - 1.14.19.1 genes: - *id378 left: - H+ - a ferrocytochrome b5 - oxygen - stearoyl-CoA name: 2 a ferrocytochrome b5 + stearoyl-CoA + oxygen + 2 H+ -> 2 a ferricytochrome b5 + oleoyl-CoA + 2 H2O pmids: [] rhea: [] right: - H2O - a ferricytochrome b5 - oleoyl-CoA yeastcyc_id: 1.14.19.1-RXN - ec: - 1.3.1.10 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - H+ - NADPH - a (2E)-but-2-enoyl-[acp] name: a (2E)-but-2-enoyl-[acp] + NADPH + H+ -> a butanoyl-[acp] + NADP+ pmids: [] rhea: [] right: - NADP+ - a butanoyl-[acp] yeastcyc_id: RXN-9515 - ec: - 4.2.1.- genes: - *id134 left: - a (3R)-3-hydroxyacyl-[acyl-carrier protein] name: a (3R)-3-hydroxyacyl-[acyl-carrier protein] -> a trans-2-enoyl-[acyl-carrier protein] + H2O pmids: [] rhea: [] right: - H2O - a trans-2-enoyl-[acyl-carrier protein] yeastcyc_id: 3-HYDROXYDECANOYL-ACP-DEHYDR-RXN - ec: - 2.3.1.86 genes: - *id135 - *id136 left: - NADP+ - a (3R)-3-hydroxyacyl-[acyl-carrier protein] name: a (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ <- a 3-oxoacyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxoacyl-[acp] yeastcyc_id: 3-OXOACYL-ACP-REDUCT-RXN - ec: - 2.3.1.86 - 4.2.1.59 genes: - *id134 left: - a (3R)-3-hydroxybutanoyl-[acp] name: a (3R)-3-hydroxybutanoyl-[acp] -> a (2E)-but-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-but-2-enoyl-[acp] yeastcyc_id: 4.2.1.58-RXN - ec: - 2.3.1.86 genes: - *id135 left: - NADP+ - a (3R)-3-hydroxybutanoyl-[acp] name: a (3R)-3-hydroxybutanoyl-[acp] + NADP+ <- an acetoacetyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - an acetoacetyl-[acp] yeastcyc_id: RXN-9514 - ec: - 4.2.1.- genes: - *id134 left: - a (3R)-3-hydroxyoctadecanoyl-[acp] name: a (3R)-3-hydroxyoctadecanoyl-[acp] -> a (2E)-octadec-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-octadec-2-enoyl-[acp] yeastcyc_id: RXN-9634 - ec: - 2.3.1.86 genes: [] left: - NADP+ - a (3R)-3-hydroxyoctadecanoyl-[acp] name: a (3R)-3-hydroxyoctadecanoyl-[acp] + NADP+ <- a 3-oxooctadecanoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxooctadecanoyl-[acp] yeastcyc_id: RXN-9633 - ec: - 1.3.1.104 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - NADP+ - a 2,3,4-saturated fatty acyl-[acp] name: a 2,3,4-saturated fatty acyl-[acp] + NADP+ <- a trans-2-enoyl-[acyl-carrier protein] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a trans-2-enoyl-[acyl-carrier protein] yeastcyc_id: ENOYL-ACP-REDUCT-NADPH-RXN - ec: - 2.3.1.179 genes: - *id137 - *id135 left: - H+ - a 2,3,4-saturated fatty acyl-[acp] - a malonyl-[acp] name: a 2,3,4-saturated fatty acyl-[acp] + a malonyl-[acp] + H+ -> acyl-carrier protein + a 3-oxoacyl-[acp] + CO2 pmids: [] rhea: [] right: - CO2 - a 3-oxoacyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: 3-OXOACYL-ACP-SYNTH-RXN - ec: - 2.3.1.179 genes: - *id137 - *id135 left: - H+ - a malonyl-[acp] - a palmitoyl-[acp] name: a palmitoyl-[acp] + a malonyl-[acp] + H+ -> a 3-oxooctadecanoyl-[acp] + CO2 + acyl-carrier protein pmids: [] rhea: [] right: - CO2 - a 3-oxooctadecanoyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: RXN3O-1803 - ec: - 2.3.1.- genes: - *id134 left: - a palmitoyl-[acp] - coenzyme A name: a palmitoyl-[acp] + coenzyme A -> palmitoyl-CoA + acyl-carrier protein pmids: - '365179' rhea: [] right: - a soluble [acyl-carrier protein] - palmitoyl-CoA yeastcyc_id: RXN3O-9780 - ec: - 2.3.1.86 genes: - *id134 left: - NADP+ - a stearoyl-[acp] name: a stearoyl-[acp] + NADP+ <- a (2E)-octadec-2-enoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a (2E)-octadec-2-enoyl-[acp] yeastcyc_id: RXN3O-5293 - ec: - 2.3.1.- genes: - *id134 left: - a stearoyl-[acp] - coenzyme A name: a stearoyl-[acp] + coenzyme A -> stearoyl-CoA + acyl-carrier protein pmids: [] rhea: [] right: - a soluble [acyl-carrier protein] - stearoyl-CoA yeastcyc_id: RXN3O-5304 - ec: - 6.4.1.2 genes: - *id354 - *id355 left: - ATP - acetyl-CoA - hydrogencarbonate name: acetyl-CoA + ATP + hydrogencarbonate -> ADP + malonyl-CoA + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - malonyl-CoA - phosphate yeastcyc_id: ACETYL-COA-CARBOXYLTRANSFER-RXN - ec: - 2.3.1.86 genes: - *id134 left: - a soluble [acyl-carrier protein] - acetyl-CoA name: acyl-carrier protein + acetyl-CoA -> an acetyl-[acp] + coenzyme A pmids: [] rhea: [] right: - an acetyl-[acp] - coenzyme A yeastcyc_id: ACP-S-ACETYLTRANSFER-RXN - ec: - 2.3.1.86 genes: - *id134 - *id356 left: - a soluble [acyl-carrier protein] - malonyl-CoA name: acyl-carrier protein + malonyl-CoA -> a malonyl-[acp] + coenzyme A pmids: [] rhea: [] right: - a malonyl-[acp] - coenzyme A yeastcyc_id: MALONYL-COA-ACP-TRANSACYL-RXN - ec: - 2.3.1.179 genes: - *id137 - *id135 left: - H+ - a malonyl-[acp] - an acetyl-[acp] name: an acetyl-[acp] + a malonyl-[acp] + H+ -> an acetoacetyl-[acp] + acyl-carrier protein + CO2 pmids: [] rhea: [] right: - CO2 - a soluble [acyl-carrier protein] - an acetoacetyl-[acp] yeastcyc_id: 3-OXOACYL-ACP-SYNTH-BASE-RXN - ec: - 3.1.2.2 genes: [] left: - H2O - oleoyl-CoA name: oleoyl-CoA + H2O -> oleate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - oleate yeastcyc_id: RXN-9666 - ec: - 3.1.2.- genes: [] left: - H2O - palmitoleoyl-CoA name: palmitoleoyl-CoA + H2O -> palmitoleate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - palmitoleate yeastcyc_id: RXN-10662 - ec: - 1.14.19.1 genes: - *id378 left: - H+ - a ferrocytochrome b5 - oxygen - palmitoyl-CoA name: palmitoyl-CoA + 2 a ferrocytochrome b5 + oxygen + 2 H+ -> palmitoleoyl-CoA + 2 a ferricytochrome b5 + 2 H2O pmids: [] rhea: [] right: - H2O - a ferricytochrome b5 - palmitoleoyl-CoA yeastcyc_id: RXN-10664 - ec: - 3.1.2.2 genes: [] left: - H2O - palmitoyl-CoA name: palmitoyl-CoA + H2O -> palmitate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - palmitate yeastcyc_id: PALMITOYL-COA-HYDROLASE-RXN - ec: - 3.1.2.2 genes: [] left: - H2O - stearoyl-CoA name: stearoyl-CoA + H2O -> stearate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - stearate yeastcyc_id: RXN-9624 yeastcyc_id: PWY3O-5962 PWY3O-6-1: all_genes: - &id464 orf: YML086C symbol: ALO1 uniprot: UniProtKB:P54783 - &id465 orf: YBR149W symbol: ARA1 uniprot: UniProtKB:P38115 - &id466 orf: YMR041C symbol: ARA2 uniprot: UniProtKB:Q04212 comment: 'Please note. There is a history of disagreement regarding the name of the 5-carbon product. It has been called D-erythroascorbic acid (D-erythroascorbate) in the literature |CITS: [17097644][17151466][10094636][11281285]|. However, in May 2008, the International Union of Biochemistry and Molecular Biology (IUBMB) changed the name from D-erythroascorbic acid to dehydro-D-arabinono-1,4-lactone because D-erythroascorbic acid is a 6-carbon compound (CAS registry number: 5776-48-7; formula: C6H8O6), and not a 5-carbon compound as indicated in the literature (see http://www.chemqmul.ac.uk/iubmb/enzyme/EC1/1/3/37.html.) Based on IUBMB''s advice ChEBI changed the name of the compound from D-erythroascorbic acid to dehydro-D-arabinono-1,4-lactone as well (see http://www.ebi.ac.uk/chebi/searchFreeText.do?searchString=17803).' name: dehydro-D-arabinono-1,4-lactone biosynthesis pmids: - '10094636' - '11281285' - '17097644' - '17151466' reactions: - ec: - 1.1.3.37 genes: - *id464 left: - D-arabinono-1,4-lactone - oxygen name: D-arabinono-1,4-lactone + oxygen -> hydrogen peroxide + dehydro-D-arabinono-1,4-lactone pmids: [] rhea: [] right: - dehydro-D-arabinono-1,4-lactone - hydrogen peroxide yeastcyc_id: 1.1.3.37-RXN - ec: - 1.1.1.117 genes: - *id465 left: - D-arabinose - NAD(P)+ name: D-arabinose + NAD(P)+ -> D-arabinono-1,4-lactone + NAD(P)H + H+ pmids: [] rhea: [] right: - D-arabinono-1,4-lactone - H+ - NAD(P)H yeastcyc_id: RXN3O-9798 - ec: - 1.1.1.116 genes: - *id466 left: - D-arabinose - NAD+ name: D-arabinose + NAD+ -> D-arabinono-1,4-lactone + NADH + H+ pmids: [] rhea: [] right: - D-arabinono-1,4-lactone - H+ - NADH yeastcyc_id: RXN3O-9797 yeastcyc_id: PWY3O-6-1 PWY3O-6336: all_genes: - *id354 - *id137 - *id134 - *id135 - *id355 - *id356 - *id136 comment: 'Fatty acids are essential to all organisms except for archaea; they are major constituents of cellular membranes, and are used for energy storage and for posttranslational protein modifications. Most organisms are capable of synthesizing long chain (C12:0-C16:0) saturated fatty acids de novo. Although the initiation and termination reactions may vary, the cyclic series of chain-lengthening reactions are essentially the same across all organisms. The fatty acid chain, which starts as a 2-carbon chain from acetyl-CoA, is extended two carbons at a time by the addition of an acetyl group from malonyl-CoA. When the final length of the fatty acid is achieved, fatty acid synthesis is terminated. Each cycle of chain elongation involves 5 reactions with the following enzymatic activities: malonyl transferase (EC: 2.3.1.39), ketoacyl synthase (EC: 2.3.1.41), ketoacyl reductase (EC: 1.1.1.100), 3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61), and enoyl-acyl reductase (EC: 1.3.1.10). In yeast, fatty acid biosynthesis is terminated with the release of fatty acyl-CoAs from fatty acid synthase (FAS), the enzyme complex that carries out de novo fatty acid biosynthesis. Palmitoyl- (C16) and stearoyl-CoA (C18) are the main products in yeast, while myristoyl-CoA (C14) is only produced in small amounts |CITS: [Lynen69]|. To synthesize palmitoyl-CoA (C16) one acetyl-CoA and 7 malonyl-CoA molecules are required. The elongation substrate, malonyl-CoA is synthesized from the carboxylation of acetyl-CoA (EC 6.4.1.2) by the biotin-containing enzyme, acetyl-CoA carboxylase (Acc1p) |CITS: [1350093]|). Acetyl-CoA carboxylase is activated by the biotin:apoprotein ligase (Bpl1p) |CITS: [7649444]|). There are two types of FAS systems based on the organization of the catalytic sites. Fungi, animals, and some bacteria have type I FASs, which are large multi-functional proteins that contain all of the requisite catalytic active sites for fatty acid biosynthesis within domains on a single polypeptide (alpha) or on two polypeptides (alpha and beta). Fungal FASs are alpha6beta6 heterododecamers, animal FASs are alpha2 homodimers, and some type I bacterial FASs are alpha6 |CITS: [17448991]|. Bacteria, plants and mitochondria, on the other hand, have type II FAS systems, which are comprised of independent proteins, whereby each protein catalyzes a single step in the cyclic series of reactions |CITS: [15952903]|. The yeast FAS complex catalyzes a total of 8 reactions. The alpha subunit(Fas2p) catalyzes 3 reactions, ketoacyl synthase (EC: 2.3.1.41),ketoacyl reductase (EC: 1.1.1.100) and self pantetheinylation and the yeast beta subunit (Fas1p) catalyzes 5 reactions, acetyltransferase (EC 2.3.1.38), malonyl transferase (EC: 2.3.1.39),3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61),enoyl-acyl reductase (EC: 1.3.1.10), and palmitoyl transferase (EC:2.3.1.-) |CITS: [365179], [1100391], [10785388], [3528750], [374077]|. FASs are regulated at the transcriptional and translational level as well as posttranslationally. In yeast, FAS is a housekeeping enzyme that is expressed constitutively at a low level, but its expression is also activated by the general yeast transcription factors Rap1, Abf1 and Reb1 |CITS: [7925441]| and theinositol/choline-responsive transcription factor heterodimer, Ino2p-Ino4p |CITS: [1461729][7862526]|. The coordinate expression of the two subunits also appears to be regulated by Fas1p controlling the expression of FAS2 |CITS: [11713312]|. The FAS subunits are further regulated by proteolytic degradation of excess subunits. While the intact FAS multimeric complex (alpha6beta6 ) is stable, its individual subunits are rapidly degraded |CITS: [1735446][8262967]|.' name: superpathway of fatty acid biosynthesis, saturated pmids: [] reactions: - ec: - 1.3.1.10 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - H+ - NADPH - a (2E)-but-2-enoyl-[acp] name: a (2E)-but-2-enoyl-[acp] + NADPH + H+ -> a butanoyl-[acp] + NADP+ pmids: [] rhea: [] right: - NADP+ - a butanoyl-[acp] yeastcyc_id: RXN-9515 - ec: - 4.2.1.- genes: - *id134 left: - a (3R)-3-hydroxyacyl-[acyl-carrier protein] name: a (3R)-3-hydroxyacyl-[acyl-carrier protein] -> a trans-2-enoyl-[acyl-carrier protein] + H2O pmids: [] rhea: [] right: - H2O - a trans-2-enoyl-[acyl-carrier protein] yeastcyc_id: 3-HYDROXYDECANOYL-ACP-DEHYDR-RXN - ec: - 2.3.1.86 genes: - *id135 - *id136 left: - NADP+ - a (3R)-3-hydroxyacyl-[acyl-carrier protein] name: a (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ <- a 3-oxoacyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxoacyl-[acp] yeastcyc_id: 3-OXOACYL-ACP-REDUCT-RXN - ec: - 2.3.1.86 - 4.2.1.59 genes: - *id134 left: - a (3R)-3-hydroxybutanoyl-[acp] name: a (3R)-3-hydroxybutanoyl-[acp] -> a (2E)-but-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-but-2-enoyl-[acp] yeastcyc_id: 4.2.1.58-RXN - ec: - 2.3.1.86 genes: - *id135 left: - NADP+ - a (3R)-3-hydroxybutanoyl-[acp] name: a (3R)-3-hydroxybutanoyl-[acp] + NADP+ <- an acetoacetyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - an acetoacetyl-[acp] yeastcyc_id: RXN-9514 - ec: - 4.2.1.- genes: - *id134 left: - a (3R)-3-hydroxyoctadecanoyl-[acp] name: a (3R)-3-hydroxyoctadecanoyl-[acp] -> a (2E)-octadec-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-octadec-2-enoyl-[acp] yeastcyc_id: RXN-9634 - ec: - 2.3.1.86 genes: [] left: - NADP+ - a (3R)-3-hydroxyoctadecanoyl-[acp] name: a (3R)-3-hydroxyoctadecanoyl-[acp] + NADP+ <- a 3-oxooctadecanoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxooctadecanoyl-[acp] yeastcyc_id: RXN-9633 - ec: - 1.3.1.104 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - NADP+ - a 2,3,4-saturated fatty acyl-[acp] name: a 2,3,4-saturated fatty acyl-[acp] + NADP+ <- a trans-2-enoyl-[acyl-carrier protein] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a trans-2-enoyl-[acyl-carrier protein] yeastcyc_id: ENOYL-ACP-REDUCT-NADPH-RXN - ec: - 2.3.1.179 genes: - *id137 - *id135 left: - H+ - a 2,3,4-saturated fatty acyl-[acp] - a malonyl-[acp] name: a 2,3,4-saturated fatty acyl-[acp] + a malonyl-[acp] + H+ -> acyl-carrier protein + a 3-oxoacyl-[acp] + CO2 pmids: [] rhea: [] right: - CO2 - a 3-oxoacyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: 3-OXOACYL-ACP-SYNTH-RXN - ec: - 2.3.1.179 genes: - *id137 - *id135 left: - H+ - a malonyl-[acp] - a palmitoyl-[acp] name: a palmitoyl-[acp] + a malonyl-[acp] + H+ -> a 3-oxooctadecanoyl-[acp] + CO2 + acyl-carrier protein pmids: [] rhea: [] right: - CO2 - a 3-oxooctadecanoyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: RXN3O-1803 - ec: - 2.3.1.- genes: - *id134 left: - a palmitoyl-[acp] - coenzyme A name: a palmitoyl-[acp] + coenzyme A -> palmitoyl-CoA + acyl-carrier protein pmids: - '365179' rhea: [] right: - a soluble [acyl-carrier protein] - palmitoyl-CoA yeastcyc_id: RXN3O-9780 - ec: - 2.3.1.86 genes: - *id134 left: - NADP+ - a stearoyl-[acp] name: a stearoyl-[acp] + NADP+ <- a (2E)-octadec-2-enoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a (2E)-octadec-2-enoyl-[acp] yeastcyc_id: RXN3O-5293 - ec: - 2.3.1.- genes: - *id134 left: - a stearoyl-[acp] - coenzyme A name: a stearoyl-[acp] + coenzyme A -> stearoyl-CoA + acyl-carrier protein pmids: [] rhea: [] right: - a soluble [acyl-carrier protein] - stearoyl-CoA yeastcyc_id: RXN3O-5304 - ec: - 6.4.1.2 genes: - *id354 - *id355 left: - ATP - acetyl-CoA - hydrogencarbonate name: acetyl-CoA + ATP + hydrogencarbonate -> ADP + malonyl-CoA + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - malonyl-CoA - phosphate yeastcyc_id: ACETYL-COA-CARBOXYLTRANSFER-RXN - ec: - 2.3.1.86 genes: - *id134 left: - a soluble [acyl-carrier protein] - acetyl-CoA name: acyl-carrier protein + acetyl-CoA -> an acetyl-[acp] + coenzyme A pmids: [] rhea: [] right: - an acetyl-[acp] - coenzyme A yeastcyc_id: ACP-S-ACETYLTRANSFER-RXN - ec: - 2.3.1.86 genes: - *id134 - *id356 left: - a soluble [acyl-carrier protein] - malonyl-CoA name: acyl-carrier protein + malonyl-CoA -> a malonyl-[acp] + coenzyme A pmids: [] rhea: [] right: - a malonyl-[acp] - coenzyme A yeastcyc_id: MALONYL-COA-ACP-TRANSACYL-RXN - ec: - 2.3.1.179 genes: - *id137 - *id135 left: - H+ - a malonyl-[acp] - an acetyl-[acp] name: an acetyl-[acp] + a malonyl-[acp] + H+ -> an acetoacetyl-[acp] + acyl-carrier protein + CO2 pmids: [] rhea: [] right: - CO2 - a soluble [acyl-carrier protein] - an acetoacetyl-[acp] yeastcyc_id: 3-OXOACYL-ACP-SYNTH-BASE-RXN - ec: - 3.1.2.2 genes: [] left: - H2O - palmitoyl-CoA name: palmitoyl-CoA + H2O -> palmitate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - palmitate yeastcyc_id: PALMITOYL-COA-HYDROLASE-RXN - ec: - 3.1.2.2 genes: [] left: - H2O - stearoyl-CoA name: stearoyl-CoA + H2O -> stearate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - stearate yeastcyc_id: RXN-9624 yeastcyc_id: PWY3O-6336 PWY3O-64: all_genes: - *id433 - *id015 - *id017 - *id080 - *id081 - *id435 - *id436 - *id437 - *id434 comment: 'Many organisms possess sulfur salvage pathways that enable recovery of the reduced sulfur atom in metabolites of S-adenosylmethionine (AdoMet) after AdoMet is consumed in a metabolic reaction. The methionine salvage pathway, also known as the 5-methylthioadenosine (MTA) cycle, is one such example. The MTA cycle regenerates methionine from the AdoMet metabolite 5-methylthioadenosine/MTA, which is formed predominantly as a byproduct of polyamine biosynthesis. The methionine salvage pathway is present in all types of organisms, and may have evolved to reuse sulfur after its costly assimilation into the cell. In the MTA cycle, four carbon atoms from the ribose moiety (C-2 through C-5) of MTA give rise to the carbon skeleton of methionine while the methylthiol group is conserved. The preferred amino group donor for the transamination reaction at the final step of pathway varies by organism; in S. cerevisiae, branched-chain and aromatic amino acids are both preferred donors. This step occurs via the branched-chain transaminases Bat1p and Bat2p or the aromatic amino acid transaminases Aro8p and Aro9p. The less-used donors for this reaction in S. cerevisiae are lysine, proline, glutamate, and glutamine. In addition to methionine, the MTA cycle may also serve as a source of purines, as adenine is cleaved off from MTA during the first reaction of the cycle. References: |CITS:[9409150]||CITS: [19946895]||CITS: [16530730]||CITS: [18625006]|' name: methionine salvage pathway pmids: - '16530730' - '18625006' - '19946895' - '9409150' reactions: - ec: - 1.13.11.54 genes: - *id433 left: - 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one - oxygen name: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + oxygen -> 4-(methylsulfanyl)-2-oxobutanoate + formate + H+ pmids: - '15938715' - '18625006' rhea: [] right: - 4-(methylsulfanyl)-2-oxobutanoate - H+ - formate yeastcyc_id: R147-RXN - ec: - 3.1.3.77 genes: - *id434 left: - 5-(methylsulfanyl)-2,3-dioxopentyl 1-phosphate - H2O name: 5-(methylsulfanyl)-2,3-dioxopentyl 1-phosphate + H2O -> 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate + H+ pmids: - '18625006' rhea: [] right: - 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one - H+ - phosphate yeastcyc_id: 3.1.3.77-RXN - ec: - 4.2.1.109 genes: - *id435 left: - 5-(methylsulfanyl)-ribulose 1-phosphate name: 5-(methylsulfanyl)-ribulose 1-phosphate -> 5-(methylsulfanyl)-2,3-dioxopentyl 1-phosphate + H2O pmids: - '18625006' rhea: [] right: - 5-(methylsulfanyl)-2,3-dioxopentyl 1-phosphate - H2O yeastcyc_id: R145-RXN - ec: - 2.6.1.88 genes: - *id015 - *id017 - *id080 - *id081 left: - L-methionine - a 2-oxo carboxylate name: L-methionine + a 2-oxo carboxylate <- 4-(methylsulfanyl)-2-oxobutanoate + a proteinogenic amino acid pmids: - '18625006' rhea: [] right: - 4-(methylsulfanyl)-2-oxobutanoate - a proteinogenic amino acid yeastcyc_id: R15-RXN - ec: - 2.4.2.28 genes: - *id436 left: - S-methyl-5'-thioadenosine - phosphate name: S-methyl-5'-thioadenosine + phosphate -> adenine + S-methyl-5-thio-α-D-ribose 1-phosphate pmids: [] rhea: [] right: - S-methyl-5-thio-α-D-ribose 1-phosphate - adenine yeastcyc_id: 5-METHYLTHIOADENOSINE-PHOSPHORYLASE-RXN - ec: - 5.3.1.23 genes: - *id437 left: - S-methyl-5-thio-α-D-ribose 1-phosphate name: S-methyl-5-thio-α-D-ribose 1-phosphate -> 5-(methylsulfanyl)-ribulose 1-phosphate pmids: - '15215245' - '18625006' rhea: [] right: - 5-(methylsulfanyl)-ribulose 1-phosphate yeastcyc_id: 5.3.1.23-RXN yeastcyc_id: PWY3O-64 PWY3O-6407: all_genes: - &id467 orf: YIL124W symbol: AYR1 uniprot: UniProtKB:P40471 - &id469 orf: YKR067W symbol: GPT2 uniprot: UniProtKB:P36148 - &id470 orf: YBL011W symbol: SCT1 uniprot: UniProtKB:P32784 - &id468 orf: YDL052C symbol: SLC1 uniprot: UniProtKB:P33333 comment: 'Phosphatidic acid (PA) is a central intermediate in the biosynthesis of phospholipids and triacylglycerols. In S. cerevisiae, de novo synthesis of PA occurs primarily through two acylation pathways: the glycerol-3-phosphate (G3P) pathway and the dihydroxyacetone phosphate (DHAP) pathway. In both routes of PA synthesis, G3P and DHAP are converted to lysophosphatidic acid (LPA) and subsequently acylated to PA by 1-acyl-sn-G3P acyltransferases (Slc1p, Ale1p, and Loa1p). G3P/DHAP acyltransferases (Sct1p and Gpt2p) catalyze the first step in both pathways, acylating G3P to LPA or DHAP to 1-acyl-DHAP. Further conversion of 1-acyl-DHAP to LPA occurs via a NADPH-dependent reaction catalyzed by 1-acyl-DHAP reductase (Ayr1p). After its formation from LPA, PA can be cleaved to diacylglycerol by phosphatidate phosphatases (Pah1p, Dpp1p, Lpp1p, and App1p) for the biosynthesis of triacylglycerols. Alternatively, PA can be converted by CDP-DAG synthases (Cds1p and Tam41p) to cytidine diphosphate diacylglycerol (CDP-DAG), the precursor to all major phospholipids in S. cerevisiae. The universal route of PA biosynthesis is the G3P pathway, which exists in prokaryotes, plants, yeast, and mammalian cells. In contrast, the DHAP pathway is present only in yeast and mammals. Aside from these de novo pathways, PA synthesis may also occur through alternative routes such as phosphorylation of diacylglycerol by DAG kinase (Dgk1p in yeast) and hydrolysis of phosphatidylcholine by phospholipase D (Spo14p in yeast). References: |CITS:[24520995]||CITS: [17726007]||CITS: [22090344]||CITS: [10542045]|' name: phosphatidate biosynthesis I (the dihydroxyacetone pathway) pmids: - '10542045' - '10617610' - '16916618' - '17726007' - '22090344' - '24520995' - '9401016' reactions: - ec: - 1.1.1.101 genes: - *id467 left: - 1-acyl-dihydroxyacetone-phosphate - NADPH name: 1-acyl-dihydroxyacetone-phosphate + NADPH -> a 1-acyl-sn-glycerol 3-phosphate + NADP+ + H+ pmids: [] rhea: [] right: - H+ - NADP+ - a 1-acyl-sn-glycerol 3-phosphate yeastcyc_id: RXN3O-9800 - ec: - 2.3.1.51 genes: - *id468 left: - a 1-acyl-sn-glycerol 3-phosphate - an acyl-CoA name: an acyl-CoA + a 1-acyl-sn-glycerol 3-phosphate -> a 1,2-diacyl-sn-glycerol 3-phosphate + coenzyme A pmids: [] rhea: [] right: - a 1,2-diacyl-sn-glycerol 3-phosphate - coenzyme A yeastcyc_id: RXN-1623 - ec: - 2.3.1.42 genes: - *id469 - *id470 left: - a long-chain acyl-CoA - glycerone phosphate name: glycerone phosphate + a long-chain acyl-CoA -> 1-acyl-dihydroxyacetone-phosphate + coenzyme A pmids: - '16916618' rhea: [] right: - 1-acyl-dihydroxyacetone-phosphate - coenzyme A yeastcyc_id: RXN3O-5279 yeastcyc_id: PWY3O-6407 PWY3O-6499: all_genes: - *id457 - *id458 - *id469 - *id470 - *id468 comment: 'Phosphatidic acid (PA) is a central intermediate in the biosynthesis of phospholipids and triacylglycerols. In S. cerevisiae, de novo synthesis of PA occurs primarily through two acylation pathways: the glycerol-3-phosphate (G3P) pathway and the dihydroxyacetone phosphate (DHAP) pathway. In both routes of PA synthesis, G3P and DHAP are converted to lysophosphatidic acid (LPA) and subsequently acylated to PA by 1-acyl-sn-G3P acyltransferases (Slc1p, Ale1p, and Loa1p). G3P/DHAP acyltransferases (Sct1p and Gpt2p) catalyze the first step in both pathways, acylating G3P to LPA or DHAP to 1-acyl-DHAP. Further conversion of 1-acyl-DHAP to LPA occurs via a NADPH-dependent reaction catalyzed by 1-acyl-DHAP reductase (Ayr1p). After its formation from LPA, PA can be cleaved to diacylglycerol by phosphatidate phosphatases (Pah1p, Dpp1p, Lpp1p, and App1p) for the biosynthesis of triacylglycerols. Alternatively, PA can be converted by CDP-DAG synthases (Cds1p and Tam41p) to cytidine diphosphate diacylglycerol (CDP-DAG), the precursor to all major phospholipids in S. cerevisiae. The universal route of PA biosynthesis is the G3P pathway, which exists in prokaryotes, plants, yeast, and mammalian cells. In contrast, the DHAP pathway is present only in yeast and mammals. Aside from these de novo pathways, PA synthesis may also occur through alternative routes such as phosphorylation of diacylglycerol by DAG kinase (Dgk1p in yeast) and hydrolysis of phosphatidylcholine by phospholipase D (Spo14p in yeast). References: |CITS:[24520995]||CITS: [17726007]||CITS: [22090344]||CITS: [10542045]|' name: phosphatidate biosynthesis II (the glycerol-3-phosphate pathway) pmids: - '10542045' - '10617610' - '16916618' - '17726007' - '22090344' - '24520995' - '9401016' reactions: - ec: - 2.3.1.51 genes: - *id468 left: - a 1-acyl-sn-glycerol 3-phosphate - an acyl-CoA name: an acyl-CoA + a 1-acyl-sn-glycerol 3-phosphate -> a 1,2-diacyl-sn-glycerol 3-phosphate + coenzyme A pmids: [] rhea: [] right: - a 1,2-diacyl-sn-glycerol 3-phosphate - coenzyme A yeastcyc_id: RXN-1623 - ec: - 1.1.1.8 genes: - *id457 - *id458 left: - NAD+ - sn-glycerol 3-phosphate name: sn-glycerol 3-phosphate + NAD+ <- glycerone phosphate + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - glycerone phosphate yeastcyc_id: 1.1.1.8-RXN - ec: - 2.3.1.15 genes: - *id469 - *id470 left: - a long-chain acyl-CoA - sn-glycerol 3-phosphate name: sn-glycerol 3-phosphate + a long-chain acyl-CoA -> a 1-acyl-sn-glycerol 3-phosphate + coenzyme A pmids: - '11544256' rhea: [] right: - a 1-acyl-sn-glycerol 3-phosphate - coenzyme A yeastcyc_id: GLYCEROL-3-P-ACYLTRANSFER-RXN yeastcyc_id: PWY3O-6499 PWY3O-661: all_genes: - *id427 comment: 'Many yeast and bacterial species ferment pyruvate to 2,3-butanediol via the intermediate, acetoin. Although acetoin is a flavorless compound, it is a precursor to some off-odor compounds, such as diacetyl, which can be unfavorable in beer and wine. Acetoin and 2,3-butanediol are both by-products of alcoholic fermentation by S. cerevisiae and other wine yeasts. Acetoin production during alcoholic fermentation depends on the yeast strain and other variables such as substrate and temperature (as reported in |CITS: [16535224]|). Wine yeasts with high fermentation power generally produce low acetoin levels and large amounts of ethanol and higher alcohols (alcohols with more than 2 carbons) (as reported in |CITS: [16535224]|). ' name: butanediol biosynthesis pmids: - '10938079' - '11306064' - '16535224' reactions: - ec: - 1.1.1.4 genes: - *id427 left: - (R,R)-2,3-butanediol - NAD+ name: (R,R)-2,3-butanediol + NAD+ <-> (R)-acetoin + NADH + H+ pmids: [] rhea: [] right: - (R)-acetoin - H+ - NADH yeastcyc_id: RR-BUTANEDIOL-DEHYDROGENASE-RXN yeastcyc_id: PWY3O-661 PWY3O-6635: all_genes: - *id467 - *id457 - *id458 - *id469 - *id470 - *id468 comment: 'Phosphatidic acid (PA) is a central intermediate in the biosynthesis of phospholipids and triacylglycerols. In S. cerevisiae, de novo synthesis of PA occurs primarily through two acylation pathways: the glycerol-3-phosphate (G3P) pathway and the dihydroxyacetone phosphate (DHAP) pathway. In both routes of PA synthesis, G3P and DHAP are converted to lysophosphatidic acid (LPA) and subsequently acylated to PA by 1-acyl-sn-G3P acyltransferases (Slc1p, Ale1p, and Loa1p). G3P/DHAP acyltransferases (Sct1p and Gpt2p) catalyze the first step in both pathways, acylating G3P to LPA or DHAP to 1-acyl-DHAP. Further conversion of 1-acyl-DHAP to LPA occurs via a NADPH-dependent reaction catalyzed by 1-acyl-DHAP reductase (Ayr1p). After its formation from LPA, PA can be cleaved to diacylglycerol by phosphatidate phosphatases (Pah1p, Dpp1p, Lpp1p, and App1p) for the biosynthesis of triacylglycerols. Alternatively, PA can be converted by CDP-DAG synthases (Cds1p and Tam41p) to cytidine diphosphate diacylglycerol (CDP-DAG), the precursor to all major phospholipids in S. cerevisiae. The universal route of PA biosynthesis is the G3P pathway, which exists in prokaryotes, plants, yeast, and mammalian cells. In contrast, the DHAP pathway is present only in yeast and mammals. Aside from these de novo pathways, PA synthesis may also occur through alternative routes such as phosphorylation of diacylglycerol by DAG kinase (Dgk1p in yeast) and hydrolysis of phosphatidylcholine by phospholipase D (Spo14p in yeast). References: |CITS:[24520995]||CITS: [17726007]||CITS: [22090344]||CITS: [10542045]|' name: superpathway of phosphatidate biosynthesis pmids: - '10542045' - '17726007' - '22090344' - '24520995' reactions: - ec: - 1.1.1.101 genes: - *id467 left: - 1-acyl-dihydroxyacetone-phosphate - NADPH name: 1-acyl-dihydroxyacetone-phosphate + NADPH -> a 1-acyl-sn-glycerol 3-phosphate + NADP+ + H+ pmids: [] rhea: [] right: - H+ - NADP+ - a 1-acyl-sn-glycerol 3-phosphate yeastcyc_id: RXN3O-9800 - ec: - 2.3.1.51 genes: - *id468 left: - a 1-acyl-sn-glycerol 3-phosphate - an acyl-CoA name: an acyl-CoA + a 1-acyl-sn-glycerol 3-phosphate -> a 1,2-diacyl-sn-glycerol 3-phosphate + coenzyme A pmids: [] rhea: [] right: - a 1,2-diacyl-sn-glycerol 3-phosphate - coenzyme A yeastcyc_id: RXN-1623 - ec: - 2.3.1.42 genes: - *id469 - *id470 left: - a long-chain acyl-CoA - glycerone phosphate name: glycerone phosphate + a long-chain acyl-CoA -> 1-acyl-dihydroxyacetone-phosphate + coenzyme A pmids: - '16916618' rhea: [] right: - 1-acyl-dihydroxyacetone-phosphate - coenzyme A yeastcyc_id: RXN3O-5279 - ec: - 1.1.1.8 genes: - *id457 - *id458 left: - NAD+ - sn-glycerol 3-phosphate name: sn-glycerol 3-phosphate + NAD+ <- glycerone phosphate + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - glycerone phosphate yeastcyc_id: 1.1.1.8-RXN - ec: - 2.3.1.15 genes: - *id469 - *id470 left: - a long-chain acyl-CoA - sn-glycerol 3-phosphate name: sn-glycerol 3-phosphate + a long-chain acyl-CoA -> a 1-acyl-sn-glycerol 3-phosphate + coenzyme A pmids: - '11544256' rhea: [] right: - a 1-acyl-sn-glycerol 3-phosphate - coenzyme A yeastcyc_id: GLYCEROL-3-P-ACYLTRANSFER-RXN yeastcyc_id: PWY3O-6635 PWY3O-69: all_genes: - *id462 - *id218 - *id215 - *id217 - *id216 - *id460 - *id461 - *id463 - *id330 - *id331 comment: 'Tetrapyrroles are a group of molecules that contain of four pyrrole rings linked together by single-atom bridges in a cyclic or linear arrangement. Biologically important cyclic tetrapyrroles, such as chlorophyll, cobalamin, heme, and siroheme, coordinate a metal ion in their central cavity and function as cofactors in numerous biological processes. The iron-containing tetrapyrroles siroheme and heme function in sulfur assimilation and oxygen sensing/utilization respectively. Both are synthesized de novo via the intermediary formation of uroporphyrinogen-III in the budding yeast S. cerevisiae. Like in mammals and photosynthetic bacteria, de novo synthesis of tetrapyrroles in S. cerevisiae begins with the condensation of glycine and succinyl-CoA to 5-aminolevulinic acid (ALA). In many plants and prokaryotes however, ALA is instead synthesized from the 5-carbon chain of glutamate. After two ALA molecules are produced, they can be condensed by ALA dehydratase (Hem2p in yeast) to form porphobilinogen (PBG), the building block of tetrapyrroles. Condensation of four molecules of PBG by PBG deaminase (Hem3p) results in a linear tetrapyrrole that can be rearranged and cyclized by uroporphyrinogen-III synthase (Hem4p) to yield uroporphyrinogen-III, the major branch point intermediate between heme and siroheme biosynthesis in yeast. The fate of uroporphyrinogen-III is determined by its subsequent modification: decarboxylation of uroporphyrinogen-III commits it to the heme biosynthesis pathway, whereas methylation commits it to the biosynthesis of siroheme. References: |CITS:[2077690]||CITS: [10051442]||CITS: [11212295]|' name: superpathway of heme and siroheme biosynthesis pmids: - '10051442' - '11212295' - '2077690' reactions: - ec: - 4.2.1.24 genes: - *id460 left: - 5-aminolevulinate name: 2 5-aminolevulinate -> porphobilinogen + H+ + 2 H2O pmids: [] rhea: [] right: - H+ - H2O - porphobilinogen yeastcyc_id: PORPHOBILSYNTH-RXN - ec: - 2.1.1.107 genes: - *id330 left: - S-adenosyl-L-methionine - uroporphyrinogen-III name: 2 S-adenosyl-L-methionine + uroporphyrinogen-III -> 2 S-adenosyl-L-homocysteine + precorrin-2 + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - precorrin-2 yeastcyc_id: RXN-13403 - ec: - 2.5.1.61 genes: - *id461 left: - H2O - porphobilinogen name: 4 porphobilinogen + H2O -> 4 ammonium + preuroporphyrinogen pmids: - '1508149' rhea: [] right: - ammonium - preuroporphyrinogen yeastcyc_id: OHMETHYLBILANESYN-RXN - ec: - 1.3.3.3 genes: - *id215 left: - H+ - coproporphyrinogen III - oxygen name: coproporphyrinogen III + oxygen + 2 H+ -> protoporphyrinogen IX + 2 CO2 + 2 H2O pmids: - '2838478' rhea: [] right: - CO2 - H2O - protoporphyrinogen IX yeastcyc_id: RXN0-1461 - ec: - 4.99.1.1 genes: - *id216 left: - H+ - ferroheme b name: ferroheme b + 2 H+ <- protoporphyrin IX + Fe2+ pmids: - '8473299' rhea: [] right: - Fe2+ - protoporphyrin IX yeastcyc_id: PROTOHEMEFERROCHELAT-RXN - ec: - 2.3.1.37 genes: - *id462 left: - H+ - glycine - succinyl-CoA name: glycine + succinyl-CoA + H+ -> CO2 + 5-aminolevulinate + coenzyme A pmids: [] rhea: [] right: - 5-aminolevulinate - CO2 - coenzyme A yeastcyc_id: 5-AMINOLEVULINIC-ACID-SYNTHASE-RXN - ec: - 1.3.1.76 genes: - *id331 left: - NAD+ - precorrin-2 name: precorrin-2 + NAD+ -> sirohydrochlorin + NADH + 2 H+ pmids: [] rhea: [] right: - H+ - NADH - sirohydrochlorin yeastcyc_id: DIMETHUROPORDEHYDROG-RXN - ec: - 4.2.1.75 genes: - *id463 left: - preuroporphyrinogen name: preuroporphyrinogen -> uroporphyrinogen-III + H2O pmids: [] rhea: [] right: - H2O - uroporphyrinogen-III yeastcyc_id: UROGENIIISYN-RXN - ec: - 1.3.3.4 genes: - *id217 left: - oxygen - protoporphyrinogen IX name: protoporphyrinogen IX + 3 oxygen -> protoporphyrin IX + 3 hydrogen peroxide pmids: - '8621563' rhea: [] right: - hydrogen peroxide - protoporphyrin IX yeastcyc_id: PROTOPORGENOXI-RXN - ec: - 4.99.1.4 genes: - *id331 left: - Fe2+ - sirohydrochlorin name: sirohydrochlorin + Fe2+ -> siroheme + 2 H+ pmids: [] rhea: [] right: - H+ - siroheme yeastcyc_id: SIROHEME-FERROCHELAT-RXN - ec: - 4.1.1.37 genes: - *id218 left: - H+ - uroporphyrinogen-III name: uroporphyrinogen-III + 4 H+ -> 4 CO2 + coproporphyrinogen III pmids: - '2180703' rhea: [] right: - CO2 - coproporphyrinogen III yeastcyc_id: UROGENDECARBOX-RXN yeastcyc_id: PWY3O-69 PWY3O-697: all_genes: - *id021 - *id026 - *id027 - *id031 - *id032 - *id033 - *id034 - *id023 - *id024 - *id022 - *id025 - *id018 - *id019 comment: 'reference for curation: (1) Cherest, H., et al J Biol Chem (2000) 275:14056-14063. (2) [for FOL2] Mancini, R., et al. Biochem Biophys Res Commun (1999) 255:521-527. (3) [sequence similarity for EC:2.7.6.3] Sen-Gupta, M, et al. Yeast (1997) 13:849-860. (4) Bayly, A.M. and I.G. Macreadie. FEMS Microbiol Lett (2002) 213:189-192. (5) [for EC:2.5.1.15] Bayly, A.M., et al. FEMS Microbiol Lett (2001) 204:387-390. (6) [for ABZ1] Castelli, L.A., et al. FEMS Microbiol Lett (2001) 199:181-184.' name: folate interconversions pmids: - '10871621' - '1916088' - '2836393' - '8852837' reactions: - ec: - 2.1.2.1 genes: - *id018 - *id019 left: - L-serine - a tetrahydrofolate name: L-serine + a tetrahydrofolate <-> glycine + a 5,10-methylenetetrahydrofolate + H2O pmids: [] rhea: [] right: - H2O - a 5,10-methylenetetrahydrofolate - glycine yeastcyc_id: GLYOHMETRANS-RXN - ec: - 3.5.4.9 genes: - *id021 - *id022 left: - H2O - a 5,10-methenyltetrahydrofolate name: a 5,10-methenyltetrahydrofolate + H2O <-> a 10-formyltetrahydrofolate + H+ pmids: [] rhea: [] right: - H+ - a 10-formyltetrahydrofolate yeastcyc_id: METHENYLTHFCYCLOHYDRO-RXN - ec: - 1.5.1.15 genes: - *id025 left: - NAD+ - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NAD+ -> a 5,10-methenyltetrahydrofolate + NADH pmids: - '8608153' rhea: [] right: - NADH - a 5,10-methenyltetrahydrofolate yeastcyc_id: 1.5.1.15-RXN - ec: - 1.5.1.5 genes: - *id021 - *id022 left: - NADP+ - a 5,10-methylenetetrahydrofolate name: a 5,10-methylenetetrahydrofolate + NADP+ <-> a 5,10-methenyltetrahydrofolate + NADPH pmids: [] rhea: [] right: - NADPH - a 5,10-methenyltetrahydrofolate yeastcyc_id: METHYLENETHFDEHYDROG-NADP-RXN - ec: - 2.1.1.45 genes: - *id026 left: - a 5,10-methylenetetrahydrofolate - dUMP name: a 5,10-methylenetetrahydrofolate + dUMP -> dTMP + a 7,8-dihydrofolate pmids: [] rhea: [] right: - a 7,8-dihydrofolate - dTMP yeastcyc_id: THYMIDYLATESYN-RXN - ec: - 1.5.1.20 genes: - *id023 - *id024 left: - NAD+ - a 5-methyltetrahydrofolate name: a 5-methyltetrahydrofolate + NAD+ <- a 5,10-methylenetetrahydrofolate + NADH + H+ pmids: - '10600168' rhea: [] right: - H+ - NADH - a 5,10-methylenetetrahydrofolate yeastcyc_id: 1.5.1.20-RXN - ec: - 6.3.4.3 genes: - *id021 - *id022 left: - ATP - a tetrahydrofolate - formate name: a tetrahydrofolate + ATP + formate <-> a 10-formyltetrahydrofolate + ADP + phosphate pmids: - '1916088' rhea: [] right: - ADP - a 10-formyltetrahydrofolate - phosphate yeastcyc_id: FORMATETHFLIG-RXN - ec: - 1.5.1.3 genes: - *id027 left: - NADP+ - a tetrahydrofolate name: a tetrahydrofolate + NADP+ <- a 7,8-dihydrofolate + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 7,8-dihydrofolate yeastcyc_id: DIHYDROFOLATEREDUCT-RXN - ec: [] genes: - *id031 - *id032 - *id033 - *id034 left: - NAD+ - a tetrahydrofolate - glycine name: glycine + a tetrahydrofolate + NAD+ -> a 5,10-methylenetetrahydrofolate + ammonium + CO2 + NADH pmids: - '1916088' rhea: [] right: - CO2 - NADH - a 5,10-methylenetetrahydrofolate - ammonium yeastcyc_id: GCVMULTI-RXN yeastcyc_id: PWY3O-697 PWY3O-7: all_genes: - *id059 - *id060 - *id232 - *id231 - *id233 - *id068 - *id069 - *id229 - *id230 comment: 'In S. cerevisiae, the TCA cycle intermediate oxaloacetate can be converted to threonine in six steps. In the first step, oxaloacetate receives an amino group from glutamate via aspartate aminotransferase (Aat1p/Aat2p) to form aspartate. Aspartate is then converted by aspartate kinase (Hom3p) to L-4-aspartyl phosphate, which in turn is sequentially reduced by aspartate semialdehyde dehydrogenase (Hom2p) and homoserine dehydrogenase (Hom6p) to form homoserine. Homoserine is subsequently phosphorylated by homoserine kinase (Thr1p) and finally converted to threonine via threonine synthase (Thr4p). Threonine itself, if not utilized for protein synthesis, can be further metabolized to isoleucine or cleaved to produce glycine. Two intermediates in this pathway represent important crossroads in amino acid metabolism: aspartate and homoserine. Aspartate can be utilized for the synthesis of asparagine, arginine, and homoserine, and homoserine can be utilized for the synthesis of sulfur-containing amino acids and threonine. The flow of aspartate and homoserine into threonine biosynthesis appears to be largely modulated by threonine levels: threonine allosterically inhibits aspartate kinase (Hom3p) and competitively inhibits homoserine kinase (Thr1p). Of the two enzyme activities, aspartate kinase activity likely plays a larger role in controlling flux, as yeast strains that possess a Hom3p variant insensitive to feedback inhibition by threonine accumulate over twenty times more threonine than the wild type. Unlike yeast, mammals lack a threonine biosynthesis pathway and must acquire threonine from the environment. To exploit this difference for medical purposes, efforts have been made to identify potential antifungal agents from compounds that inhibit the enzymes involved in threonine biosynthesis in yeast. References: |CITS:[(JONES)]||CITS: [9163906]||CITS: [25408465]||CITS: [1847111]||CITS: [6821505]|' name: superpathway of threonine biosynthesis pmids: - '1847111' - '25408465' - '6821505' - '9163906' reactions: - ec: - 2.6.1.1 genes: - *id059 - *id060 left: - 2-oxoglutarate - L-aspartate name: 2-oxoglutarate + L-aspartate <-> oxaloacetate + L-glutamate pmids: [] rhea: [] right: - L-glutamate - oxaloacetate yeastcyc_id: ASPAMINOTRANS-RXN - ec: - 2.7.2.4 genes: - *id231 left: - ATP - L-aspartate name: L-aspartate + ATP -> L-aspartyl-4-phosphate + ADP pmids: [] rhea: [] right: - ADP - L-aspartyl-4-phosphate yeastcyc_id: ASPARTATEKIN-RXN - ec: - 1.2.1.11 genes: - *id232 left: - L-aspartate 4-semialdehyde - NADP+ - phosphate name: L-aspartate 4-semialdehyde + NADP+ + phosphate <- L-aspartyl-4-phosphate + NADPH + H+ pmids: [] rhea: [] right: - H+ - L-aspartyl-4-phosphate - NADPH yeastcyc_id: ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN - ec: - 2.7.1.39 genes: - *id229 left: - ATP - L-homoserine name: L-homoserine + ATP -> O-phospho-L-homoserine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - O-phospho-L-homoserine yeastcyc_id: HOMOSERKIN-RXN - ec: - 1.1.1.3 genes: - *id233 left: - L-homoserine - NAD(P)+ name: L-homoserine + NAD(P)+ <- L-aspartate 4-semialdehyde + NAD(P)H + H+ pmids: [] rhea: [] right: - H+ - L-aspartate 4-semialdehyde - NAD(P)H yeastcyc_id: HOMOSERDEHYDROG-RXN - ec: - 4.2.3.1 genes: - *id230 left: - H2O - O-phospho-L-homoserine name: O-phospho-L-homoserine + H2O -> L-threonine + phosphate pmids: [] rhea: [] right: - L-threonine - phosphate yeastcyc_id: THRESYN-RXN - ec: - 6.4.1.1 genes: - *id068 - *id069 left: - ATP - hydrogencarbonate - pyruvate name: hydrogencarbonate + pyruvate + ATP -> oxaloacetate + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - oxaloacetate - phosphate yeastcyc_id: PYRUVATE-CARBOXYLASE-RXN yeastcyc_id: PWY3O-7 PWY3O-70: all_genes: - &id471 orf: YLR307W symbol: CDA1 uniprot: UniProtKB:Q06702 - &id472 orf: YLR308W symbol: CDA2 uniprot: UniProtKB:Q06703 comment: Chitosan, a beta-1,4 -D-glucosamine homopolymer, is a component of the yeast spore wall (ascospore) and is produced by the deacetylation of nascent chains of chitin, a beta-1,4-N-acetyl-D- glucosamine homopolymer. The CDA1 and CDA2 genes, expressed specifically during sporulation, account for the total chitin deacetylase activity in S. cerevisiae (|CITS:[8940152]|). name: chitosan biosynthesis pmids: - '16760306' reactions: - ec: - 3.5.1.41 genes: - *id471 - *id472 left: - H2O - chitin name: chitin + n H2O -> n acetate + chitosan pmids: [] rhea: [] right: - acetate - chitosan yeastcyc_id: CHITIN-DEACETYLASE-RXN yeastcyc_id: PWY3O-70 PWY3O-743: all_genes: - *id352 - *id348 - *id349 comment: 'Purine bases (guanine, adenine, etc.) acquired from the environment or formed as a product of nucleic acid degradation can be recycled for purine nucleotide synthesis via purine salvage pathways. In the salvage pathway for guanine, guanine is converted to guanosine monophosphate (GMP) by hypoxanthine-guanine phosphoribosyltransferase (HPRT). Alternatively, guanine can be converted to xanthine by guanine deaminase. In S. cerevisiae, these enzymes are encoded by HPT1 and GUD1, respectively. Xanthine itself can be salvaged to form XMP by xanthine phosphoribosyltransferase (Xpt1p in yeast) and further converted to GMP by GMP synthase (Gua1p). S. cerevisiae mutants defective in the de novo GMP biosynthesis pathway are viable when supplied with guanine, demonstrating that the salvage pathway can act as a sufficient source of guanylic nucleotides in this organism. Because overproduction or starvation of purine nucleotides is deleterious to cells, the intracellular pool of these compounds must be carefully balanced. Purine salvage appears to be an important factor in this regard. Deletion of HPT1 in S. cerevisiae leads to de-repression of enzymes involved in the de novo pathway, resulting in constitutively active purine nucleotide biosynthesis. On the other hand, overexpression of feedback-insensitive mutant hpt1 in the presence of guanine leads to guanylic nucleotide overaccumulation and massive cell death. Notably, deficiency of HPRT activity in humans results in increased production of purine nucleotides and is also regarded as the cause of Lesch-Nyhan syndrome. References: |CITS:[17052198]||CITS: [15565584]||CITS: [10217799]||CITS: [12746440]||CITS: [9335580]||CITS: [18245832]||CITS: [18067674]|' name: salvage pathways of guanine, xanthine and their nucleosides pmids: - '10217799' - '11223943' - '12746440' - '15565584' - '1577682' - '17052198' - '18067674' - '18245832' - '9335580' reactions: - ec: - 2.4.2.8 genes: - *id348 left: - GMP - diphosphate name: GMP + diphosphate <- guanine + 5-phospho-α-D-ribose 1-diphosphate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - guanine yeastcyc_id: GUANPRIBOSYLTRAN-RXN - ec: - 2.4.2.22 genes: - *id349 left: - XMP - diphosphate name: XMP + diphosphate <- xanthine + 5-phospho-α-D-ribose 1-diphosphate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - xanthine yeastcyc_id: XANPRIBOSYLTRAN-RXN - ec: - 3.5.4.3 genes: - *id352 left: - H+ - H2O - guanine name: guanine + H+ + H2O -> ammonium + xanthine pmids: [] rhea: [] right: - ammonium - xanthine yeastcyc_id: GUANINE-DEAMINASE-RXN yeastcyc_id: PWY3O-743 PWY3O-8: all_genes: - &id474 orf: YHR104W symbol: GRE3 uniprot: UniProtKB:P38715 - &id473 orf: YLR070C symbol: XYL2 uniprot: UniProtKB:Q07993 comment: 'Xylose is a pentose sugar and the second most abundant monosaccharide in nature. Because of the high abundance of xylose in wood and dry plant matter, engineering organisms for efficient fermentation of xylose to biofuel ethanol is of major industrial interest. Degradation of xylose in yeasts and filamentous fungi generally proceeds through its conversion to xylulose, phosphorylation to xylulose-5-phosphate, and subsequent metabolism in the pentose phosphate pathway. Although enzyme activities for all necessary steps in xylose utilization have been detected in S. cerevisiae, the conversion of xylose to xylulose does not occur in this organism at a rate sufficient for growth on xylose. As a consequence, S. cerevisiae can utilize xylulose but not xylose for growth and carbon in vivo. In xylose-utilizing yeasts, conversion of xylose to xylulose occurs in two steps: reduction of xylose to xylitol by xylose reductase, and oxidation of xylitol to xylulose by xylitol dehydrogenase. In S. cerevisiae, the first step can be catalyzed by the unspecific aldose reductase Gre3p while the second step can be catalyzed by the xylitol dehydrogenase Xyl2p. Overexpression of both GRE3 and XYL2 enables S. cerevisiae to grow on xylose as the sole carbon source. Wild type S. cerevisiae cells accumulate xylitol when cultured on xylose, suggesting that S. cerevisiae metabolizes xylose to xylitol and little further in vivo. This may be due to the NAD+ requirement for xylitol dehydrogenase; NADH is thought to accumulate due to xylitol dehydrogenase activity and create a cofactor imbalance severe enough to obstruct to continuous conversion of xylitol to xylulose. References: |CITS:[20171088]||CITS: [18555359]||CITS: [7747971]||CITS: [10486580]||CITS: [15184173]|' name: xylose metabolism pmids: - '10486580' - '12271459' - '15184173' - '16911508' - '18555359' - '20171088' - '20485559' - '7747971' reactions: - ec: - 1.1.1.9 genes: - *id473 left: - NAD+ - xylitol name: xylitol + NAD+ -> D-xylulose + NADH + H+ pmids: [] rhea: [] right: - D-xylulose - H+ - NADH yeastcyc_id: D-XYLULOSE-REDUCTASE-RXN - ec: - 1.1.1.21 genes: - *id474 left: - NADP+ - xylitol name: xylitol + NADP+ <-> D-xylopyranose + NADPH + H+ pmids: [] rhea: [] right: - D-xylopyranose - H+ - NADPH yeastcyc_id: RXN-8773 yeastcyc_id: PWY3O-8 PWY3O-8514: all_genes: - *id134 - *id135 comment: 'Fatty acids are essential to all organisms except for archaea; they are major constituents of cellular membranes, and are used for energy storage and for posttranslational protein modifications. Most organisms are capable of synthesizing long chain (C12:0-C16:0) saturated fatty acids de novo. Although the initiation and termination reactions may vary, the cyclic series of chain-lengthening reactions are essentially the same across all organisms. The fatty acid chain, which starts as a 2-carbon chain from acetyl-CoA, is extended two carbons at a time by the addition of an acetyl group from malonyl-CoA. When the final length of the fatty acid is achieved, fatty acid synthesis is terminated. Each cycle of chain elongation involves 5 reactions with the following enzymatic activities: malonyl transferase (EC: 2.3.1.39), ketoacyl synthase (EC: 2.3.1.41), ketoacyl reductase (EC: 1.1.1.100), 3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61), and enoyl-acyl reductase (EC: 1.3.1.10). In yeast, fatty acid biosynthesis is terminated with the release of fatty acyl-CoAs from fatty acid synthase (FAS), the enzyme complex that carries out de novo fatty acid biosynthesis. Palmitoyl- (C16) and stearoyl-CoA (C18) are the main products in yeast, while myristoyl-CoA (C14) is only produced in small amounts |CITS: [Lynen69]|. To synthesize palmitoyl-CoA (C16) one acetyl-CoA and 7 malonyl-CoA molecules are required. The elongation substrate, malonyl-CoA is synthesized from the carboxylation of acetyl-CoA (EC 6.4.1.2) by the biotin-containing enzyme, acetyl-CoA carboxylase (Acc1p) |CITS: [1350093]|). Acetyl-CoA carboxylase is activated by the biotin:apoprotein ligase (Bpl1p) |CITS: [7649444]|). There are two types of FAS systems based on the organization of the catalytic sites. Fungi, animals, and some bacteria have type I FASs, which are large multi-functional proteins that contain all of the requisite catalytic active sites for fatty acid biosynthesis within domains on a single polypeptide (alpha) or on two polypeptides (alpha and beta). Fungal FASs are alpha6beta6 heterododecamers, animal FASs are alpha2 homodimers, and some type I bacterial FASs are alpha6 |CITS: [17448991]|. Bacteria, plants and mitochondria, on the other hand, have type II FAS systems, which are comprised of independent proteins, whereby each protein catalyzes a single step in the cyclic series of reactions |CITS: [15952903]|. The yeast FAS complex catalyzes a total of 8 reactions. The alpha subunit(Fas2p) catalyzes 3 reactions, ketoacyl synthase (EC: 2.3.1.41),ketoacyl reductase (EC: 1.1.1.100) and self pantetheinylation and the yeast beta subunit (Fas1p) catalyzes 5 reactions, acetyltransferase (EC 2.3.1.38), malonyl transferase (EC: 2.3.1.39),3-hydroxyacyl dehydratase (EC: 4.2.1.58, 4.2.1.59, and 4.2.1.61),enoyl-acyl reductase (EC: 1.3.1.10), and palmitoyl transferase (EC:2.3.1.-) |CITS: [365179], [1100391], [10785388], [3528750], [374077]|. FASs are regulated at the transcriptional and translational level as well as posttranslationally. In yeast, FAS is a housekeeping enzyme that is expressed constitutively at a low level, but its expression is also activated by the general yeast transcription factors Rap1, Abf1 and Reb1 |CITS: [7925441]| and theinositol/choline-responsive transcription factor heterodimer, Ino2p-Ino4p |CITS: [1461729][7862526]|. The coordinate expression of the two subunits also appears to be regulated by Fas1p controlling the expression of FAS2 |CITS: [11713312]|. The FAS subunits are further regulated by proteolytic degradation of excess subunits. While the intact FAS multimeric complex (alpha6beta6 ) is stable, its individual subunits are rapidly degraded |CITS: [1735446][8262967]|.' name: palmitate biosynthesis pmids: [] reactions: - ec: - 2.3.1.86 - 4.2.1.59 genes: - *id134 left: - a (3R)-3-hydroxyhexadecanoyl-[acp] name: a (3R)-3-hydroxyhexadecanoyl-[acp] -> a (2E)-hexadec-2-enoyl-[acp] + H2O pmids: [] rhea: [] right: - H2O - a (2E)-hexadec-2-enoyl-[acp] yeastcyc_id: 4.2.1.61-RXN - ec: - 2.3.1.86 genes: [] left: - NADP+ - a (3R)-3-hydroxyhexadecanoyl-[acp] name: a (3R)-3-hydroxyhexadecanoyl-[acp] + NADP+ <- a 3-oxohexadecanoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a 3-oxohexadecanoyl-[acp] yeastcyc_id: RXN-9540 - ec: - 2.3.1.179 genes: - *id135 left: - H+ - a malonyl-[acp] - a myristoyl-[acp] name: a myristoyl-[acp] + a malonyl-[acp] + H+ -> a 3-oxohexadecanoyl-[acp] + CO2 + acyl-carrier protein pmids: [] rhea: [] right: - CO2 - a 3-oxohexadecanoyl-[acp] - a soluble [acyl-carrier protein] yeastcyc_id: RXN-9539 - ec: - 1.3.1.10 - 1.3.1.39 - 2.3.1.85 - 2.3.1.86 genes: - *id134 left: - NADP+ - a palmitoyl-[acp] name: a palmitoyl-[acp] + NADP+ <- a (2E)-hexadec-2-enoyl-[acp] + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - a (2E)-hexadec-2-enoyl-[acp] yeastcyc_id: RXN-9542 - ec: - 2.3.1.- genes: - *id134 left: - a palmitoyl-[acp] - coenzyme A name: a palmitoyl-[acp] + coenzyme A -> palmitoyl-CoA + acyl-carrier protein pmids: - '365179' rhea: [] right: - a soluble [acyl-carrier protein] - palmitoyl-CoA yeastcyc_id: RXN3O-9780 - ec: - 3.1.2.2 genes: [] left: - H2O - palmitoyl-CoA name: palmitoyl-CoA + H2O -> palmitate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - coenzyme A - palmitate yeastcyc_id: PALMITOYL-COA-HYDROLASE-RXN yeastcyc_id: PWY3O-8514 PWY3O-862: all_genes: - *id220 - *id407 - *id219 - *id410 - *id409 - *id408 - *id406 - *id126 comment: 'Ubiquinone (Coenzyme Q; CoQ) is a lipophilic, redox-active molecule present in cell membranes. For its ability to sustain continuous oxidation-reduction cycles, ubiquinone functions as both a membrane antioxidant and an electron carrier in many cellular pathways. In the electron transport chain, it transfers electrons from complex I and complex II to complex III. Ubiquinone is composed of a quinone core and a polyisoprenoid tail whose chain length varies according to species. The principal ubiquinone in S. cerevisiae has six subunits (CoQ6), whereas mice and humans have nine (CoQ9) and ten (CoQ10) subunits, respectively. In yeast, the polyisoprenoid tail of ubiquinone derives from the two main products of the mevalonate pathway: dimethylallyl-pyrophosphate (DPP) and isopentenyl-pyrophosphate (IPP). The condensation of DPP with one or more units of IPP produces short-chain polyprenyl diphosphates, such as farnesyl-PP (FPP) and geranylgeranyl-PP (GGPP), which serve as precursors for many primary metabolites. In the CoQ biosynthetic pathway, these short-chain molecules are further extended by long-chain polyprenyl diphosphate synthases. S. cerevisiae Coq1p (hexaprenyl pyrophosphate synthase) extends the isoprenoid subunit length of FPP or GGPP to six subunits, forming the hexaprenyl precursor to the polyprenyl tail of CoQ6. S. cerevisiae derives the quinone component of ubiquinone from either para-aminobenzoic acid (pABA) or 4-hydroxybenzoate (4-HB). While it is known that pABA synthesis from chorismate occurs via Abz1p and Abz2p in S. cerevisiae, the pathway of 4-HB synthesis is not fully characterized in this organism. It has been proposed that S. cerevisiae possesses a three-step pathway that converts tyrosine to 4-HB. This takes place through the following reactions: 1) deamination of tyrosine to 4-hydroxyphenylpyruvate (4-HPP) by Aro8p and Aro9p, 2) conversion of 4-HPP to 4-hydroxybenzaldehyde (4-Hbz) by an unknown enzyme, and 3) oxidation of 4-Hbz to 4-HB by Hfd1p. To synthesize CoQ6 in yeast, 4-HB is condensed with hexaprenyl-diphosphate via Coq2p to form 3-hexaprenyl-4-hydroxybenzoate. This molecule then undergoes a series of methylation, decarboxylation, and hydroxylation reactions in a pathway involving enzymes encoded by COQ genes. Of all the COQ genes known to be important for the biosynthesis of ubiquinone, several members (e.g. COQ4 and COQ9) have yet to be assigned a specific role in the pathway. References: |CITS:[27060254]||CITS: [19531029]||CITS: [20592037]||CITS: [27693056]|' name: superpathway of ubiquinone biosynthesis pmids: - '17482885' - '19531029' - '20592037' - '27060254' - '27693056' reactions: - ec: [] genes: [] left: - (E)-4-coumaroyl-CoA - H2O - NAD+ - coenzyme A name: (E)-4-coumaroyl-CoA + coenzyme A + NAD+ + H2O -> 4-hydroxybenzoyl-CoA + acetyl-CoA + NADH + H+ pmids: [] rhea: [] right: - 4-hydroxybenzoyl-CoA - H+ - NADH - acetyl-CoA yeastcyc_id: RXN3O-1120 - ec: [] genes: [] left: - (R)-3-(4-hydroxyphenyl)lactate name: (R)-3-(4-hydroxyphenyl)lactate -> 4-coumarate + H2O pmids: [] rhea: [] right: - 4-coumarate - H2O yeastcyc_id: RXN3O-1118 - ec: - 1.1.1.110 genes: [] left: - (R)-3-(4-hydroxyphenyl)lactate - NAD+ name: (R)-3-(4-hydroxyphenyl)lactate + NAD+ <- 3-(4-hydroxyphenyl)pyruvate + NADH + H+ pmids: [] rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - H+ - NADH yeastcyc_id: HYDROXYPHENYLPYRUVATE-REDUCTASE-RXN - ec: - 1.14.13.- genes: - *id406 left: - 2-hexaprenyl-6-methoxyphenol - H+ - NADPH - oxygen name: 2-hexaprenyl-6-methoxyphenol + NADPH + oxygen + H+ -> 2-methoxy-6-all trans-hexaprenyl-1,4-benzoquinol + NADP+ + H2O pmids: [] rhea: [] right: - 2-methoxy-6-all trans-hexaprenyl-1,4-benzoquinol - H2O - NADP+ yeastcyc_id: RXN3O-12 - ec: - 1.14.15.- genes: - *id406 left: - 3-hexaprenyl-4-hydroxybenzoate - H+ - a reduced ferredoxin [iron-sulfur] cluster - oxygen name: 3-hexaprenyl-4-hydroxybenzoate + 2 a reduced ferredoxin [iron-sulfur] cluster + oxygen + 2 H+ -> 3,4-dihydroxy-5-all-trans-hexaprenylbenzoate + 2 an oxidized ferredoxin [iron-sulfur] cluster + H2O pmids: [] rhea: [] right: - 3,4-dihydroxy-5-all-trans-hexaprenylbenzoate - H2O - an oxidized ferredoxin [iron-sulfur] cluster yeastcyc_id: RXN3O-58 - ec: - 4.1.1.- genes: [] left: - 3-methoxy-4-hydroxy-5-all-trans-hexaprenylbenzoate - H+ name: 3-methoxy-4-hydroxy-5-all-trans-hexaprenylbenzoate + H+ -> 2-hexaprenyl-6-methoxyphenol + CO2 pmids: [] rhea: [] right: - 2-hexaprenyl-6-methoxyphenol - CO2 yeastcyc_id: RXN3O-73 - ec: - 6.2.1.12 genes: [] left: - 4-coumarate - ATP - coenzyme A name: 4-coumarate + ATP + coenzyme A -> (E)-4-coumaroyl-CoA + AMP + diphosphate pmids: [] rhea: [] right: - (E)-4-coumaroyl-CoA - AMP - diphosphate yeastcyc_id: 4-COUMARATE--COA-LIGASE-RXN - ec: [] genes: [] left: - 4-hydroxybenzoyl-CoA - acetyl-CoA name: 4-hydroxybenzoyl-CoA + acetyl-CoA -> 4-hydroxybenzoate pmids: [] rhea: [] right: - 4-hydroxybenzoate yeastcyc_id: RXN3O-1121 - ec: - 1.14.99.60 genes: - *id407 left: - 6-methoxy-3-methyl-2-all-trans-hexaprenyl-1,4-benzoquinol - a reduced electron acceptor - oxygen name: 6-methoxy-3-methyl-2-all-trans-hexaprenyl-1,4-benzoquinol + a reduced electron acceptor + oxygen -> 3-demethylubiquinol-6 + an oxidized electron acceptor + H2O pmids: [] rhea: [] right: - 3-demethylubiquinol-6 - H2O - an oxidized electron acceptor yeastcyc_id: RXN3O-75 - ec: [] genes: [] left: - L-tyrosine name: L-tyrosine -> 3-(4-hydroxyphenyl)pyruvate + ammonia pmids: [] rhea: [] right: - 3-(4-hydroxyphenyl)pyruvate - ammonia yeastcyc_id: RXN3O-1116 - ec: - 2.1.1.201 genes: - *id408 left: - 2-methoxy-6-all trans-hexaprenyl-1,4-benzoquinol - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + 2-methoxy-6-all trans-hexaprenyl-1,4-benzoquinol -> 6-methoxy-3-methyl-2-all-trans-hexaprenyl-1,4-benzoquinol + S-adenosyl-L-homocysteine + H+ pmids: [] rhea: [] right: - 6-methoxy-3-methyl-2-all-trans-hexaprenyl-1,4-benzoquinol - H+ - S-adenosyl-L-homocysteine yeastcyc_id: RXN3O-54 - ec: - 2.1.1.114 genes: - *id409 left: - 3,4-dihydroxy-5-all-trans-hexaprenylbenzoate - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + 3,4-dihydroxy-5-all-trans-hexaprenylbenzoate -> S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-5-all-trans-hexaprenylbenzoate + H+ pmids: [] rhea: [] right: - 3-methoxy-4-hydroxy-5-all-trans-hexaprenylbenzoate - H+ - S-adenosyl-L-homocysteine yeastcyc_id: 2.1.1.114-RXN - ec: - 2.1.1.64 genes: - *id409 left: - 3-demethylubiquinol-6 - S-adenosyl-L-methionine name: S-adenosyl-L-methionine + 3-demethylubiquinol-6 -> S-adenosyl-L-homocysteine + ubiquinol-6 + H+ pmids: [] rhea: [] right: - H+ - S-adenosyl-L-homocysteine - ubiquinol-6 yeastcyc_id: RXN3O-102 - ec: - 2.5.1.39 genes: - *id410 left: - 4-hydroxybenzoate - all-trans-hexaprenyl diphosphate name: all-trans-hexaprenyl diphosphate + 4-hydroxybenzoate -> 3-hexaprenyl-4-hydroxybenzoate + diphosphate pmids: [] rhea: [] right: - 3-hexaprenyl-4-hydroxybenzoate - diphosphate yeastcyc_id: RXN-9003 - ec: - 4.1.3.40 genes: [] left: - chorismate name: chorismate -> 4-hydroxybenzoate + pyruvate pmids: [] rhea: [] right: - 4-hydroxybenzoate - pyruvate yeastcyc_id: CHORPYRLY-RXN - ec: - 2.5.1.1 genes: - *id126 left: - dimethylallyl diphosphate - isopentenyl diphosphate name: dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - geranyl diphosphate yeastcyc_id: GPPSYN-RXN - ec: - 2.5.1.10 genes: - *id126 left: - geranyl diphosphate - isopentenyl diphosphate name: geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate pmids: [] rhea: [] right: - (2E,6E)-farnesyl diphosphate - diphosphate yeastcyc_id: FPPSYN-RXN - ec: - 2.5.1.- genes: - *id219 left: - geranylfarnesyl diphosphate - isopentenyl diphosphate name: geranylfarnesyl diphosphate + isopentenyl diphosphate -> all-trans-hexaprenyl diphosphate + diphosphate pmids: [] rhea: [] right: - all-trans-hexaprenyl diphosphate - diphosphate yeastcyc_id: RXN3O-9805 - ec: - 2.5.1.81 genes: [] left: - geranylgeranyl diphosphate - isopentenyl diphosphate name: geranylgeranyl diphosphate + isopentenyl diphosphate -> geranylfarnesyl diphosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - geranylfarnesyl diphosphate yeastcyc_id: RXN-8813 - ec: - 2.5.1.29 genes: - *id220 left: - (2E,6E)-farnesyl diphosphate - isopentenyl diphosphate name: isopentenyl diphosphate + (2E,6E)-farnesyl diphosphate -> geranylgeranyl diphosphate + diphosphate pmids: [] rhea: [] right: - diphosphate - geranylgeranyl diphosphate yeastcyc_id: FARNESYLTRANSTRANSFERASE-RXN yeastcyc_id: PWY3O-862 PWY3O-94: all_genes: - *id208 - *id209 - *id210 - *id211 - *id212 - *id206 - &id475 orf: YPL262W symbol: FUM1 uniprot: UniProtKB:P08417 - *id205 - &id476 orf: YNL037C symbol: IDH1 uniprot: UniProtKB:P28834 - &id477 orf: YOR136W symbol: IDH2 uniprot: UniProtKB:P28241 - *id328 - *id329 - *id034 - &id478 orf: YOR142W symbol: LSC1 uniprot: UniProtKB:P53598 - &id479 orf: YGR244C symbol: LSC2 uniprot: UniProtKB:P53312 - *id170 - *id171 - *id172 - *id207 - *id068 - *id069 - *id401 - *id402 - *id403 - *id404 - *id405 comment: 'The tricarboxylic acid (TCA) cycle is a catabolic pathway that functions to generate energy and reduced cofactors from the oxidative decarboxylation of acetyl (C2) units. It occupies a central role in the metabolism of aerobic organisms, enabling the production of energy from carbohydrates, fatty acids, amino acids, and potentially any other molecule that can be converted or broken down to acetyl-CoA. In addition to its role in catabolism, the TCA cycle can also serve a biosynthetic role, as several intermediates in the pathway (e.g. oxaloacetate, succinate) provide carbon for the synthesis of amino acids or other biological compounds. The glyoxylate cycle is similar to the TCA cycle in that both pathways share the same initial steps, namely the conversion of oxaloacetate and acetyl-CoA to the six-carbon molecule isocitrate. Here the pathways diverge- instead of catalyzing the decarboxylation of isocitrate, the glyoxylate cycle catalyzes the cleavage of isocitrate to the 4-carbon molecule succinate and the 2-carbon molecule glyoxylate. Glyoxylate is then condensed with another molecule of acetyl-CoA to form the 4-carbon molecule malate. These two steps are catalyzed by isocitrate lyase and malate synthase, respectively. Malate can then be converted back to oxaloacetate for another round through the pathway. Ultimately, the glyoxylate cycle leads to the net condensation of acetyl units into 4-carbon molecules, whereas the TCA cycle results in the net dissimilation of acetyl carbons as CO2. The existence of both pathways in S. cerevisiae enables this organism to utilize acetyl units not only for energy (via the TCA cycle), but also for the synthesis of 4-carbon precursors (via the glyoxylate cycle). Consequently, S. cerevisiae is able to use C2 carbon sources (e.g. ethanol, acetate) and fatty acids as sole sources of carbon. The key enzymes of the glyoxylate cycle- isocitrate lyase and malate synthase- are encoded in S. cerevisiae by ICL1 and MLS1, respectively. Both ICL1 and MLS1 are highly induced by ethanol, acetate, and fatty acids; furthermore, disruption of either gene results in a growth defect on these carbon sources. Whereas the TCA cycle exists in virtually all aerobic organisms, the glyoxylate cycle is unique to plants, fungi, and other microorganisms such as E. coli. References: |CITS: [20889721]||CITS: [23966945]||CITS: [1551398]||CITS: [1454530]|' name: superpathway of TCA cycle and glyoxylate cycle pmids: - '12455685' - '1454530' - '1551398' - '20889721' - '23966945' reactions: - ec: - 4.2.1.2 genes: - *id475 left: - (S)-malate name: (S)-malate <- fumarate + H2O pmids: [] rhea: [] right: - H2O - fumarate yeastcyc_id: FUMHYDR-RXN - ec: - 1.1.1.37 genes: - *id170 - *id171 - *id172 left: - (S)-malate - NAD+ name: (S)-malate + NAD+ <-> oxaloacetate + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - oxaloacetate yeastcyc_id: MALATE-DEH-RXN - ec: - 1.2.1.- genes: - *id328 - *id329 - *id034 left: - 2-oxoglutarate - NAD+ - coenzyme A name: 2-oxoglutarate + coenzyme A + NAD+ -> succinyl-CoA + CO2 + NADH pmids: [] rhea: [] right: - CO2 - NADH - succinyl-CoA yeastcyc_id: 2OXOGLUTARATEDEH-RXN - ec: - 4.1.3.1 genes: - *id205 left: - D-threo-isocitrate name: D-threo-isocitrate -> glyoxylate + succinate pmids: [] rhea: [] right: - glyoxylate - succinate yeastcyc_id: ISOCIT-CLEAV-RXN - ec: - 1.1.1.286 - 1.1.1.41 genes: - *id476 - *id477 left: - D-threo-isocitrate - NAD+ name: D-threo-isocitrate + NAD+ -> 2-oxoglutarate + CO2 + NADH pmids: [] rhea: [] right: - 2-oxoglutarate - CO2 - NADH yeastcyc_id: ISOCITRATE-DEHYDROGENASE-NAD+-RXN - ec: - 2.3.3.9 genes: - *id206 - *id207 left: - H2O - acetyl-CoA - glyoxylate name: acetyl-CoA + glyoxylate + H2O -> (S)-malate + coenzyme A + H+ pmids: [] rhea: [] right: - (S)-malate - H+ - coenzyme A yeastcyc_id: MALSYN-RXN - ec: [] genes: - *id208 left: - H2O - cis-aconitate name: cis-aconitate + H2O <-> D-threo-isocitrate pmids: [] rhea: [] right: - D-threo-isocitrate yeastcyc_id: ACONITATEHYDR-RXN - ec: [] genes: - *id208 - *id209 left: - citrate name: citrate <-> cis-aconitate + H2O pmids: [] rhea: [] right: - H2O - cis-aconitate yeastcyc_id: ACONITATEDEHYDR-RXN - ec: - 6.4.1.1 genes: - *id068 - *id069 left: - ATP - hydrogencarbonate - pyruvate name: hydrogencarbonate + pyruvate + ATP -> oxaloacetate + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - oxaloacetate - phosphate yeastcyc_id: PYRUVATE-CARBOXYLASE-RXN - ec: - 2.3.3.1 - 2.3.3.16 genes: - *id210 - *id211 - *id212 left: - H2O - acetyl-CoA - oxaloacetate name: oxaloacetate + acetyl-CoA + H2O -> citrate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - citrate - coenzyme A yeastcyc_id: CITSYN-RXN - ec: - 6.2.1.5 genes: - *id478 - *id479 left: - ATP - coenzyme A - succinate name: succinate + ATP + coenzyme A <-> succinyl-CoA + ADP + phosphate pmids: [] rhea: [] right: - ADP - phosphate - succinyl-CoA yeastcyc_id: SUCCCOASYN-RXN - ec: - 1.3.5.1 genes: - *id401 - *id402 - *id403 - *id404 - *id405 left: - a ubiquinone - succinate name: succinate[inner membrane] + a ubiquinone[inner membrane] -> fumarate[inner membrane] + an ubiquinol[inner membrane] pmids: [] rhea: [] right: - an ubiquinol - fumarate yeastcyc_id: SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN yeastcyc_id: PWY3O-94 PWY3O-954: all_genes: - *id232 - *id231 - *id233 - *id264 - *id263 - *id262 - *id265 comment: 'Aspartate, inorganic sulfur, and a methyl group from one-carbon metabolism can be used by S. cerevisiae cells to synthesize methionine de novo. Here, the four-carbon chain of methionine comes from aspartate, which undergoes a three-step conversion to homoserine followed by acetylation to O-acetylhomoserine. The sulfur of methionine is acquired from inorganic sulfate, which is reduced to sulfide via the sulfate assimilation pathway and incorporated into the carbon chain of O-acetyl-L-homoserine to form homocysteine. To synthesize methionine, homocysteine receives a methyl group from 5-methyltetrahydrofolate (5-methyl-THF) in a reaction catalyzed by methionine synthase (Met6p). 5-methyl-THF is a folate coenzyme that exists in both monoglutamated and polyglutamated forms, however only the latter can be used by Met6p as the methyl donor for this reaction. In addition to inorganic sulfur, cysteine can also be used as a sulfur source for methionine biosynthesis in S. cerevisiae. This occurs through the transsulfuration pathway, where cysteine reacts with O-acetylhomoserine to form cystathionine. Cleavage of cystathionine produces homocysteine, which can undergo conversion to methionine or reverse-transsulfuration to regenerate cysteine. The transsulfuration pathway enables S. cerevisiae to exchange sulfur between methionine, homocysteine, and cysteine. References: |CITS:[9409150]||CITS: [16700064]|' name: superpathway of methionine biosynthesis pmids: - '16700064' - '9409150' reactions: - ec: - 2.7.2.4 genes: - *id231 left: - ATP - L-aspartate name: L-aspartate + ATP -> L-aspartyl-4-phosphate + ADP pmids: [] rhea: [] right: - ADP - L-aspartyl-4-phosphate yeastcyc_id: ASPARTATEKIN-RXN - ec: - 1.2.1.11 genes: - *id232 left: - L-aspartate 4-semialdehyde - NADP+ - phosphate name: L-aspartate 4-semialdehyde + NADP+ + phosphate <- L-aspartyl-4-phosphate + NADPH + H+ pmids: [] rhea: [] right: - H+ - L-aspartyl-4-phosphate - NADPH yeastcyc_id: ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN - ec: - 2.1.1.14 genes: - *id262 left: - 5-methyltetrahydropteroyl tri-L-glutamate - L-homocysteine name: L-homocysteine + 5-methyltetrahydropteroyl tri-L-glutamate <-> L-methionine + tetrahydropteroyl tri-L-glutamate pmids: [] rhea: [] right: - L-methionine - tetrahydropteroyl tri-L-glutamate yeastcyc_id: HOMOCYSMET-RXN - ec: - 1.1.1.3 genes: - *id233 left: - L-homoserine - NAD(P)+ name: L-homoserine + NAD(P)+ <- L-aspartate 4-semialdehyde + NAD(P)H + H+ pmids: [] rhea: [] right: - H+ - L-aspartate 4-semialdehyde - NAD(P)H yeastcyc_id: HOMOSERDEHYDROG-RXN - ec: - 2.3.1.31 genes: - *id263 left: - L-homoserine - acetyl-CoA name: L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A pmids: [] rhea: [] right: - O-acetyl-L-homoserine - coenzyme A yeastcyc_id: HOMOSERINE-O-ACETYLTRANSFERASE-RXN - ec: - 2.5.1.49 genes: - *id264 left: - O-acetyl-L-homoserine - hydrogen sulfide name: O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H+ pmids: [] rhea: [] right: - H+ - L-homocysteine - acetate yeastcyc_id: ACETYLHOMOSER-CYS-RXN - ec: - 6.3.2.17 genes: - *id265 left: - ATP - L-glutamate - a 5-methyltetrahydrofolate name: a 5-methyltetrahydrofolate + L-glutamate + ATP -> a 5-methyltetrahydrofolate + ADP + phosphate pmids: [] rhea: [] right: - ADP - a 5-methyltetrahydrofolate - phosphate yeastcyc_id: RXN3O-22 yeastcyc_id: PWY3O-954 PWY3O-96: all_genes: - *id353 - *id413 comment: 'Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and energy metabolism. NAD also has been shown to be an important substrate in a variety of biological processes, including transcriptional regulation, DNA repair, calcium-dependent signaling pathways, calorie-restriction-mediated life-span extension and age-associated diseases |CITS: [12736687],[12648681]|. NAD appears to affect these processes by regulating the Sir2p family of NAD-dependent deacetylases (Sirtuins) |CITS: [12648681]|. There are a number of pathways for NAD biosynthesis. In yeast and most other organisms, the two major pathways are de novo synthesis of NAD (the de novo pathway) and regeneration of NAD from its nicotinamide degradation products (the NAD salvage pathway) |CITS: [12972620], [12648681]|. NAD is synthesized de novo from tryptophan via kynurenine |CITS: [12972620]|. In this pathway tryptophan is converted to nicotinic acid mononucleotide (NAMN) in 6 enzymatic steps (catalyzed by Bna1-2p, and Bna4-7p) and one non-enzymatic step |CITS: [12972620]|. At NAMN the de novo pathway converges with the NAD salvage pathway and the last two steps to NAD are shared |CITS: [12972620], [12648681]|. In the yeast NAD salvage pathway, the vitamin precursors nicotinamide and nicotinic acid are converted to NAMN, the point of convergence with the de novo pathway |CITS: [12648681]|. The steps from nicotinic acid to NAD were elucidated by Preiss and Handler and are sometimes referred to as the Preiss-Handler pathway |CITS: [13416279], [13563526]|. Yeast can also import extracellular nicotinic acid into the cell by the permease Tna1p and then convert it into NAD via the Preiss-Handler pathway |CITS: [12648681]|. There are four additional pathways for synthesizing NAD in yeast: two salvage pathways from the vitamin precursor nicotinamide riboside (NR) and two salvage pathways from nicotinic acid riboside (NaR) |CITS: [15137942], [17482543], [17914902]|. Three of these salvage pathways converge first with the NAD salvage pathway and then with the de novo pathway, while the fourth, the NR salvage pathway I, is independent of both of these pathways. In the NR salvage pathway I, NR is phosphorylated to nicotinamide mononucleotide by the kinase Nrk1p, and then adenylated to NAD by Nma1p or Nma2p |CITS: [15137942]|. Bacteria such as Haemophilus influenza that lack the enzymes of the de novo and Preiss-Handler pathway can synthesize NAD from NR and nicotinamide mononucleotide as well |CITS: [15137942]|. Humans also appear to have this NR salvage pathway |CITS: [15137942]|. Yeast have a second NR salvage pathway (NR salvage pathway II) that is independent of Nrk1p; in NR salvage pathway II NR is split into a ribosyl product and nicotinamide, which is subsequently converted to NAD via enzymes of the NAD salvage pathway and de novo pathway |CITS: [17482543]|. The initial steps in the two NaR salvage pathways are similar to those of the NR salvage pathways and are catalyzed by the same enzymes; Nrk1p catalyzes the first step in the NR and NaR salvage pathways I and Urh1p and Pnp1p catalyze the first steps of the NR and NaR salvage pathways II |CITS: [17914902]|.' name: nicotinamide riboside salvage pathway II pmids: - '17482543' reactions: - ec: - 3.2.2.3 genes: - *id413 left: - 1-(β-D ribofuranosyl)nicotinamide - H2O name: 1-(β-D ribofuranosyl)nicotinamide + H2O -> D-ribofuranose + nicotinamide + H+ pmids: - '17482543' rhea: [] right: - D-ribofuranose - H+ - nicotinamide yeastcyc_id: RXN-8441 - ec: - 2.4.2.- genes: - *id353 left: - H+ - nicotinamide - α-D-ribose-1-phosphate name: 1-(β-D ribofuranosyl)nicotinamide + phosphate -> nicotinamide + α-D-ribose-1-phosphate + H+ pmids: - '17482543' rhea: [] right: - 1-(β-D ribofuranosyl)nicotinamide - phosphate yeastcyc_id: RXN0-7092 yeastcyc_id: PWY3O-96 PWY3O-981: all_genes: - *id427 - *id076 - *id077 - *id164 - *id165 - *id166 comment: 'Many yeast and bacterial species ferment pyruvate to 2,3-butanediol via the intermediate, acetoin. Although acetoin is a flavorless compound, it is a precursor to some off-odor compounds, such as diacetyl, which can be unfavorable in beer and wine. Acetoin and 2,3-butanediol are both by-products of alcoholic fermentation by S. cerevisiae and other wine yeasts. Acetoin production during alcoholic fermentation depends on the yeast strain and other variables such as substrate and temperature (as reported in |CITS: [16535224]|). Wine yeasts with high fermentation power generally produce low acetoin levels and large amounts of ethanol and higher alcohols (alcohols with more than 2 carbons) (as reported in |CITS: [16535224]|). ' name: superpathway of acetoin and butanediol biosynthesis pmids: - '10938079' - '16535224' - '2180695' - '2404950' - '6383467' reactions: - ec: - 1.1.1.4 genes: - *id427 left: - (R,R)-2,3-butanediol - NAD+ name: (R,R)-2,3-butanediol + NAD+ <-> (R)-acetoin + NADH + H+ pmids: [] rhea: [] right: - (R)-acetoin - H+ - NADH yeastcyc_id: RR-BUTANEDIOL-DEHYDROGENASE-RXN - ec: [] genes: [] left: - (S)-2-acetolactate - H+ - an oxidized electron acceptor name: (S)-2-acetolactate + an oxidized electron acceptor + H+ -> diacetyl + CO2 + a reduced electron acceptor pmids: [] rhea: [] right: - CO2 - a reduced electron acceptor - diacetyl yeastcyc_id: RXN-6081 - ec: [] genes: - *id164 - *id165 - *id166 left: - acetaldehyde name: 2 acetaldehyde -> acetoin pmids: - '6383467' rhea: [] right: - acetoin yeastcyc_id: RXN3O-470 - ec: - 2.2.1.6 genes: - *id076 - *id077 left: - H+ - pyruvate name: 2 pyruvate + H+ -> (S)-2-acetolactate + CO2 pmids: [] rhea: [] right: - (S)-2-acetolactate - CO2 yeastcyc_id: ACETOLACTSYN-RXN - ec: - 1.1.1.- genes: - *id427 left: - NAD+ - acetoin name: acetoin + NAD+ <- diacetyl + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - diacetyl yeastcyc_id: ACETOINDEHYDROG-RXN - ec: - 4.1.1.1 genes: - *id164 - *id165 - *id166 left: - H+ - pyruvate name: pyruvate + H+ -> acetaldehyde + CO2 pmids: - '9123965' rhea: [] right: - CO2 - acetaldehyde yeastcyc_id: RXN-6161 - ec: [] genes: - *id164 - *id165 - *id166 left: - H+ - acetaldehyde - pyruvate name: pyruvate + acetaldehyde + H+ -> acetoin + CO2 pmids: - '6383467' rhea: [] right: - CO2 - acetoin yeastcyc_id: RXN0-2022 yeastcyc_id: PWY3O-981 PWYQT-4432: all_genes: - *id357 - *id358 comment: 'The tripeptide glutathione (GSH: L-γ-glutamyl-L-cysteinylglycine) is a prevalent intracellular thiol that is able to act as a cellular redox buffer due to its low redox potential (as reviewed in |CITS: [12702279]|). GSH is involved in many biological processes including: protein and DNA synthesis; amino acid transport; enzyme regulation; protection of cells against reactive oxygen compounds and free radicals, xenobiotics and heavy metals (as reviewed in |CITS: [12702279]|). GSH can also be used as a source of sulfur and cysteine in |CITS: [1674526], [10514563]|. Although GSH biosynthesis is well characterized in yeast, the pathway(s) of GSH degradation are not yet fully characterized. Plants and animals are known to metabolize GSH via the γ-glutamyl cycle, but the presence of this complete cycle in yeast and other microorganisms is still open to debate |CITS: [5076], [JASPERS85]|. Saccharomyces cerevisiae is believed to hydrolyze GSH to its constitutive amino acids glutamate, cysteine and glycine in two steps catalyzed by the vacuolar-membrane-bound enzymes, γ-glutamyl transpeptidase (Ecm38p) and cysteinylglycine dipeptidase (CGase), respectively |CITS: [JASPERS85], [6143574], [11672438]|. Ecm38p catalyzes the cleavage and transfer of the γ-glutamyl moiety from GSH to an acceptor amino acid (or its hydrolysis to glutamate) and the release of cysteinylglycine |CITS: [JASPERS85]|. Cellular levels of Ecm38p are low in the presence of ammonium ions as the sole nitrogen source, but they are increased in the presence of other nitrogen sources, such as amino acids and urea |CITS: [6102906]|. Ecm38p production is derepressed during nitrogen starvation |CITS: [9202464]|. CGase is proposed to hydrolyze the cysteinylglycine to the amino acids cysteine and glycine. Although enzymatic activity for CGase was observed in S. cerevisiae |CITS: [JASPERS85]|, the open reading frame for CGase has yet to be identified in S. cerevisiae. S. cerevisiae also has been proposed to have an alternative pathway for degrading GSH that involves a novel GSH degradosomal protein complex comprised of the three gene products Dug1p, Dug2p, and Dug3p |CITS: [17179087]|. ' name: glutathione degradation pmids: - '11169096' - '12620619' reactions: - ec: - 3.4.13.18 genes: - *id357 left: - H2O - L-cysteinylglycine name: L-cysteinylglycine + H2O -> L-cysteine + glycine pmids: - '19346245' rhea: [] right: - L-cysteine - glycine yeastcyc_id: RXN-6622 - ec: - 2.3.2.2 genes: - *id358 left: - a proteinogenic amino acid - glutathione name: glutathione + a proteinogenic amino acid -> an α-(γ-L-glutamyl)-L-amino acid + L-cysteinylglycine pmids: [] rhea: [] right: - L-cysteinylglycine - an α-(γ-L-glutamyl)-L-amino acid yeastcyc_id: RXN-6601 yeastcyc_id: PWYQT-4432 PYRIMID-RNTSYN-PWY: all_genes: - *id049 - *id050 - *id300 - *id310 - *id051 - *id309 - *id299 - *id311 - *id301 - *id307 - *id308 comment: 'Purine and pyrimidine nucleotides serve many diverse and essential roles in the cell. They are precursors to DNA, RNA, and many important metabolites (e.g. CDP-diacylglycerol). In addition, nucleotides can be used as an energy source (primarily as ATP), signaling molecules, and cofactor components (e.g. coenzyme A). In S. cerevisiae, the initial steps of de novo pyrimidine biosynthesis are catalyzed by the bifunctional carbamoylphosphate synthetase/aspartate transcarbamylase Ura2p. In the first step, Ura2p catalyzes the synthesis of carbamoylphosphate from CO2, ATP, and glutamine. In the second, Ura2p condenses carbamoylphosphate with aspartate to yield ureidosuccinate/carbamoyl-L-aspartate. Third, dihydroorotase (Ura4p) catalyzes closure of the pyrimidine ring of ureidosuccinate to form dihydroorotate (DHO). DHO, in turn, is oxidized to orotic acid (OA), condensed with phosphoribosyl pyrophosphate to form orotidine 5-monophosphate, and finally decarboxylated to yield UMP. These three steps are catalyzed by Ura1p, Ura5p/Ura10p, and Ura3p, respectively. UMP may then undergo further processing to form other pyrimidines. The de novo pyrimidine pathway is regulated at both the enzymatic and transcriptional levels. Ura2p, which catalyzes the first committed step of the pathway, is subject to end product feedback inhibition by UTP. Transcription of URA2 is repressed by UTP and uracil. Furthermore, transcription of URA2 and several other genes in the pathway is upregulated in response to pyrimidine starvation. Upregulation of URA1, URA3, and URA4 during pyrimidine starvation depends upon the zinc finger transcription factor Ppr1p. Two intermediates in the pyrimidine pathway regulate the transcriptional activity of Ppr1p: DHO and OA. At low concentrations, these intermediates convert Ppr1p into its active state, resulting in transcription of URA genes. High concentrations of DHO and OA, however, inhibit Ppr1p activity in vitro. References: |CITS:[22419079]||CITS: [(JONES]||CITS: [2283036]||CITS: [9858611]|' name: de novo biosynthesis of pyrimidine ribonucleotides pmids: - '22419079' - '2283036' - '9485596' - '9858611' reactions: - ec: - 3.5.2.3 genes: - *id299 left: - (S)-dihydroorotate - H2O name: (S)-dihydroorotate + H2O <-> N-carbamoyl-L-aspartate + H+ pmids: [] rhea: [] right: - H+ - N-carbamoyl-L-aspartate yeastcyc_id: DIHYDROOROT-RXN - ec: - 1.3.5.2 genes: - *id300 left: - (S)-dihydroorotate - an electron-transfer quinone name: (S)-dihydroorotate + an electron-transfer quinone[inner membrane] -> orotate + an electron-transfer quinol[inner membrane] pmids: [] rhea: [] right: - an electron-transfer quinol - orotate yeastcyc_id: DIHYDROOROTATE-DEHYDROGENASE-RXN - ec: - 6.3.5.5 genes: - *id049 - *id050 - *id051 left: - ATP - H2O - L-glutamine - hydrogencarbonate name: 2 ATP + L-glutamine + hydrogencarbonate + H2O -> L-glutamate + carbamoyl phosphate + 2 ADP + phosphate + 2 H+ pmids: - '8626695' rhea: [] right: - ADP - H+ - L-glutamate - carbamoyl phosphate - phosphate yeastcyc_id: CARBPSYN-RXN - ec: - 2.7.4.14 - 2.7.4.22 - 2.7.4.4 genes: - *id301 left: - ATP - UMP name: ATP + UMP -> ADP + UDP pmids: [] rhea: [] right: - ADP - UDP yeastcyc_id: RXN-12002 - ec: - 2.1.3.2 genes: - *id051 left: - L-aspartate - carbamoyl phosphate name: L-aspartate + carbamoyl phosphate <-> N-carbamoyl-L-aspartate + phosphate + H+ pmids: [] rhea: [] right: - H+ - N-carbamoyl-L-aspartate - phosphate yeastcyc_id: ASPCARBTRANS-RXN - ec: - 6.3.4.2 genes: - *id307 - *id308 left: - ATP - H2O - L-glutamine - UTP name: L-glutamine + UTP + ATP + H2O -> ADP + CTP + L-glutamate + phosphate + 2 H+ pmids: [] rhea: [] right: - ADP - CTP - H+ - L-glutamate - phosphate yeastcyc_id: CTPSYN-RXN - ec: - 2.7.4.6 genes: [] left: - ATP - UDP name: UDP + ATP -> UTP + ADP pmids: [] rhea: [] right: - ADP - UTP yeastcyc_id: UDPKIN-RXN - ec: - 4.1.1.23 genes: - *id309 left: - H+ - orotidine 5'-phosphate name: orotidine 5'-phosphate + H+ -> CO2 + UMP pmids: [] rhea: [] right: - CO2 - UMP yeastcyc_id: OROTPDECARB-RXN - ec: - 2.4.2.10 genes: - *id310 - *id311 left: - diphosphate - orotidine 5'-phosphate name: orotidine 5'-phosphate + diphosphate <-> 5-phospho-α-D-ribose 1-diphosphate + orotate pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - orotate yeastcyc_id: OROPRIBTRANS-RXN yeastcyc_id: PYRIMID-RNTSYN-PWY PYRUVDEHYD-PWY: all_genes: - &id480 orf: YNL071W symbol: LAT1 uniprot: UniProtKB:P12695 - *id034 - &id481 orf: YER178W symbol: PDA1 uniprot: UniProtKB:P16387 - &id482 orf: YBR221C symbol: PDB1 uniprot: UniProtKB:P32473 comment: 'The overall conversion of pyruvate to acetyl-CoA is catalyzed by the multienzyme pyruvate dehydrogenase complex. The pyruvate dehydrogenase complex is composed of: pyruvate dehydrogenase (E1α subunit (Pda1p) and E1β subunit (Pdb1p)), dihydrolipoyllysine-residue acetyltransferase (E2 subunit (Lat1p)), and dihydrolipoyl dehydrogenase (E3 subunit (Lpd1p)). A fifth subunit (Protein X (Pdx1p)) of the pyruvate dehydrogenase complex links Lat1p to Lpd1p.' name: pyruvate decarboxylation to acetyl CoA pmids: - '9123965' reactions: - ec: - 1.8.1.4 genes: - *id034 left: - NAD+ - a [pyruvate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine name: a [pyruvate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine + NAD+ -> a [pyruvate dehydrogenase E2 protein] N6-lipoyl-L-lysine + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - a [pyruvate dehydrogenase E2 protein] N6-lipoyl-L-lysine yeastcyc_id: RXN0-1132 - ec: - 2.3.1.12 genes: - *id480 left: - a [pyruvate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine - acetyl-CoA name: acetyl-CoA + a [pyruvate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine <- a [pyruvate dehydrogenase E2 protein] N6-S-acetyldihydrolipoyl-L-lysine + coenzyme A pmids: [] rhea: [] right: - a [pyruvate dehydrogenase E2 protein] N6-S-acetyldihydrolipoyl-L-lysine - coenzyme A yeastcyc_id: RXN0-1133 - ec: - 1.2.4.1 genes: - *id481 - *id482 left: - H+ - a [pyruvate dehydrogenase E2 protein] N6-lipoyl-L-lysine - pyruvate name: pyruvate + a [pyruvate dehydrogenase E2 protein] N6-lipoyl-L-lysine + H+ -> a [pyruvate dehydrogenase E2 protein] N6-S-acetyldihydrolipoyl-L-lysine + CO2 pmids: - '9123965' rhea: [] right: - CO2 - a [pyruvate dehydrogenase E2 protein] N6-S-acetyldihydrolipoyl-L-lysine yeastcyc_id: RXN0-1134 yeastcyc_id: PYRUVDEHYD-PWY SAM-PWY: all_genes: - *id320 - *id321 name: S-adenosyl-L-methionine biosynthesis pmids: - '9409150' reactions: - ec: - 2.5.1.6 genes: - *id320 - *id321 left: - ATP - H2O - L-methionine name: ATP + L-methionine + H2O -> S-adenosyl-L-methionine + phosphate + diphosphate pmids: [] rhea: [] right: - S-adenosyl-L-methionine - diphosphate - phosphate yeastcyc_id: S-ADENMETSYN-RXN yeastcyc_id: SAM-PWY SERDEG-PWY: all_genes: [] name: L-serine degradation pmids: - '1628804' reactions: - ec: [] genes: [] left: - 2-aminoprop-2-enoate name: 2-aminoprop-2-enoate -> 2-iminopropanoate pmids: [] rhea: [] right: - 2-iminopropanoate yeastcyc_id: RXN-15124 - ec: - 3.5.99.10 genes: [] left: - 2-iminopropanoate - H2O name: 2-iminopropanoate + H2O -> pyruvate + ammonium pmids: [] rhea: [] right: - ammonium - pyruvate yeastcyc_id: RXN-15127 - ec: [] genes: [] left: - L-serine name: L-serine -> 2-aminoprop-2-enoate + H2O pmids: [] rhea: [] right: - 2-aminoprop-2-enoate - H2O yeastcyc_id: RXN-15125 yeastcyc_id: SERDEG-PWY SERSYN-PWY: all_genes: - *id428 - *id431 - *id429 - *id430 name: L-serine biosynthesis I pmids: - '12525494' reactions: - ec: - 2.6.1.52 genes: - *id428 left: - 2-oxoglutarate - 3-phospho-L-serine name: 2-oxoglutarate + 3-phospho-L-serine <- 3-phosphooxypyruvate + L-glutamate pmids: [] rhea: [] right: - 3-phosphooxypyruvate - L-glutamate yeastcyc_id: PSERTRANSAM-RXN - ec: - 1.1.1.95 genes: - *id429 - *id430 left: - 3-phospho-D-glycerate - NAD+ name: 3-phospho-D-glycerate + NAD+ <-> 3-phosphooxypyruvate + NADH + H+ pmids: [] rhea: [] right: - 3-phosphooxypyruvate - H+ - NADH yeastcyc_id: PGLYCDEHYDROG-RXN - ec: - 3.1.3.3 genes: - *id431 left: - 3-phospho-L-serine - H2O name: 3-phospho-L-serine + H2O -> L-serine + phosphate pmids: [] rhea: [] right: - L-serine - phosphate yeastcyc_id: RXN0-5114 yeastcyc_id: SERSYN-PWY SO4ASSIM-PWY: all_genes: - *id340 - *id332 - *id339 - *id333 - *id341 name: assimilatory sulfate reduction I pmids: [] reactions: - ec: - 1.8.4.8 genes: - *id339 left: - H+ - adenosine 3',5'-bisphosphate - an oxidized thioredoxin - sulfite name: adenosine 3',5'-bisphosphate + sulfite + an oxidized thioredoxin + 2 H+ <-> 3'-phosphoadenylyl-sulfate + a reduced thioredoxin pmids: - '3060034' rhea: [] right: - 3'-phosphoadenylyl-sulfate - a reduced thioredoxin yeastcyc_id: 1.8.4.8-RXN - ec: - 2.7.1.25 genes: - *id332 left: - ATP - adenosine 5'-phosphosulfate name: adenosine 5'-phosphosulfate + ATP <-> 3'-phosphoadenylyl-sulfate + ADP + H+ pmids: [] rhea: [] right: - 3'-phosphoadenylyl-sulfate - ADP - H+ yeastcyc_id: ADENYLYLSULFKIN-RXN - ec: - 1.8.1.2 genes: - *id340 - *id341 left: - H2O - NADP+ - hydrogen sulfide name: hydrogen sulfide + 3 NADP+ + 3 H2O <- sulfite + 3 NADPH + 5 H+ pmids: [] rhea: [] right: - H+ - NADPH - sulfite yeastcyc_id: SULFITE-REDUCT-RXN - ec: - 2.7.7.4 genes: - *id333 left: - ATP - H+ - sulfate name: sulfate + ATP + H+ <-> adenosine 5'-phosphosulfate + diphosphate pmids: [] rhea: [] right: - adenosine 5'-phosphosulfate - diphosphate yeastcyc_id: SULFATE-ADENYLYLTRANS-RXN yeastcyc_id: SO4ASSIM-PWY SPHINGOLIPID-SYN-PWY-1: all_genes: - &id491 orf: YKL004W symbol: AUR1 uniprot: UniProtKB:P36107 - &id494 orf: YBR036C symbol: CSG2 uniprot: UniProtKB:P35206 - &id501 orf: YDR294C symbol: DPL1 uniprot: UniProtKB:Q05567 - &id492 orf: YDR072C symbol: IPT1 uniprot: UniProtKB:P38954 - &id496 orf: YKL008C symbol: LAC1 uniprot: UniProtKB:P28496 - &id497 orf: YHL003C symbol: LAG1 uniprot: UniProtKB:P38703 - &id487 orf: YMR296C symbol: LCB1 uniprot: UniProtKB:P25045 - &id488 orf: YDR062W symbol: LCB2 uniprot: UniProtKB:P40970 - &id499 orf: YJL134W symbol: LCB3 uniprot: UniProtKB:P47013 - &id484 orf: YOR171C symbol: LCB4 uniprot: UniProtKB:Q12246 - &id485 orf: YLR260W symbol: LCB5 uniprot: UniProtKB:Q06147 - &id498 orf: YMR298W symbol: LIP1 uniprot: UniProtKB:Q03579 - &id493 orf: YMR272C symbol: SCS7 uniprot: UniProtKB:Q03529 - &id495 orf: YPL057C symbol: SUR1 uniprot: UniProtKB:P33300 - &id483 orf: YDR297W symbol: SUR2 uniprot: UniProtKB:P38992 - &id486 orf: YBR265W symbol: TSC10 uniprot: UniProtKB:P38342 - &id489 orf: YPL087W symbol: YDC1 uniprot: UniProtKB:Q02896 - &id490 orf: YBR183W symbol: YPC1 uniprot: UniProtKB:P38298 - &id500 orf: YKR053C symbol: YSR3 uniprot: UniProtKB:P23501 comment: 'Sphingolipids are essential components of the plasma membrane in all eukaryotic cells. S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide (IPC), mannose-inositol-phosphoceramide (MIPC), and mannose-(inositol phosphate)2-ceramide (M(IP)2C)|CITS: [12069845]|. In the yeast plasma membrane sphingolipids concentrate with ergosterol to form lipid rafts, specialized membrane microdomains implicated in a variety of cellular processes, including sorting of membrane proteins and lipids, as well as organizing and regulating signaling cascades |CITS: [12452424]|. Intermediates in sphingolipid biosynthesis have been shown to play important roles as signaling molecules and growth regulators. Sphingolipid long chain bases (LCBs), dihydrosphingosine (DHS) and phytosphingosine (PHS), have been implicated as secondary messengers in signaling pathways that regulate heat stress response |CITS: [9405471]||CITS: [11967828]|. Other intermediates, phytoceramide and long-chain base phosphates (LCBPs), have been shown to be components of the tightly-controlled ceramide/LCBP rheostat, which regulates cell growth |CITS: [12684378]|. Since phosphoinositol-containing sphingolipids are unique to fungi, the sphingolipid biosynthesis pathway is considered a target for antifungal drugs |CITS: [9092515]||CITS: [15578972]|.' name: sphingolipid biosynthesis (yeast) pmids: - '11113186' - '12034738' - '12069845' - '15692566' reactions: - ec: - 1.14.18.5 genes: - *id483 left: - D-erythro-sphinganine - H+ - a ferrocytochrome b5 - oxygen name: D-erythro-sphinganine + 2 a ferrocytochrome b5 + oxygen + 2 H+ -> phytosphingosine + 2 a ferricytochrome b5 + H2O pmids: [] rhea: [] right: - H2O - a ferricytochrome b5 - phytosphingosine yeastcyc_id: RXN3O-1380 - ec: - 2.7.1.91 genes: - *id484 - *id485 left: - ATP - D-erythro-sphinganine name: D-erythro-sphinganine + ATP -> sphinganine 1-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - sphinganine 1-phosphate yeastcyc_id: SPHINGANINE-KINASE-RXN - ec: - 1.1.1.102 genes: - *id486 left: - D-erythro-sphinganine - NADP+ name: D-erythro-sphinganine + NADP+ <- 3-dehydrosphinganine + NADPH + H+ pmids: [] rhea: [] right: - 3-dehydrosphinganine - H+ - NADPH yeastcyc_id: 3-DEHYDROSPHINGANINE-REDUCTASE-RXN - ec: - 2.3.1.50 genes: - *id487 - *id488 left: - H+ - L-serine - palmitoyl-CoA name: L-serine + palmitoyl-CoA + H+ -> CO2 + 3-dehydrosphinganine + coenzyme A pmids: [] rhea: [] right: - 3-dehydrosphinganine - CO2 - coenzyme A yeastcyc_id: SERINE-C-PALMITOYLTRANSFERASE-RXN - ec: - 3.5.1.23 genes: - *id489 - *id490 left: - H2O - a (2'R)-2'-hydroxy-phytoceramide name: a (2'R)-2'-hydroxy-phytoceramide + H2O <-> phytosphingosine + a 2-hydroxy fatty acid pmids: [] rhea: [] right: - a 2-hydroxy fatty acid - phytosphingosine yeastcyc_id: CERAMIDASE-YEAST-RXN - ec: - 2.7.1.- genes: - *id491 left: - a (2'R)-2'-hydroxy-phytoceramide - a 1-phosphatidyl-1D-myo-inositol name: a (2'R)-2'-hydroxy-phytoceramide + a 1-phosphatidyl-1D-myo-inositol -> an inositol-phospho-α hydroxyphytoceramide + a 1,2-diacyl-sn-glycerol pmids: [] rhea: [] right: - a 1,2-diacyl-sn-glycerol - an inositol-phospho-α hydroxyphytoceramide yeastcyc_id: RXN3O-581 - ec: - 2.7.1.- genes: - *id492 left: - a 1-phosphatidyl-1D-myo-inositol - a mannosyl-inositol-phospho-α hydroxyphytoceramide name: a mannosyl-inositol-phospho-α hydroxyphytoceramide + a 1-phosphatidyl-1D-myo-inositol -> a mannosyl-diphosphoinositol-α hydroxyphytoceramide + a 1,2-diacyl-sn-glycerol pmids: [] rhea: [] right: - a 1,2-diacyl-sn-glycerol - a mannosyl-diphosphoinositol-α hydroxyphytoceramide yeastcyc_id: RXN3O-680 - ec: - 1.14.18.6 genes: - *id493 left: - H+ - a ferrocytochrome b5 - a phytoceramide - oxygen name: a phytoceramide + 2 a ferrocytochrome b5 + oxygen + 2 H+ -> a (2'R)-2'-hydroxy-phytoceramide + 2 a ferricytochrome b5 + H2O pmids: [] rhea: [] right: - H2O - a (2'R)-2'-hydroxy-phytoceramide - a ferricytochrome b5 yeastcyc_id: RXN3O-4042 - ec: - 2.4.1.- genes: - *id494 - *id495 left: - GDP-α-D-mannose - an inositol-phospho-α hydroxyphytoceramide name: an inositol-phospho-α hydroxyphytoceramide + GDP-α-D-mannose -> a mannosyl-inositol-phospho-α hydroxyphytoceramide + GDP + H+ pmids: [] rhea: [] right: - GDP - H+ - a mannosyl-inositol-phospho-α hydroxyphytoceramide yeastcyc_id: RXN3O-663 - ec: - 2.7.1.91 genes: - *id484 - *id485 left: - ATP - phytosphingosine name: phytosphingosine + ATP -> phytosphingosine 1-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - phytosphingosine 1-phosphate yeastcyc_id: RXN3O-458 - ec: - 2.3.1.24 genes: - *id496 - *id497 - *id498 left: - a very long chain fatty acyl-CoA - phytosphingosine name: phytosphingosine + a very long chain fatty acyl-CoA -> a phytoceramide + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - a phytoceramide - coenzyme A yeastcyc_id: RXN3O-328 - ec: - 3.1.3.- genes: - *id499 - *id500 left: - H2O - phytosphingosine 1-phosphate name: phytosphingosine 1-phosphate + H2O -> phytosphingosine + phosphate pmids: [] rhea: [] right: - phosphate - phytosphingosine yeastcyc_id: RXN3O-504 - ec: - 4.1.2.27 genes: - *id501 left: - sphinganine 1-phosphate name: sphinganine 1-phosphate -> palmitaldehyde + O-phosphoethanolamine pmids: [] rhea: [] right: - O-phosphoethanolamine - palmitaldehyde yeastcyc_id: SPHINGANINE-1-PHOSPHATE-ALDOLASE-RXN - ec: - 3.1.3.- genes: - *id499 - *id500 left: - H2O - sphinganine 1-phosphate name: sphinganine 1-phosphate + H2O -> D-erythro-sphinganine + phosphate pmids: [] rhea: [] right: - D-erythro-sphinganine - phosphate yeastcyc_id: DHS-PHOSPHATASE-RXN yeastcyc_id: SPHINGOLIPID-SYN-PWY-1 SUCUTIL-PWY-2: all_genes: - &id502 orf: YIL162W symbol: SUC2 uniprot: UniProtKB:P00724 name: sucrose degradation pmids: - '9467897' reactions: - ec: - 3.2.1.26 genes: - *id502 left: - H2O - sucrose name: sucrose + H2O -> β-D-glucopyranose + D-fructose pmids: [] rhea: [] right: - D-fructose - β-D-glucopyranose yeastcyc_id: RXN3O-9807 yeastcyc_id: SUCUTIL-PWY-2 TCA-EUK-PWY: all_genes: - *id208 - *id209 - *id210 - *id211 - *id212 - *id475 - *id476 - *id477 - *id328 - *id329 - *id034 - *id478 - *id479 - *id170 - *id171 - *id172 - *id068 - *id069 - *id401 - *id402 - *id403 - *id404 - *id405 comment: Eukaryotes have both NADP(+)-dependent isocitrate dehydrogenases (EC 1.1.1.42) and NAD(+)-dependent isocitrate dehydrogenases (EC 1.1.1.41). It has been shown that NAD(+)-IDH is involved in respiration while NADP(+)-IDH is involved in glutamate biosynthesis. name: TCA cycle, aerobic respiration pmids: - '12855708' - '8099357' - '9395469' reactions: - ec: - 4.2.1.2 genes: - *id475 left: - (S)-malate name: (S)-malate <- fumarate + H2O pmids: [] rhea: [] right: - H2O - fumarate yeastcyc_id: FUMHYDR-RXN - ec: - 1.1.1.37 genes: - *id170 - *id171 - *id172 left: - (S)-malate - NAD+ name: (S)-malate + NAD+ <-> oxaloacetate + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - oxaloacetate yeastcyc_id: MALATE-DEH-RXN - ec: - 1.2.1.- genes: - *id328 - *id329 - *id034 left: - 2-oxoglutarate - NAD+ - coenzyme A name: 2-oxoglutarate + coenzyme A + NAD+ -> succinyl-CoA + CO2 + NADH pmids: [] rhea: [] right: - CO2 - NADH - succinyl-CoA yeastcyc_id: 2OXOGLUTARATEDEH-RXN - ec: - 1.1.1.286 - 1.1.1.41 genes: - *id476 - *id477 left: - D-threo-isocitrate - NAD+ name: D-threo-isocitrate + NAD+ -> 2-oxoglutarate + CO2 + NADH pmids: [] rhea: [] right: - 2-oxoglutarate - CO2 - NADH yeastcyc_id: ISOCITRATE-DEHYDROGENASE-NAD+-RXN - ec: [] genes: - *id208 left: - H2O - cis-aconitate name: cis-aconitate + H2O <-> D-threo-isocitrate pmids: [] rhea: [] right: - D-threo-isocitrate yeastcyc_id: ACONITATEHYDR-RXN - ec: [] genes: - *id208 - *id209 left: - citrate name: citrate <-> cis-aconitate + H2O pmids: [] rhea: [] right: - H2O - cis-aconitate yeastcyc_id: ACONITATEDEHYDR-RXN - ec: - 6.4.1.1 genes: - *id068 - *id069 left: - ATP - hydrogencarbonate - pyruvate name: hydrogencarbonate + pyruvate + ATP -> oxaloacetate + ADP + phosphate + H+ pmids: [] rhea: [] right: - ADP - H+ - oxaloacetate - phosphate yeastcyc_id: PYRUVATE-CARBOXYLASE-RXN - ec: - 2.3.3.1 - 2.3.3.16 genes: - *id210 - *id211 - *id212 left: - H2O - acetyl-CoA - oxaloacetate name: oxaloacetate + acetyl-CoA + H2O -> citrate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - citrate - coenzyme A yeastcyc_id: CITSYN-RXN - ec: - 6.2.1.5 genes: - *id478 - *id479 left: - ATP - coenzyme A - succinate name: succinate + ATP + coenzyme A <-> succinyl-CoA + ADP + phosphate pmids: [] rhea: [] right: - ADP - phosphate - succinyl-CoA yeastcyc_id: SUCCCOASYN-RXN - ec: - 1.3.5.1 genes: - *id401 - *id402 - *id403 - *id404 - *id405 left: - a ubiquinone - succinate name: succinate[inner membrane] + a ubiquinone[inner membrane] -> fumarate[inner membrane] + an ubiquinol[inner membrane] pmids: [] rhea: [] right: - an ubiquinol - fumarate yeastcyc_id: SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN yeastcyc_id: TCA-EUK-PWY THIOREDOX-PWY: all_genes: - &id503 orf: YDR353W symbol: TRR1 uniprot: UniProtKB:P29509 - &id504 orf: YHR106W symbol: TRR2 uniprot: UniProtKB:P38816 comment: 'The thioredoxin and glutathione/glutaredoxin systems help maintain the reduced environment of the cell and play a significant role in defending the cell against oxidative stress. They also have been proposed to play a role in the biosynthesis of purines and pyrimidines as required for DNA synthesis, protein folding and regulation, and sulfur metabolism |CITS:[11169096],[2668278]|. Thioredoxins and glutaredoxins are small heat-stable proteins with redox-active cysteines that facilitate the reduction of other proteins by catalyzing cysteine thiol-disulfide exchange reactions |CITS:[2668278]|. Thioredoxins contain two conserved cysteines that exist in either a reduced form as in thioredoxin-(SH)2 or in an oxidized form as in thioredoxin-S2 when they form an intramolecular disulfide bridge |CITS:[2668278]|. Thioredoxins donate electrons from their active center dithiol to protein disulfide bonds (Protein-S2) that are then reduced to dithiols (Protein-(SH)2). The resulting oxidized thioredoxin disulfide is reduced directly by thioredoxin reductase with electrons donated by NADPH |CITS:[2668278]|. Hence the thioredoxin reduction system consists of thioredoxin, thioredoxin reductase, and NADPH. Oxidized glutaredoxins, on the other hand, are reduced by the tripeptide glutathione (gamma-Glu-Cys-Gly, known as GSH) using electrons donated by NADPH |CITS:[2668278]|. Hence the glutathione/glutaredoxin system consists of glutaredoxin, glutathione, glutathione reductase and NADPH. S. cerevisiae contains a cytoplasmic thioredoxin system comprised of the thioredoxins Trx1p and Trx2p and the thioredoxin reductase Trr1p, and a complete mitochondrial thioredoxin system comprised of the thioredoxin Trx3p and the thioredoxin reductase Trr2p |CITS:[15701801]|. Evidence suggests that the cytoplasmic thioredoxin system may have overlapping function with the glutathione/glutaredoxin system |CITS:[8930901], [10844700]|. The mitochondrial thioredoxin system, on the other hand, does not appear to be able to substitute for either the cytoplasmic thioredoxin or glutathione/glutaredoxin systems |CITS:[10844700]|. Instead, the mitochondrial thioredoxn proteins, thioredoxin (Trx3p) and thioredoxin reductase (Trr2p) have been implicated in the defense against oxidative stress generated during respiratory metabolism |CITS:[10037727]|. The two cytoplasmic thioredoxins (Trx1p and Trx2p) are believed to supply reducing equivalents to the enzymes ribonucleotide reductase (Rnr1p, Rnr2p, Rnr3p, Rnr4p) and 3''-phosphoadenosine 5''-phosphosulfate (PAPS) reductase (Met16p) |CITS:[4392601],[5442277]|. Deletion of either TRX1 or TRX2 has no effect on cell growth or morphology |CITS:[2026619]|, but, deletion of both genes affects the cell cycle, and makes the cells auxotrophic for methionine/cysteine |CITS:[2026619],[7929110]|. Deletion of the single gene TRX2 does result in extreme sensitivity to H2O2 and is thereby believed to be involved in the response against H2O2 |CITS:[8313910]|. The expression of TRX2 and TRR1 are regulated by the transcription factors Yap1p and Skn7p in response to H2O2 |CITS:[8313910],[9118942]|. ' name: thioredoxin pathway pmids: - '10037727' - '11169096' - '13785690' - '2668278' - '4392601' - '5442277' reactions: - ec: - 1.8.1.9 genes: - *id503 - *id504 left: - NADP+ - a reduced thioredoxin name: a reduced thioredoxin + NADP+ <- an oxidized thioredoxin + NADPH + H+ pmids: [] rhea: [] right: - H+ - NADPH - an oxidized thioredoxin yeastcyc_id: THIOREDOXIN-REDUCT-NADPH-RXN - ec: [] genes: [] left: - a reduced electron acceptor - an oxidized thioredoxin name: an oxidized thioredoxin + a reduced electron acceptor <- a reduced thioredoxin + an oxidized electron acceptor pmids: [] rhea: [] right: - a reduced thioredoxin - an oxidized electron acceptor yeastcyc_id: THIOREDOXIN-RXN yeastcyc_id: THIOREDOX-PWY THREOCAT2-PWY: all_genes: - &id505 orf: YCL064C symbol: CHA1 uniprot: UniProtKB:P25379 - *id084 comment: 'Threonine degradation can occur via several routes in the budding yeast S. cerevisiae. In the first route, threonine is deaminated to produce ammonia and -ketobutyrate. This reaction is catalyzed by the so-called ""catabolic threonine (and serine) deaminase Cha1p or the biosynthetic threonine deaminase Ilv1p. Cha1p enables S. cerevisiae to produce ammonia from the catabolism of serine or threonine, consequently enabling the use of either amino acid as a sole source of nitrogen. In contrast, Ilv1p is thought to serve a mainly biosynthetic role by degrading threonine to -ketobutyrate, the initial substrate for isoleucine biosynthesis. CHA1 is transcriptionally induced by serine and threonine, whereas ILV1 is regulated by general control of amino acid biosynthesis. The second route of threonine degradation occurs via threonine aldolase, encoded by GLY1 in S. cerevisiae. Threonine aldolase directly cleaves threonine to form glycine and acetaldehyde. Disruption of GLY1 leads to strongly reduced growth in minimal media lacking glycine, suggesting that threonine catabolism via threonine aldolase is the major source of glycine in S. cerevisiae. The third, putative route of threonine degradation in S. cerevisiae is the NAD-dependent oxidation of threonine to 2-amino-3-oxobutanoate. In many organisms, this reaction is catalyzed by threonine dehydrogenase (TDH). The existence of this enzyme in S. cerevisiae is uncertain, however low levels of TDH activity have been reported in one study (see Murata et al., 1986). S. cerevisiae also lacks 2-amino-3-ketobutyrate CoA ligase (KBL), the enzyme responsible for converting the product of TDH (2-amino-3-oxobutanoate) to glycine. Because 2-amino-3-oxobutanoate is unstable, the fate of this product in S. cerevisiae is presumed to be spontaneous decarboxylation to aminoacetate. References: |CITS:[2841185]||CITS: [3289762]||CITS: [8132653]||CITS: [3086094]||CITS: [3117785]|' name: threonine degradation pmids: - '1628804' - '2841185' - '3086094' - '3117785' - '3289762' - '8132653' reactions: - ec: - 1.1.1.75 genes: [] left: - (R)-1-aminopropan-2-ol - NAD+ name: (R)-1-aminopropan-2-ol + NAD+ <- aminoacetone + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - aminoacetone yeastcyc_id: AMINOPROPDEHYDROG-RXN - ec: - 2.3.1.- genes: [] left: - 2-oxobutanoate - coenzyme A name: 2-oxobutanoate + coenzyme A -> propanoyl-CoA + formate pmids: [] rhea: [] right: - formate - propanoyl-CoA yeastcyc_id: KETOBUTFORMLY-RXN - ec: - 2.7.2.15 genes: [] left: - ATP - propanoate name: ATP + propanoate <- ADP + propanoyl phosphate pmids: [] rhea: [] right: - ADP - propanoyl phosphate yeastcyc_id: PROPKIN-RXN - ec: [] genes: [] left: - H+ - L-2-amino-3-oxobutanoate name: L-2-amino-3-oxobutanoate + H+ -> aminoacetone + CO2 pmids: [] rhea: [] right: - CO2 - aminoacetone yeastcyc_id: THREOSPON-RXN - ec: - 4.4.1.1 genes: - *id084 left: - H2O - L-cystathionine name: L-cystathionine + H2O <-> 2-oxobutanoate + L-cysteine + ammonia pmids: [] rhea: [] right: - 2-oxobutanoate - L-cysteine - ammonia yeastcyc_id: CYSTAGLY-RXN - ec: - 4.4.1.1 genes: [] left: - L-homoserine name: L-homoserine <-> 2-oxobutanoate + ammonium pmids: [] rhea: [] right: - 2-oxobutanoate - ammonium yeastcyc_id: HOMOSERDEAM-RXN - ec: - 4.3.1.19 genes: - *id505 left: - H2O - L-threonine name: L-threonine + H2O -> 2-oxobutanoate + ammonia + H2O pmids: [] rhea: [] right: - 2-oxobutanoate - H2O - ammonia yeastcyc_id: THREDEHYD2-RXN - ec: - 1.1.1.103 genes: [] left: - L-threonine - NAD+ name: L-threonine + NAD+ -> L-2-amino-3-oxobutanoate + NADH + H+ pmids: [] rhea: [] right: - H+ - L-2-amino-3-oxobutanoate - NADH yeastcyc_id: THREODEHYD-RXN - ec: - 4.3.1.- genes: [] left: - H2O - O-succinyl-L-homoserine name: O-succinyl-L-homoserine + H2O <-> 2-oxobutanoate + succinate + ammonium + H+ pmids: [] rhea: [] right: - 2-oxobutanoate - H+ - ammonium - succinate yeastcyc_id: METBALT-RXN - ec: - 1.4.3.21 genes: [] left: - H2O - aminoacetone - oxygen name: aminoacetone + H2O + oxygen -> methylglyoxal + ammonium + hydrogen peroxide pmids: [] rhea: [] right: - ammonium - hydrogen peroxide - methylglyoxal yeastcyc_id: AMACETOXID-RXN - ec: - 2.3.1.29 genes: [] left: - acetyl-CoA - glycine name: glycine + acetyl-CoA <-> L-2-amino-3-oxobutanoate + coenzyme A pmids: [] rhea: [] right: - L-2-amino-3-oxobutanoate - coenzyme A yeastcyc_id: AKBLIG-RXN - ec: - 2.3.1.222 genes: [] left: - phosphate - propanoyl-CoA name: propanoyl-CoA + phosphate -> propanoyl phosphate + coenzyme A pmids: [] rhea: [] right: - coenzyme A - propanoyl phosphate yeastcyc_id: PTAALT-RXN yeastcyc_id: THREOCAT2-PWY THRESYN-PWY: all_genes: - *id059 - *id060 - *id232 - *id231 - *id233 - *id229 - *id230 name: superpathway of L-threonine biosynthesis pmids: - '2176637' - '8082795' reactions: - ec: - 2.6.1.1 genes: - *id059 - *id060 left: - 2-oxoglutarate - L-aspartate name: 2-oxoglutarate + L-aspartate <-> oxaloacetate + L-glutamate pmids: [] rhea: [] right: - L-glutamate - oxaloacetate yeastcyc_id: ASPAMINOTRANS-RXN - ec: - 2.7.2.4 genes: - *id231 left: - ATP - L-aspartate name: L-aspartate + ATP -> L-aspartyl-4-phosphate + ADP pmids: [] rhea: [] right: - ADP - L-aspartyl-4-phosphate yeastcyc_id: ASPARTATEKIN-RXN - ec: - 1.2.1.11 genes: - *id232 left: - L-aspartate 4-semialdehyde - NADP+ - phosphate name: L-aspartate 4-semialdehyde + NADP+ + phosphate <- L-aspartyl-4-phosphate + NADPH + H+ pmids: [] rhea: [] right: - H+ - L-aspartyl-4-phosphate - NADPH yeastcyc_id: ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN - ec: - 2.7.1.39 genes: - *id229 left: - ATP - L-homoserine name: L-homoserine + ATP -> O-phospho-L-homoserine + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - O-phospho-L-homoserine yeastcyc_id: HOMOSERKIN-RXN - ec: - 1.1.1.3 genes: - *id233 left: - L-homoserine - NAD(P)+ name: L-homoserine + NAD(P)+ <- L-aspartate 4-semialdehyde + NAD(P)H + H+ pmids: [] rhea: [] right: - H+ - L-aspartate 4-semialdehyde - NAD(P)H yeastcyc_id: HOMOSERDEHYDROG-RXN - ec: - 4.2.3.1 genes: - *id230 left: - H2O - O-phospho-L-homoserine name: O-phospho-L-homoserine + H2O -> L-threonine + phosphate pmids: [] rhea: [] right: - L-threonine - phosphate yeastcyc_id: THRESYN-RXN yeastcyc_id: THRESYN-PWY TREDEG-YEAST-PWY: all_genes: - &id506 orf: YPR026W symbol: ATH1 uniprot: UniProtKB:P48016 - &id507 orf: YDR001C symbol: NTH1 uniprot: UniProtKB:P32356 comment: 'Trehalose is a storage carbohydrate that can either be synthesized or obtained from the external environment. To be utilized as a carbon source, trehalase (EC:3.2.1.28) must convert trehalose and water into two molecules of glucose |CITS: 11152943|. S. cerevisiae has two trehalase enzymes, one is an acid trehalase encoded by ATH1 |CITS: 8764988| and the other is a neutral trehalase encoded by NTH1 |CITS: 8444853|. The name "acid" or "neutral" are based on the optimal pH of each enzyme (pH 4.5-5.0 and pH 6.8-7.0, respectively) |CITS: 11152943|. Each trehalase enzyme is active in a different subcellular location. Nth1p occurs as homodimer that is located in the cytoplasm, and is required for the hydrolysis of intracellular trehalose |CITS: 15128531|. Intracellular trehalose either results from trehalose biosynthesis, or to a lesser degree from uptake of trehalose from the environment via the Mal11p transporter. Ath1p was originally predicted to be a vacuolar protein, but has been experimentally shown to mainly localize in the periplasmic space, with a small fraction also occurring in the cell wall |CITS: 15128531|. Extracellular trehalose is hydrolysed into 2 glucose molecules by Ath1p |CITS: 15128531|. ' name: trehalose degradation pmids: - '11152943' reactions: - ec: - 3.2.1.28 genes: - *id506 - *id507 left: - H2O - α,α-trehalose name: α,α-trehalose + H2O -> β-D-glucopyranose + α-D-glucopyranose pmids: [] rhea: [] right: - α-D-glucopyranose - β-D-glucopyranose yeastcyc_id: TREHALA-RXN yeastcyc_id: TREDEG-YEAST-PWY TRESYN-PWY: all_genes: - &id508 orf: YBR126C symbol: TPS1 uniprot: UniProtKB:Q00764 - &id509 orf: YDR074W symbol: TPS2 uniprot: UniProtKB:P31688 comment: In Saccharomyces cerevisiae, trehalose is a major reserve carbohydrate that has been shown to stabilize proteins during heat shock and to suppress the aggregation of denatured proteins |CITS:9660948|. Trehalose has also been shown to be important for surviving osmotic, ethanol, and oxidative stresses |CITS:11483159|. Trehalose biosynthesis also influences glycolysis because trehalose-6-phosphate inhibits hexokinases, which restricts the influx of sugars into glycolysis during a switch to fermentative metabolism |CITS:8809751|. Trehalose biosynthesis is a two step process in which glucose 6-phosphate plus UDP-glucose is converted to alpha,alpha-trehalose 6-phosphate by trehalose-6-phosphate synthase (TPS), and then alpha,alpha-trehalose 6-phosphate and water are converted to trehalose and phosphate by trehalose-6-phosphate phosphatase (TPP) |CITS:11152943|. In S. cerevisiae, both of these steps occur in a single alpha,alpha-trehalose-phosphate synthase complex which is composed of four protein subunits, Tps1p |CITS:1425702|, Tps2p |CITS:8444170|, Tsl1p |CITS:8404905|, and Tps3p |CITS:9837904|. Tps1p contains the TPS catalytic activity, Tps2p contains the TPP activity, and Tps3p and Tsl1p are regulatory proteins with partially overlapping functions |CITS:9837904|. Deletion of TPS1 results in loss of both TPS activity and trehalose biosynthesis while deletion of TPS2 results in loss of TPP activity. Deletion of either TSL1 or TPS3 result in mild effects, but deletion of both TSL1 and TSL3 results in significant reductions in TPS and TPP activities as well as reduced trehalose biosynthesis |CITS:9837904|. name: trehalose biosynthesis I pmids: - '11152943' reactions: - ec: - 2.4.1.15 genes: - *id508 left: - D-glucopyranose 6-phosphate - UDP-α-D-glucose name: UDP-α-D-glucose + D-glucopyranose 6-phosphate -> α,α-trehalose 6-phosphate + UDP + H+ pmids: [] rhea: [] right: - H+ - UDP - α,α-trehalose 6-phosphate yeastcyc_id: TREHALOSE6PSYN-RXN - ec: - 3.1.3.12 genes: - *id509 left: - H2O - α,α-trehalose 6-phosphate name: α,α-trehalose 6-phosphate + H2O -> α,α-trehalose + phosphate pmids: [] rhea: [] right: - phosphate - α,α-trehalose yeastcyc_id: TREHALOSEPHOSPHA-RXN yeastcyc_id: TRESYN-PWY TRIGLSYN-PWY: all_genes: - &id510 orf: YOR245C symbol: DGA1 uniprot: UniProtKB:Q08650 - &id511 orf: YDR284C symbol: DPP1 uniprot: UniProtKB:Q05521 - *id469 - &id512 orf: YDR503C symbol: LPP1 uniprot: UniProtKB:Q04396 - &id514 orf: YNR008W symbol: LRO1 uniprot: UniProtKB:P40345 - &id513 orf: YMR165C symbol: PAH1 uniprot: UniProtKB:P32567 - *id470 - *id468 name: diacylglycerol and triacylglycerol biosynthesis pmids: - '16916618' reactions: - ec: - 2.3.1.- genes: [] left: - a 1,2-diacyl-sn-glycerol name: 2 a 1,2-diacyl-sn-glycerol <-> a triacyl-sn-glycerol + a 2-acylglycerol pmids: [] rhea: [] right: - a 2-acylglycerol - a triacyl-sn-glycerol yeastcyc_id: RXN-12383 - ec: - 2.7.1.174 genes: [] left: - CTP - a 1,2-diacyl-sn-glycerol name: CTP + a 1,2-diacyl-sn-glycerol -> CDP + a 1,2-diacyl-sn-glycerol 3-phosphate + H+ pmids: [] rhea: [] right: - CDP - H+ - a 1,2-diacyl-sn-glycerol 3-phosphate yeastcyc_id: RXN-12959 - ec: - 2.3.1.20 genes: - *id510 left: - a 1,2-diacyl-sn-glycerol - an acyl-CoA name: a 1,2-diacyl-sn-glycerol + an acyl-CoA -> a triacyl-sn-glycerol + coenzyme A pmids: [] rhea: [] right: - a triacyl-sn-glycerol - coenzyme A yeastcyc_id: DIACYLGLYCEROL-O-ACYLTRANSFERASE-RXN - ec: - 3.1.3.4 genes: - *id511 - *id512 - *id513 left: - H2O - a 1,2-diacyl-sn-glycerol 3-phosphate name: a 1,2-diacyl-sn-glycerol 3-phosphate + H2O -> a 1,2-diacyl-sn-glycerol + phosphate pmids: [] rhea: [] right: - a 1,2-diacyl-sn-glycerol - phosphate yeastcyc_id: PHOSPHATIDATE-PHOSPHATASE-RXN - ec: - 2.3.1.158 genes: - *id514 left: - a 1,2-diacyl-sn-glycerol - a phosphatidylcholine name: a phosphatidylcholine + a 1,2-diacyl-sn-glycerol -> a triacyl-sn-glycerol + a 1-acyl-sn-glycero-3-phosphocholine pmids: [] rhea: [] right: - a 1-acyl-sn-glycero-3-phosphocholine - a triacyl-sn-glycerol yeastcyc_id: RXN-1641 - ec: - 2.3.1.51 genes: - *id468 left: - a 1-acyl-sn-glycerol 3-phosphate - an acyl-CoA name: an acyl-CoA + a 1-acyl-sn-glycerol 3-phosphate -> a 1,2-diacyl-sn-glycerol 3-phosphate + coenzyme A pmids: [] rhea: [] right: - a 1,2-diacyl-sn-glycerol 3-phosphate - coenzyme A yeastcyc_id: RXN-1623 - ec: - 2.3.1.15 genes: - *id469 - *id470 left: - an acyl-CoA - sn-glycerol 3-phosphate name: an acyl-CoA + sn-glycerol 3-phosphate -> a 1-acyl-sn-glycerol 3-phosphate + coenzyme A pmids: [] rhea: [] right: - a 1-acyl-sn-glycerol 3-phosphate - coenzyme A yeastcyc_id: RXN-1381 yeastcyc_id: TRIGLSYN-PWY TRPSYN-PWY-1: all_genes: - *id020 - *id030 - *id007 - *id028 - *id006 comment: Biosynthesis of the aromatic amino acids tryptophan, tyrosine, and phenylalanine proceeds via a common pathway to chorismate, at which point the pathway branches |CITS:[Jones][1943992]|. One branch proceeds to tryptophan, and the other to tyrosine and phenylalanine |CITS:[Jones]|. The series of reactions to chorismate, called the shikimate pathway, and the series of reactions from chorismate to tryptophan have been found to be common to all eukaryotes and prokaryotes studied thus far (as reported in |CITS:[1943992]|). In contrast, there appears to be two separate routes from chorismate to tyrosine and phenylalanine, only one of which has been found in S. cerevisiae |CITS:[1943992]|. Aromatic amino acid biosynthesis in S. cerevisiae is controlled by a combination of feedback inhibition, activation of enzyme activity, and regulation of enzyme synthesis |CITS:[Jones][1943992]|. The first step in the tryptophan branch is feedback inhibited by tryptophan, and the first step in the phenylalanine-tyrosine branch is feedback inhibited by tyrosine and activated by tryptophan |CITS:[1943992]|. The transcriptional activator GCN4 regulates most of the genes encoding for the aromatic amino acid biosynthetic enzymes; however, no GCN4 regulation was found for TRP1 of the tryptophan branch, TYR1 of the tyrosine branch or ARO7 of the tyrosine and phenylalanine branch |CITS:[1943992]|. name: L-tryptophan biosynthesis pmids: - '10790693' - '1943992' - '6323449' reactions: - ec: - 4.2.1.20 genes: - *id006 left: - (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate - L-serine name: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine -> L-tryptophan + D-glyceraldehyde 3-phosphate + H2O pmids: [] rhea: [] right: - D-glyceraldehyde 3-phosphate - H2O - L-tryptophan yeastcyc_id: TRYPSYN-RXN - ec: - 4.1.1.48 genes: - *id007 left: - 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate - H+ name: 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate + H+ -> (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O pmids: [] rhea: [] right: - (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate - CO2 - H2O yeastcyc_id: IGPSYN-RXN - ec: - 5.3.1.24 genes: - *id020 left: - N-(5-phosphoribosyl)-anthranilate name: N-(5-phosphoribosyl)-anthranilate -> 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate pmids: [] rhea: [] right: - 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate yeastcyc_id: PRAISOM-RXN - ec: - 2.4.2.18 genes: - *id028 left: - 5-phospho-α-D-ribose 1-diphosphate - anthranilate name: anthranilate + 5-phospho-α-D-ribose 1-diphosphate -> N-(5-phosphoribosyl)-anthranilate + diphosphate pmids: [] rhea: [] right: - N-(5-phosphoribosyl)-anthranilate - diphosphate yeastcyc_id: PRTRANS-RXN - ec: - 4.1.3.27 genes: - *id030 - *id007 left: - L-glutamine - chorismate name: chorismate + L-glutamine -> anthranilate + L-glutamate + pyruvate + H+ pmids: [] rhea: [] right: - H+ - L-glutamate - anthranilate - pyruvate yeastcyc_id: ANTHRANSYN-RXN yeastcyc_id: TRPSYN-PWY-1 TRYPTOPHAN-DEGRADATION-1: all_genes: - *id245 - *id249 - *id250 - *id248 - *id244 - *id247 - *id251 - *id252 - *id253 - *id246 name: L-tryptophan degradation III (eukaryotic) pmids: - '12062417' reactions: - ec: [] genes: [] left: - 2-amino-3-carboxymuconate-6-semialdehyde name: 2-amino-3-carboxymuconate-6-semialdehyde -> quinolinate + H2O pmids: [] rhea: [] right: - H2O - quinolinate yeastcyc_id: RXN-5721 - ec: - 3.7.1.3 genes: - *id244 left: - 3-hydroxy-L-kynurenine - H2O name: 3-hydroxy-L-kynurenine + H2O -> 3-hydroxyanthranilate + L-alanine + H+ pmids: [] rhea: [] right: - 3-hydroxyanthranilate - H+ - L-alanine yeastcyc_id: 3-HYDROXY-KYNURENINASE-RXN - ec: - 1.13.11.6 genes: - *id245 left: - 3-hydroxyanthranilate - oxygen name: 3-hydroxyanthranilate + oxygen -> 2-amino-3-carboxymuconate-6-semialdehyde + H+ pmids: [] rhea: [] right: - 2-amino-3-carboxymuconate-6-semialdehyde - H+ yeastcyc_id: 1.13.11.6-RXN - ec: - 6.3.5.1 genes: - *id246 left: - ATP - H2O - L-glutamine - nicotinate adenine dinucleotide name: ATP + nicotinate adenine dinucleotide + L-glutamine + H2O -> L-glutamate + AMP + NAD+ + diphosphate + H+ pmids: [] rhea: [] right: - AMP - H+ - L-glutamate - NAD+ - diphosphate yeastcyc_id: NAD-SYNTH-GLN-RXN - ec: - 2.4.2.19 genes: - *id247 left: - CO2 - diphosphate - β-nicotinate D-ribonucleotide name: CO2 + β-nicotinate D-ribonucleotide + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + quinolinate + 2 H+ pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - H+ - quinolinate yeastcyc_id: QUINOPRIBOTRANS-RXN - ec: - 1.14.13.9 genes: - *id248 left: - H+ - L-kynurenine - NADPH - oxygen name: L-kynurenine + NADPH + oxygen + H+ -> 3-hydroxy-L-kynurenine + NADP+ + H2O pmids: [] rhea: [] right: - 3-hydroxy-L-kynurenine - H2O - NADP+ yeastcyc_id: KYNURENINE-3-MONOOXYGENASE-RXN - ec: - 1.13.11.11 - 1.13.11.52 genes: - *id249 left: - L-tryptophan - oxygen name: L-tryptophan + oxygen -> N-Formyl-L-kynurenine pmids: [] rhea: [] right: - N-Formyl-L-kynurenine yeastcyc_id: RXN-8665 - ec: - 3.5.1.9 genes: - *id250 - *id251 left: - H2O - N-Formyl-L-kynurenine name: N-Formyl-L-kynurenine + H2O -> L-kynurenine + formate + H+ pmids: [] rhea: [] right: - H+ - L-kynurenine - formate yeastcyc_id: ARYLFORMAMIDASE-RXN - ec: - 2.7.7.18 genes: - *id252 - *id253 left: - ATP - H+ - β-nicotinate D-ribonucleotide name: β-nicotinate D-ribonucleotide + ATP + H+ -> nicotinate adenine dinucleotide + diphosphate pmids: [] rhea: [] right: - diphosphate - nicotinate adenine dinucleotide yeastcyc_id: NICONUCADENYLYLTRAN-RXN yeastcyc_id: TRYPTOPHAN-DEGRADATION-1 UDPNAGSYN-YEAST-PWY: all_genes: - &id518 orf: YKL104C symbol: GFA1 uniprot: UniProtKB:P14742 - &id515 orf: YFL017C symbol: GNA1 uniprot: UniProtKB:P43577 - &id516 orf: YEL058W symbol: PCM1 uniprot: UniProtKB:P38628 - &id517 orf: YDL103C symbol: QRI1 uniprot: UniProtKB:P43123 comment: 'UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) is a sugar nucleotide utilized for the biosynthesis of chitin, a major structural polysaccharide in the yeast cell wall. UDP-GlcNAc also provides GlcNAc moieties for N-linked glycosylation of proteins and for the biosynthesis of glycosylphosphatidylinositol (GPI), a lipid anchor involved in tethering proteins to the cell membrane. Synthesis of UDP-GlcNAc is an essential process in S. cerevisiae; conditional depletion of several of the enzymes in the pathway (Gna1p, Pcm1p, Qri1p) results in aberrant cell morphology and increased cell lysis. In S. cerevisiae, UDP-GlcNAc is synthesized in four steps from fructose-6-phosphate (F6P). First, F6P is converted to glucosamine-6-phosphate (GlcN6P) by glutamine:fructose-6-phosphate amidotransferase (GFAT). Second, GlcN6P is N-acetylated by GlcN6P acetyltransferase (Gna1p). This forms GlcNAc-6-P, which in the third step of the pathway is isomerized to GlcNAc-1-P by phosphoacetylglucosamine mutase (Pcm1p). Finally, GlcNAc-1-P is condensed with UTP via UDP-GlcNAc pyrophosphorylase (Qri1p), yielding UDP-GlcNAc. The UDP-GlcNAc biosynthesis pathway described in yeast occurs similarly in other eukaryotes, however in the bacterial pathway GlcN-6-P is initially isomerized to GlcN-1-P prior to N-acetylation. References: |CITS:[23135325]||CITS: [9867860]||CITS: [16408321]|' name: UDP-N-acetylglucosamine biosynthesis pmids: - '16408321' - '23135325' - '2656689' - '8174553' - '9603950' - '9867860' reactions: - ec: - 2.3.1.4 genes: - *id515 left: - D-glucosamine 6-phosphate - acetyl-CoA name: D-glucosamine 6-phosphate + acetyl-CoA -> N-acetyl-D-glucosamine 6-phosphate + coenzyme A + H+ pmids: [] rhea: [] right: - H+ - N-acetyl-D-glucosamine 6-phosphate - coenzyme A yeastcyc_id: GLUCOSAMINEPNACETYLTRANS-RXN - ec: - 5.4.2.3 genes: - *id516 left: - N-acetyl-D-glucosamine 6-phosphate name: N-acetyl-D-glucosamine 6-phosphate -> N-acetyl-α-D-glucosamine 1-phosphate pmids: [] rhea: [] right: - N-acetyl-α-D-glucosamine 1-phosphate yeastcyc_id: PHOSACETYLGLUCOSAMINEMUT-RXN - ec: - 2.7.7.23 genes: - *id517 left: - H+ - N-acetyl-α-D-glucosamine 1-phosphate - UTP name: UTP + N-acetyl-α-D-glucosamine 1-phosphate + H+ -> UDP-N-acetyl-α-D-glucosamine + diphosphate pmids: [] rhea: [] right: - UDP-N-acetyl-α-D-glucosamine - diphosphate yeastcyc_id: NAG1P-URIDYLTRANS-RXN - ec: - 2.6.1.16 genes: - *id518 left: - L-glutamine - β-D-fructofuranose 6-phosphate name: β-D-fructofuranose 6-phosphate + L-glutamine <-> D-glucosamine 6-phosphate + L-glutamate pmids: [] rhea: [] right: - D-glucosamine 6-phosphate - L-glutamate yeastcyc_id: L-GLN-FRUCT-6-P-AMINOTRANS-RXN yeastcyc_id: UDPNAGSYN-YEAST-PWY VALSYN-PWY: all_genes: - *id080 - *id081 - *id076 - *id073 - *id074 - *id077 name: L-valine biosynthesis pmids: - '3289762' reactions: - ec: - 4.2.1.9 genes: - *id073 left: - (2R)-2,3-dihydroxy-3-methylbutanoate name: (2R)-2,3-dihydroxy-3-methylbutanoate -> 3-methyl-2-oxobutanoate + H2O pmids: [] rhea: [] right: - 3-methyl-2-oxobutanoate - H2O yeastcyc_id: DIHYDROXYISOVALDEHYDRAT-RXN - ec: - 1.1.1.86 genes: - *id074 left: - (2R)-2,3-dihydroxy-3-methylbutanoate - NADP+ name: (2R)-2,3-dihydroxy-3-methylbutanoate + NADP+ <- (S)-2-acetolactate + NADPH + H+ pmids: [] rhea: [] right: - (S)-2-acetolactate - H+ - NADPH yeastcyc_id: ACETOLACTREDUCTOISOM-RXN - ec: - 2.2.1.6 genes: - *id076 - *id077 left: - H+ - pyruvate name: 2 pyruvate + H+ -> (S)-2-acetolactate + CO2 pmids: [] rhea: [] right: - (S)-2-acetolactate - CO2 yeastcyc_id: ACETOLACTSYN-RXN - ec: - 2.6.1.42 genes: - *id080 - *id081 left: - 2-oxoglutarate - L-valine name: L-valine + 2-oxoglutarate <-> L-glutamate + 3-methyl-2-oxobutanoate pmids: - '10989445' - '8702755' - '8798704' rhea: [] right: - 3-methyl-2-oxobutanoate - L-glutamate yeastcyc_id: BRANCHED-CHAINAMINOTRANSFERVAL-RXN yeastcyc_id: VALSYN-PWY YEAST-4AMINOBUTMETAB-PWY: all_genes: - *id186 - *id188 comment: 'The non-protein amino acid gamma-aminobutyrate (GABA) plays an important role in mammalian neurotransmission, plant development, and in S.cerevisiae, nitrogen utilization and oxidative stress tolerance |CITS: [11031268]|, |CITS:[3888627]|. In yeast, GABA accumulation occurs either through permease-mediated uptake by Uga4p, Put4p, and Gap1p, or it is produced intracellularly via glutamate degradation by the glutamate decarboxylase Gad1p |CITS: [11031268]|, |CITS: [3888627]|. The presence of GABA causes an increase in expression of the genes UGA1 and UGA2, which encode the enzymes responsible for degrading GABA into succinate |CITS:[3888627]|. This GABA-induced upregulation is mediated by the transcriptional activators Uga3p and Uga35p/Dal81p |CITS:[2653828]|. These transcription factors bind to upstream activation sites in the promoters of GABA-regulated genes known as the UAS-GABA |CITS:[12235130]|, |CITS: [2653828]|. Levels of UGA2 transcript are also upregulated under conditions of oxidative stress |CITS:[11031268]|. S.cerevisiae cells in which GABA degradation is blocked are more sensitive to oxidative stress and can no longer grow on GABA as their sole nitrogen source |CITS:[11031268]|, |CITS:[3888627]|.' name: 4-aminobutyrate degradation pmids: - '3888627' reactions: - ec: - 2.6.1.19 genes: - *id186 left: - 2-oxoglutarate - 4-aminobutanoate name: 2-oxoglutarate + 4-aminobutanoate <-> L-glutamate + succinate semialdehyde pmids: - '3888627' rhea: [] right: - L-glutamate - succinate semialdehyde yeastcyc_id: GABATRANSAM-RXN - ec: - 1.2.1.16 genes: - *id188 left: - H2O - NAD(P)+ - succinate semialdehyde name: succinate semialdehyde + NAD(P)+ + H2O -> succinate + NAD(P)H + 2 H+ pmids: [] rhea: [] right: - H+ - NAD(P)H - succinate yeastcyc_id: RXN0-5293 yeastcyc_id: YEAST-4AMINOBUTMETAB-PWY YEAST-DE-NOVO-PYRMID-DNT: all_genes: - *id026 - &id519 orf: YJR057W symbol: CDC8 uniprot: UniProtKB:P00572 - &id520 orf: YBR252W symbol: DUT1 uniprot: UniProtKB:P33317 - *id104 - *id105 - *id106 - *id107 - *id094 comment: 'Deoxyribonucleoside triphosphates (dNTPs) are the monomeric building blocks of DNA. In all cellular organisms, synthesis of the four canonical dNTPs (dATP, dGTP, dCTP, dTTP) required for DNA replication and repair involves the action of ribonucleotide reductase, which converts ribonucleotides to their corresponding deoxy- forms by substituting their 2-hydroxyl group with a hydrogen atom. S. cerevisiae contains a class Ia RNR that is composed of two large and two small subunits. RNR2 and RNR4 encode the small subunits, while the large subunits are encoded by either RNR1 (major isoform) or RNR3 (minor isoform). Budding yeast RNR accepts ribonucleoside diphosphates (e.g. ADP, UDP) as substrate and converts them to their corresponding deoxy- forms (e.g. dADP, dUDP). These dNDPs can then be phosphorylated by NDP kinase (Ynk1p) to yield dNTPs. In contrast to the class I RNRs in yeast and other eukaryotes, class II and class III RNRs found in archaea and many bacteria can produce dNTPs directly by using NTPs as substrates. In S. cerevisiae, the only dNDP that cannot be synthesized directly by RNR is dTDP. Synthesis of thymine-containing nucleotides requires dUMP, which can be formed via the removal of pyrophosphate from dUTP by dUTP pyrophosphatase (Dut1p). dTMP is synthesized from dUMP when the latter molecule receives a methyl group from 5,10-methylene-tetrahydrofolate via thymidylate synthase (Cdc21p). The subsequent phosphorylation of dTMP by thymidylate kinase (Cdc8p) yields dTDP, which can be phosphorylated once more by Ynk1p to yield the end product dTTP. References: |CITS:[16756507]||CITS: [9759483]||CITS: [1659321]||CITS: [8223452]||CITS: [6287238]||CITS: [6088527]|' name: de novo biosynthesis of pyrimidine deoxyribonucleotides pmids: - '12472466' - '1659321' - '6094555' reactions: - ec: - 2.7.4.13 - 2.7.4.14 - 2.7.4.25 genes: [] left: - ATP - dCMP name: ATP + dCMP -> ADP + dCDP pmids: [] rhea: [] right: - ADP - dCDP yeastcyc_id: RXN-7913 - ec: - 2.7.4.13 genes: - *id519 left: - ATP - dUMP name: ATP + dUMP -> ADP + dUDP pmids: [] rhea: [] right: - ADP - dUDP yeastcyc_id: RXN-14122 - ec: - 2.1.1.45 genes: - *id026 left: - a 5,10-methylenetetrahydrofolate - dUMP name: a 5,10-methylenetetrahydrofolate + dUMP -> dTMP + a 7,8-dihydrofolate pmids: [] rhea: [] right: - a 7,8-dihydrofolate - dTMP yeastcyc_id: THYMIDYLATESYN-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dCDP name: dCDP + ATP -> dCTP + ADP pmids: [] rhea: [] right: - ADP - dCTP yeastcyc_id: DCDPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dCDP name: dCDP + an oxidized thioredoxin + H2O <- CDP + a reduced thioredoxin pmids: [] rhea: [] right: - CDP - a reduced thioredoxin yeastcyc_id: CDPREDUCT-RXN - ec: - 3.5.4.13 genes: [] left: - H+ - H2O - dCTP name: dCTP + H+ + H2O -> ammonium + dUTP pmids: [] rhea: [] right: - ammonium - dUTP yeastcyc_id: DCTP-DEAM-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dTDP name: dTDP + ATP -> dTTP + ADP pmids: [] rhea: [] right: - ADP - dTTP yeastcyc_id: DTDPKIN-RXN - ec: - 2.7.4.12 - 2.7.4.13 - 2.7.4.9 genes: - *id519 left: - ATP - dTMP name: dTMP + ATP -> dTDP + ADP pmids: [] rhea: [] right: - ADP - dTDP yeastcyc_id: DTMPKI-RXN - ec: - 2.7.4.6 genes: - *id094 left: - ATP - dUDP name: dUDP + ATP -> dUTP + ADP pmids: [] rhea: [] right: - ADP - dUTP yeastcyc_id: DUDPKIN-RXN - ec: - 1.17.4.1 genes: - *id104 - *id105 - *id106 - *id107 left: - H2O - an oxidized thioredoxin - dUDP name: dUDP + an oxidized thioredoxin + H2O <- UDP + a reduced thioredoxin pmids: [] rhea: [] right: - UDP - a reduced thioredoxin yeastcyc_id: UDPREDUCT-RXN - ec: - 3.6.1.23 - 3.6.1.9 genes: - *id520 left: - H2O - dUTP name: dUTP + H2O -> dUMP + diphosphate + H+ pmids: [] rhea: [] right: - H+ - dUMP - diphosphate yeastcyc_id: DUTP-PYROP-RXN yeastcyc_id: YEAST-DE-NOVO-PYRMID-DNT YEAST-FAO-PWY: all_genes: - &id522 orf: YOR180C symbol: DCI1 uniprot: UniProtKB:Q08558 - &id523 orf: YLR284C symbol: ECI1 uniprot: UniProtKB:Q05871 - &id524 orf: YOR317W symbol: FAA1 uniprot: UniProtKB:P30624 - &id525 orf: YER015W symbol: FAA2 uniprot: UniProtKB:P39518 - &id526 orf: YIL009W symbol: FAA3 uniprot: UniProtKB:P39002 - &id527 orf: YMR246W symbol: FAA4 uniprot: UniProtKB:P47912 - &id528 orf: YBR041W symbol: FAT1 uniprot: UniProtKB:P38225 - &id521 orf: YKR009C symbol: FOX2 uniprot: UniProtKB:Q02207 - &id529 orf: YIL160C symbol: POT1 uniprot: UniProtKB:P27796 - &id530 orf: YGL205W symbol: POX1 uniprot: UniProtKB:P13711 comment: 'In most organisms, the primary mode of fatty acid catabolism is -oxidation. The -oxidation cycle catalyzes the complete oxidation of a fatty acid molecule, removing two carbon atoms (in the form of acetyl-CoA) with each turn of the cycle. The subcellular location in which -oxidation occurs varies by organism; in bacteria, -oxidation occurs in the cytoplasm, whereas in mammalian cells it occurs in both the mitochondria and the peroxisome. In contrast, -oxidation in S. cerevisiae, plants, and most other fungi occurs exclusively in the peroxisome. -oxidation begins with the activation of a fatty acid with coenzyme A, producing an acyl-CoA. In S. cerevisiae, the uptake of free fatty acids as well as their activation with coenzyme A occurs via the acyl-CoA synthases Fat1p and Faa1p-Faa4p. The acyl-CoA molecule is then oxidized, introducing a double bond between C2 (the -carbon) and C3 (the -carbon). This step is catalyzed by acyl-CoA oxidase, encoded by POX1 in yeast. In the third step, the double bond is hydrated, leading to the formation of a hydroxyl group on C3. The stereochemistry of the 3-hydroxyacyl-CoA intermediate is specific to the type of -oxidation pathway. In fungal peroxisomes, -oxidation proceeds via (3R)-hydroxy intermediates; in contrast, mitochondrial -oxidation in mammals proceeds via the (3S) enantiomer. In the fourth step, the hydroxyl group is oxidized to a carbonyl group, forming a 3-ketoacyl-CoA intermediate. Steps 3-4 are both catalyzed by the multifunctional enzyme Fox2p in S. cerevisiae. Lastly, the 3-ketoacyl-CoA intermediate undergoes thiolytic cleavage between C2 and C3, yielding one acetyl-CoA and an acyl-CoA molecule shortened by two carbon atoms. This step is catalyzed by 3-ketoacyl-CoA thiolase, encoded by POT1 in S. cerevisiae. References: |CITS:[17028011]||CITS: [24520995]||CITS: [12697341]|' name: fatty acid oxidation pathway pmids: - '12697341' - '1551874' - '17028011' - '24520995' reactions: - ec: - 4.2.1.17 genes: - *id521 left: - a (3S)-3-hydroxyacyl-CoA name: a (3S)-3-hydroxyacyl-CoA <- a trans-2-enoyl-CoA + H2O pmids: [] rhea: [] right: - H2O - a trans-2-enoyl-CoA yeastcyc_id: ENOYL-COA-HYDRAT-RXN - ec: - 1.1.1.35 genes: - *id521 left: - NAD+ - a (3S)-3-hydroxyacyl-CoA name: a (3S)-3-hydroxyacyl-CoA + NAD+ -> a 3-oxoacyl-CoA + NADH + H+ pmids: [] rhea: [] right: - H+ - NADH - a 3-oxoacyl-CoA yeastcyc_id: OHACYL-COA-DEHYDROG-RXN - ec: - 5.3.3.8 genes: - *id522 - *id523 left: - a (3Z)-alk-3-enoyl-CoA name: a (3Z)-alk-3-enoyl-CoA -> a trans-2-enoyl-CoA pmids: [] rhea: [] right: - a trans-2-enoyl-CoA yeastcyc_id: ENOYL-COA-DELTA-ISOM-RXN - ec: - 6.2.1.3 genes: - *id524 - *id525 - *id526 - *id527 - *id528 left: - ATP - a 2,3,4-saturated fatty acid - coenzyme A name: a 2,3,4-saturated fatty acid + ATP + coenzyme A -> a 2,3,4-saturated fatty acyl CoA + AMP + diphosphate pmids: [] rhea: [] right: - AMP - a 2,3,4-saturated fatty acyl CoA - diphosphate yeastcyc_id: ACYLCOASYN-RXN - ec: - 2.3.1.16 genes: - *id529 left: - a 2,3,4-saturated fatty acyl CoA - acetyl-CoA name: a 2,3,4-saturated fatty acyl CoA + acetyl-CoA <- a 3-oxoacyl-CoA + coenzyme A pmids: [] rhea: [] right: - a 3-oxoacyl-CoA - coenzyme A yeastcyc_id: KETOACYLCOATHIOL-RXN - ec: - 1.3.3.6 genes: - *id530 left: - a 2,3,4-saturated fatty acyl CoA - oxygen name: a 2,3,4-saturated fatty acyl CoA + oxygen -> a trans-2-enoyl-CoA + hydrogen peroxide pmids: [] rhea: [] right: - a trans-2-enoyl-CoA - hydrogen peroxide yeastcyc_id: RXN-11026 yeastcyc_id: YEAST-FAO-PWY YEAST-GALACT-METAB-PWY: all_genes: - &id533 orf: YBR020W symbol: GAL1 uniprot: UniProtKB:P04385 - &id531 orf: YBR019C symbol: GAL10 uniprot: UniProtKB:P04397 - &id532 orf: YBR018C symbol: GAL7 uniprot: UniProtKB:P08431 - *id203 - *id204 comment: 'Yeast and most other microorganisms initiate the degradation of galactose via the enzymes of the Leloir pathway, which convert galactose into glucose-6-phosphate for subsequent entry into glycolysis. In the yeast Leloir pathway, galactokinase (Gal1p) phosphorylates galactose to galactose-1-phosphate. Galactokinase is specific for the -anomer of galactose; if the galactose substrate is in the -form, then it must first be converted to the -form through the mutarotase activity of Gal10p. After its conversion to galactose-1-phosphate, galactose is subsequently swapped with a glucose moiety from UDP-glucose via Gal7p, forming UDP-galactose and glucose-1-phosphate. The glucose-1-phosphate product can then be converted to glucose-6-phosphate, a substrate of glycolysis, via phosphoglucomutase (Pgm2p or Pgm1p). On the other hand, the UDP-galactose product- which contains carbon from the original galactose substrate- can be converted to UDP-glucose via the epimerase activity of Gal10p. The glucose unit of this UDP-glucose molecule may then be converted to glucose-6-phosphate during a second round of the Leloir pathway. In S. cerevisiae, the genes involved in the Leloir pathway- GAL1, GAL7, and GAL10- are transcriptionally regulated in response to galactose by Gal4p, Gal80p, and Gal3p. Gal4p functions as a transcriptional activator of GAL genes, whereas Gal80p functions to inhibit this activity by binding to Gal4p in the absence of galactose. In the presence of galactose, Gal3p binds to Gal80p in an ATP-dependent manner and relieves inhibition of Gal4p, resulting in GAL gene expression. References: |CITS:[18779058]||CITS: [8119301]|' name: galactose degradation pmids: - '14764091' - '18779058' - '8119301' reactions: - ec: - 5.1.3.2 genes: - *id531 left: - UDP-α-D-glucose name: UDP-α-D-glucose <-> UDP-α-D-galactose pmids: - '14764091' rhea: [] right: - UDP-α-D-galactose yeastcyc_id: UDPGLUCEPIM-RXN - ec: - 2.7.7.12 genes: - *id532 left: - UDP-α-D-glucose - α-D-galactose 1-phosphate name: UDP-α-D-glucose + α-D-galactose 1-phosphate -> UDP-α-D-galactose + α-D-glucopyranose 1-phosphate pmids: [] rhea: [] right: - UDP-α-D-galactose - α-D-glucopyranose 1-phosphate yeastcyc_id: GALACTURIDYLYLTRANS-RXN - ec: - 2.7.1.6 genes: - *id533 left: - ATP - α-D-galactopyranose name: α-D-galactopyranose + ATP -> α-D-galactose 1-phosphate + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - α-D-galactose 1-phosphate yeastcyc_id: GALACTOKIN-RXN - ec: - 5.4.2.2 genes: - *id203 - *id204 left: - α-D-glucopyranose 1-phosphate name: α-D-glucopyranose 1-phosphate <-> D-glucopyranose 6-phosphate pmids: [] rhea: [] right: - D-glucopyranose 6-phosphate yeastcyc_id: PHOSPHOGLUCMUT-RXN - ec: - 5.1.3.3 genes: - *id531 left: - β-D-galactopyranose name: β-D-galactopyranose -> α-D-galactopyranose pmids: - '14764091' rhea: [] right: - α-D-galactopyranose yeastcyc_id: ALDOSE1EPIM-RXN yeastcyc_id: YEAST-GALACT-METAB-PWY YEAST-RIBOSYN-PWY: all_genes: - &id538 orf: YDL045C symbol: FAD1 uniprot: UniProtKB:P38913 - &id541 orf: YDR236C symbol: FMN1 uniprot: UniProtKB:Q03778 - &id540 orf: YBL033C symbol: RIB1 uniprot: UniProtKB:P38066 - &id535 orf: YOL066C symbol: RIB2 uniprot: UniProtKB:Q12362 - &id539 orf: YDR487C symbol: RIB3 uniprot: UniProtKB:Q99258 - &id537 orf: YOL143C symbol: RIB4 uniprot: UniProtKB:P50861 - &id534 orf: YBR256C symbol: RIB5 uniprot: UniProtKB:P38145 - &id536 orf: YBR153W symbol: RIB7 uniprot: UniProtKB:P33312 comment: 'The first committed step of riboflavin biosynthesis in S. cerevisiae is the conversion of GTP to 2,5-diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5-phosphate (DRAP) via GTP cyclohydrolase II (Rib1p). DRAP is then converted to 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione 5-phosphate in two steps: reduction of the ribosyl side chain of DRAP by Rib7p, followed by deamination of the pyrimidine ring via Rib2p. These two steps occur in the reverse order relative to the riboflavin synthesis pathway in bacteria, where deamination of DRAP precedes reduction. The product of the Rib2p reaction is then dephosphorylated and condensed via lumazine synthase (Rib4p) with 4-dihydroxy-2-butanone-4-phosphate, a metabolite of ribulose-5-phosphate. This condensation reaction results in the formation of 6,7-dimethyl-8-(1-D-ribityl)-lumazine. In the final step of the pathway, one molecule of 6,7-dimethyl-8-(1-D-ribityl)-lumazine donates a four-carbon moiety to a second molecule via riboflavin synthase (Rib5p), transforming the xylene ring of 6,7-dimethyl-8-(1-D-ribityl)-lumazine into the isoalloxazine ring of riboflavin. Riboflavin may then go on to be phosphorylated by riboflavin kinase (Fmn1p) to form FMN, and FMN itself can be converted to FAD via FAD synthetase (Fad1p). References: |CITS:[24373875]||CITS: [7814407]|' name: riboflavin, FMN and FAD biosynthesis pmids: - '2437875' - '7559556' - '7814407' - '9068650' reactions: - ec: - 2.5.1.9 genes: - *id534 left: - 6,7-dimethyl-8-(1-D-ribityl)lumazine - H+ name: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H+ -> 5-amino-6-(D-ribitylamino)uracil + riboflavin pmids: [] rhea: [] right: - 5-amino-6-(D-ribitylamino)uracil - riboflavin yeastcyc_id: RIBOFLAVIN-SYN-RXN - ec: [] genes: - *id535 left: - 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one name: 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one -> 5-amino-6-(D-ribitylamino)uracil pmids: [] rhea: [] right: - 5-amino-6-(D-ribitylamino)uracil yeastcyc_id: RXN3O-164 - ec: - 3.5.4.- genes: [] left: - 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one - H+ - H2O name: 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one + H+ + H2O -> 5-amino-6-(5-phospho-D-ribitylamino)uracil + ammonium pmids: [] rhea: [] right: - 5-amino-6-(5-phospho-D-ribitylamino)uracil - ammonium yeastcyc_id: RXN-10058 - ec: - 1.1.1.302 genes: [] left: - 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one - NAD+ name: 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one + NAD+ <- 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + NADH + H+ pmids: [] rhea: [] right: - 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one - H+ - NADH yeastcyc_id: RXN-10057 - ec: [] genes: - *id536 left: - 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one name: 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one -> 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one pmids: [] rhea: [] right: - 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one yeastcyc_id: RXN3O-110 - ec: - 3.1.3.104 genes: [] left: - 5-amino-6-(5-phospho-D-ribitylamino)uracil - H2O name: 5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O -> 5-amino-6-(D-ribitylamino)uracil + phosphate pmids: [] rhea: [] right: - 5-amino-6-(D-ribitylamino)uracil - phosphate yeastcyc_id: RIBOPHOSPHAT-RXN - ec: - 2.5.1.78 genes: - *id537 left: - 1-deoxy-L-glycero-tetrulose 4-phosphate - 5-amino-6-(D-ribitylamino)uracil name: 5-amino-6-(D-ribitylamino)uracil + 1-deoxy-L-glycero-tetrulose 4-phosphate -> 6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + H+ + 2 H2O pmids: [] rhea: [] right: - 6,7-dimethyl-8-(1-D-ribityl)lumazine - H+ - H2O - phosphate yeastcyc_id: LUMAZINESYN-RXN - ec: - 2.7.7.2 genes: - *id538 left: - ATP - FMN - H+ name: ATP + FMN + H+ -> FAD + diphosphate pmids: [] rhea: [] right: - FAD - diphosphate yeastcyc_id: FADSYN-RXN - ec: - 4.1.99.12 genes: - *id539 left: - D-ribulose 5-phosphate name: D-ribulose 5-phosphate -> formate + 1-deoxy-L-glycero-tetrulose 4-phosphate + H+ pmids: [] rhea: [] right: - 1-deoxy-L-glycero-tetrulose 4-phosphate - H+ - formate yeastcyc_id: DIOHBUTANONEPSYN-RXN - ec: - 3.5.4.25 genes: - *id540 left: - GTP - H2O name: GTP + 3 H2O -> 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + formate + diphosphate + 2 H+ pmids: [] rhea: [] right: - 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one - H+ - diphosphate - formate yeastcyc_id: GTP-CYCLOHYDRO-II-RXN - ec: - 2.7.1.26 genes: - *id541 left: - ATP - riboflavin name: riboflavin + ATP -> ADP + FMN + H+ pmids: [] rhea: [] right: - ADP - FMN - H+ yeastcyc_id: RIBOFLAVINKIN-RXN yeastcyc_id: YEAST-RIBOSYN-PWY YEAST-RNT-SALV: all_genes: - &id544 orf: YLR245C symbol: CDD1 uniprot: UniProtKB:Q06549 - &id545 orf: YPR062W symbol: FCY1 uniprot: UniProtKB:Q12178 - &id542 orf: YHR128W symbol: FUR1 uniprot: UniProtKB:P18562 - *id301 - *id413 - &id543 orf: YNR012W symbol: URK1 uniprot: UniProtKB:P27515 - *id094 comment: 'Pyrimidine nucleotides are essential as components of nucleic acids, as substrates for amino acid synthesis and as energy sources, but defects in the de novo biosynthesis of pyrimidines are not lethal in S. cerevisiae cells |CITS:10501935|. This is because salvage pathways are able to utilize preformed bases (either from exogenous sources or internal turnover sources) for the synthesis of pyrimidines |CITS:2189783|. If the required substrates are available, salvage pathways are preferred over de novo synthesis pathways for pyrimidine biosynthesis |CITS:12111094|. The salvage pathways of pyrimidine ribonucleotides consist of 1) importing exogenous bases into the cell, and 2) the interconversion of various bases |CITS:2189783||CITS:12111094|. Three proteins are involved in the import of exogenous bases used by the salvage pathway for pyrimidine ribonucleotide biosynthesis. Uracil enters the cell via the Fur4p uracil permease |CITS:6290876||CITS:3276521|, cytosine enters the cell via the Fcy2p purine-cytosine transporter |CITS:6387700||CITS:2191181|, and uridine enters the cell via the Fui1p uridine permease |CITS:9485596|. As with many of the metabolic pathways of S. cerevisiae, the pathways for the salvage of pyrimidine ribonucleotides are under both transcriptional and post-transcriptional catabolite repression at a variety of points |CITS:10074071||CITS:11125145||CITS:12111094||CITS:12570998||CITS:12791685||CITS:1429716||CITS:14657252|. This pathway is of biomedical interest because cytosine deaminase (Fcy1p) is not found in mammals |CITS:12637534| and is capable of catalyzing the deamination of the prodrug 5-fluorocytosine (5FC) to form the anticancer drug 5-fluorouracil (5FU) |CITS:15823054|. Expression of Fcy1p in tumor cells increases their sensitivity to 5FC, and expression of Fur1p increases tumor cell sensitivity to 5FU |CITS:10919655|. Tumor cells expressing a novel chimeric protein, produced from a gene containing the FCY1 and FUR1 coding sequences fused in frame, display significantly increased sensitivity to 5-FC suggesting that this novel suicide gene may constitute an original and potent candidate therapeutic gene for cancer gene therapy |CITS:10919655|. ' name: salvage pathways of pyrimidine ribonucleotides pmids: - '10501935' - '12111094' reactions: - ec: - 2.7.4.6 genes: - *id094 left: - ATP - CDP name: CDP + ATP -> CTP + ADP pmids: [] rhea: [] right: - ADP - CTP yeastcyc_id: CDPKIN-RXN - ec: - 2.7.4.14 - 2.7.4.25 genes: - *id301 left: - ATP - CMP name: CMP + ATP <-> CDP + ADP pmids: [] rhea: [] right: - ADP - CDP yeastcyc_id: RXN-11832 - ec: - 2.4.2.9 genes: - *id542 left: - UMP - diphosphate name: UMP + diphosphate <- 5-phospho-α-D-ribose 1-diphosphate + uracil pmids: [] rhea: [] right: - 5-phospho-α-D-ribose 1-diphosphate - uracil yeastcyc_id: URACIL-PRIBOSYLTRANS-RXN - ec: - 2.7.1.213 genes: - *id543 left: - GTP - cytidine name: cytidine + GTP -> CMP + GDP + H+ pmids: [] rhea: [] right: - CMP - GDP - H+ yeastcyc_id: CYTIDINEKIN-RXN - ec: - 3.5.4.5 genes: - *id544 left: - H+ - H2O - cytidine name: cytidine + H+ + H2O -> uridine + ammonium pmids: [] rhea: [] right: - ammonium - uridine yeastcyc_id: CYTIDEAM2-RXN - ec: - 3.2.2.3 genes: - *id413 left: - H2O - cytidine name: cytidine + H2O -> D-ribofuranose + cytosine pmids: [] rhea: [] right: - D-ribofuranose - cytosine yeastcyc_id: RXN0-361 - ec: - 3.5.4.1 genes: - *id545 left: - H+ - H2O - cytosine name: cytosine + H2O + H+ -> uracil + ammonium pmids: [] rhea: [] right: - ammonium - uracil yeastcyc_id: CYTDEAM-RXN - ec: - 2.7.1.48 genes: - *id543 left: - ATP - uridine name: uridine + ATP -> UMP + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - UMP yeastcyc_id: URIDINEKIN-RXN - ec: - 3.2.2.3 genes: - *id413 left: - H2O - uridine name: uridine + H2O -> D-ribofuranose + uracil pmids: [] rhea: [] right: - D-ribofuranose - uracil yeastcyc_id: URIDINE-NUCLEOSIDASE-RXN yeastcyc_id: YEAST-RNT-SALV YEAST-SALV-PYRMID-DNTP: all_genes: - *id544 - *id413 - *id543 comment: 'The deoxynucleotides required for DNA synthesis can either be made de novo, or they can be salvaged from endogenous degradation processes |CITS: 10501935||CITS: 2189783|. If the required substrates are available, the salvage pathways of pyrimidine deoxyribonucleotides are preferred over de novo synthesis pathways for pyrimidine biosynthesis |CITS:12111094|. As with many of the metabolic pathways of S. cerevisiae, the pathways for the salvage of pyrimidine deoxyribonucleotides are regulated by a variety of processes, including transcription regulation |CITS: 11292850||CITS: 12570998|. Saccharomyces cerevisiae contains three enzymes (Urk1p, Urh1p, and Cdd1p) that are able to salvage deoxycytidine in vitro |CITS: 12111094|. However of these three enzymes, only Urk1p and Urh1p have been shown to metabolize deoxycytidine in vivo |CITS: 12111094|. In vitro Cdd1p has been shown to deaminate deoxycytidine to form deoxyuridine, however the biological significance of this is doubtful |CITS:10501935||CITS:12111094|. Evidence that Cdd1p is not important for deoxypyrimidine salvage comes from the observation that fyc1 urh1 urk1 triple mutants are resistant to 5-fluorodeoxycytidine, indicating that these cells are not able to metabolize deoxycytidine |CITS:12111094|. Also deoxyuridine does not allow growth of ura- strains, indicating that deoxyuridine cannot be utilized as a sole source of pyrimidines in S. cerevisiae |CITS:12111094|.' name: salvage pathways of pyrimidine deoxyribonucleotides pmids: - '10501935' - '12111094' reactions: - ec: - 2.7.1.- - 2.7.1.145 - 2.7.1.74 genes: - *id543 left: - 2'-deoxycytidine - ATP name: 2'-deoxycytidine + ATP -> dCMP + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - dCMP yeastcyc_id: RXN-14093 - ec: - 3.5.4.5 genes: - *id544 left: - 2'-deoxycytidine - H+ - H2O name: 2'-deoxycytidine + H+ + H2O -> 2'-deoxyuridine + ammonium pmids: [] rhea: [] right: - 2'-deoxyuridine - ammonium yeastcyc_id: CYTIDEAM-RXN - ec: - 3.2.2.- genes: - *id413 left: - 2'-deoxycytidine - H2O name: 2'-deoxycytidine + H2O -> cytosine + 2'-deoxyribose pmids: [] rhea: [] right: - 2'-deoxyribose - cytosine yeastcyc_id: RXN3O-314 - ec: - 2.7.1.145 - 2.7.1.21 genes: [] left: - 2'-deoxyuridine - ATP name: 2'-deoxyuridine + ATP -> dUMP + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - dUMP yeastcyc_id: DURIDKI-RXN - ec: - 2.4.2.2 - 2.4.2.3 genes: [] left: - 2'-deoxyuridine - phosphate name: 2'-deoxyuridine + phosphate -> 2-deoxy-α-D-ribose 1-phosphate + uracil pmids: [] rhea: [] right: - 2-deoxy-α-D-ribose 1-phosphate - uracil yeastcyc_id: URA-PHOSPH-RXN - ec: - 2.7.1.145 - 2.7.1.21 genes: [] left: - ATP - thymidine name: thymidine + ATP -> dTMP + ADP + H+ pmids: [] rhea: [] right: - ADP - H+ - dTMP yeastcyc_id: THYKI-RXN - ec: - 2.4.2.2 - 2.4.2.4 genes: [] left: - phosphate - thymidine name: thymidine + phosphate <-> 2-deoxy-α-D-ribose 1-phosphate + thymine pmids: [] rhea: [] right: - 2-deoxy-α-D-ribose 1-phosphate - thymine yeastcyc_id: THYM-PHOSPH-RXN yeastcyc_id: YEAST-SALV-PYRMID-DNTP