Ade2 (YOR128C) is the phosphoribosylaminoimidazole (AIR) carboxylase of Saccharomyces cerevisiae, catalysing step 6 of de novo IMP synthesis. Like other fungal and plant enzymes it is a two-domain fusion: an N-terminal PurK-like ATP-grasp domain that carboxylates AIR with bicarbonate and ATP to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR), and a C-terminal class I PurE domain that rearranges N5-CAIR to CAIR. ade2 mutants require adenine and accumulate a red vacuolar pigment derived from AIR, the basis of the widely used red/white colony colour assay. Ade2 is cytoplasmic.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004638 phosphoribosylaminoimidazole carboxylase activity | IBA GO_REF:0000033 | MODIFY | Summary: PAINT IBA (PANTHER:PTN000549205) for AIR carboxylase activity. Right step, but the term is the class II direct-carboxylase reaction. Reason: GO:0004638 (EC 4.1.1.21) describes direct CO2-dependent carboxylation of AIR, the class II (animal PAICS) chemistry. Ade2 is the fungal/plant fusion of a PurK-type ATP-grasp N5-CAIR synthetase and a class I PurE N5-CAIR mutase (InterPro IPR005875 PurK, IPR033747 PurE_ClassI); the Cryptococcus ortholog was shown to use AIR + ATP + HCO3- and to make N5-CAIR. The two specific activities describe Ade2 correctly. Proposed replacements: 5-(carboxyamino)imidazole ribonucleotide synthase activity 5-(carboxyamino)imidazole ribonucleotide mutase activity Supporting Evidence: PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. PMID:9500840 Amino acid sequence alignments, C-terminal deletion mutants, and biochemical assays indicate that the ADE2 enzyme is a two-domain, bifunctional protein. |
| GO:0004638 phosphoribosylaminoimidazole carboxylase activity | IEA GO_REF:0000120 | MODIFY | Summary: Combined IEA (ARBA:ARBA00028462, InterPro:IPR005875, InterPro:IPR016301, RHEA:10792, EC:4.1.1.21) for EC 4.1.1.21. Right step, but EC 4.1.1.21 is the class II single-step reaction. Reason: GO:0004638 (EC 4.1.1.21) describes direct CO2-dependent carboxylation of AIR, the class II (animal PAICS) chemistry. Ade2 is the fungal/plant fusion of a PurK-type ATP-grasp N5-CAIR synthetase and a class I PurE N5-CAIR mutase (InterPro IPR005875 PurK, IPR033747 PurE_ClassI); the Cryptococcus ortholog was shown to use AIR + ATP + HCO3- and to make N5-CAIR. The two specific activities describe Ade2 correctly. Proposed replacements: 5-(carboxyamino)imidazole ribonucleotide synthase activity 5-(carboxyamino)imidazole ribonucleotide mutase activity Supporting Evidence: PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. PMID:9500840 The biosynthetic product of the ADE2-PurK reaction was identified as N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) by 1H NMR, thus confirming that the C-terminal domain contains a catalytic activity similar to that of the E. coli PurE. |
| GO:0004638 phosphoribosylaminoimidazole carboxylase activity | IMP PMID:5767024 Functional blocks of the ad-1 and ad-2 mutants of Saccharomy... | MODIFY | Summary: IMP from Silver & Eaton 1969: ade2 mutants are blocked at AIR carboxylation (abstract-only). The block is real (ade2 cells accumulate the red AIR-derived pigment), but the yeast enzyme performs the reaction in two ATP-dependent steps. Reason: GO:0004638 (EC 4.1.1.21) describes direct CO2-dependent carboxylation of AIR, the class II (animal PAICS) chemistry. Ade2 is the fungal/plant fusion of a PurK-type ATP-grasp N5-CAIR synthetase and a class I PurE N5-CAIR mutase (InterPro IPR005875 PurK, IPR033747 PurE_ClassI); the Cryptococcus ortholog was shown to use AIR + ATP + HCO3- and to make N5-CAIR. The two specific activities describe Ade2 correctly. Proposed replacements: 5-(carboxyamino)imidazole ribonucleotide synthase activity 5-(carboxyamino)imidazole ribonucleotide mutase activity Supporting Evidence: PMID:5767024 Functional blocks of the ad-1 and ad-2 mutants of Saccharomyces cerevisiae. PMID:8939809 In the yeast Saccharomyces cerevisiae the ade2, and/or the ade1, mutation in the adenine biosynthetic pathway leads to the accumulation of a cell-limited red pigment PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. |
| GO:0004638 phosphoribosylaminoimidazole carboxylase activity | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA (SGD_PWY:DENOVOPURINE2-PWY, superpathway of purine nucleotides de novo biosynthesis II) assigning Ade2 to AIR carboxylation (EC 4.1.1.21). Right step, but YeastCyc models it as the class II direct carboxylation rather than the fungal PurK/PurE two-step route. Reason: GO:0004638 (EC 4.1.1.21) describes direct CO2-dependent carboxylation of AIR, the class II (animal PAICS) chemistry. Ade2 is the fungal/plant fusion of a PurK-type ATP-grasp N5-CAIR synthetase and a class I PurE N5-CAIR mutase (InterPro IPR005875 PurK, IPR033747 PurE_ClassI); the Cryptococcus ortholog was shown to use AIR + ATP + HCO3- and to make N5-CAIR. The two specific activities describe Ade2 correctly. Proposed replacements: 5-(carboxyamino)imidazole ribonucleotide synthase activity 5-(carboxyamino)imidazole ribonucleotide mutase activity Supporting Evidence: PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. PMID:9500840 The biosynthetic product of the ADE2-PurK reaction was identified as N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) by 1H NMR, thus confirming that the C-terminal domain contains a catalytic activity similar to that of the E. coli PurE. |
| GO:0004638 phosphoribosylaminoimidazole carboxylase activity | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA (SGD_PWY:DENOVOPURINE3-PWY, de novo biosynthesis of purine nucleotides) assigning Ade2 to AIR carboxylation (EC 4.1.1.21). Right step, but YeastCyc models it as the class II direct carboxylation rather than the fungal PurK/PurE two-step route. Reason: GO:0004638 (EC 4.1.1.21) describes direct CO2-dependent carboxylation of AIR, the class II (animal PAICS) chemistry. Ade2 is the fungal/plant fusion of a PurK-type ATP-grasp N5-CAIR synthetase and a class I PurE N5-CAIR mutase (InterPro IPR005875 PurK, IPR033747 PurE_ClassI); the Cryptococcus ortholog was shown to use AIR + ATP + HCO3- and to make N5-CAIR. The two specific activities describe Ade2 correctly. Proposed replacements: 5-(carboxyamino)imidazole ribonucleotide synthase activity 5-(carboxyamino)imidazole ribonucleotide mutase activity Supporting Evidence: PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. PMID:9500840 The biosynthetic product of the ADE2-PurK reaction was identified as N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) by 1H NMR, thus confirming that the C-terminal domain contains a catalytic activity similar to that of the E. coli PurE. |
| GO:0004638 phosphoribosylaminoimidazole carboxylase activity | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA (SGD_PWY:PRPP-PWY-1, superpathway of histidine, purine, and pyrimidine biosynthesis) assigning Ade2 to AIR carboxylation (EC 4.1.1.21). Right step, but YeastCyc models it as the class II direct carboxylation rather than the fungal PurK/PurE two-step route. Reason: GO:0004638 (EC 4.1.1.21) describes direct CO2-dependent carboxylation of AIR, the class II (animal PAICS) chemistry. Ade2 is the fungal/plant fusion of a PurK-type ATP-grasp N5-CAIR synthetase and a class I PurE N5-CAIR mutase (InterPro IPR005875 PurK, IPR033747 PurE_ClassI); the Cryptococcus ortholog was shown to use AIR + ATP + HCO3- and to make N5-CAIR. The two specific activities describe Ade2 correctly. Proposed replacements: 5-(carboxyamino)imidazole ribonucleotide synthase activity 5-(carboxyamino)imidazole ribonucleotide mutase activity Supporting Evidence: PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. PMID:9500840 The biosynthetic product of the ADE2-PurK reaction was identified as N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) by 1H NMR, thus confirming that the C-terminal domain contains a catalytic activity similar to that of the E. coli PurE. |
| GO:0004638 phosphoribosylaminoimidazole carboxylase activity | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA (SGD_PWY:PWY-6123-1, inosine-5'-phosphate biosynthesis I) assigning Ade2 to AIR carboxylation (EC 4.1.1.21). Right step, but YeastCyc models it as the class II direct carboxylation rather than the fungal PurK/PurE two-step route. Reason: GO:0004638 (EC 4.1.1.21) describes direct CO2-dependent carboxylation of AIR, the class II (animal PAICS) chemistry. Ade2 is the fungal/plant fusion of a PurK-type ATP-grasp N5-CAIR synthetase and a class I PurE N5-CAIR mutase (InterPro IPR005875 PurK, IPR033747 PurE_ClassI); the Cryptococcus ortholog was shown to use AIR + ATP + HCO3- and to make N5-CAIR. The two specific activities describe Ade2 correctly. Proposed replacements: 5-(carboxyamino)imidazole ribonucleotide synthase activity 5-(carboxyamino)imidazole ribonucleotide mutase activity Supporting Evidence: PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. PMID:9500840 The biosynthetic product of the ADE2-PurK reaction was identified as N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) by 1H NMR, thus confirming that the C-terminal domain contains a catalytic activity similar to that of the E. coli PurE. |
| GO:0004638 phosphoribosylaminoimidazole carboxylase activity | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA (SGD_PWY:PWY3O-285, superpathway of purine biosynthesis and salvage pathways) assigning Ade2 to AIR carboxylation (EC 4.1.1.21). Right step, but YeastCyc models it as the class II direct carboxylation rather than the fungal PurK/PurE two-step route. Reason: GO:0004638 (EC 4.1.1.21) describes direct CO2-dependent carboxylation of AIR, the class II (animal PAICS) chemistry. Ade2 is the fungal/plant fusion of a PurK-type ATP-grasp N5-CAIR synthetase and a class I PurE N5-CAIR mutase (InterPro IPR005875 PurK, IPR033747 PurE_ClassI); the Cryptococcus ortholog was shown to use AIR + ATP + HCO3- and to make N5-CAIR. The two specific activities describe Ade2 correctly. Proposed replacements: 5-(carboxyamino)imidazole ribonucleotide synthase activity 5-(carboxyamino)imidazole ribonucleotide mutase activity Supporting Evidence: PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. PMID:9500840 The biosynthetic product of the ADE2-PurK reaction was identified as N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) by 1H NMR, thus confirming that the C-terminal domain contains a catalytic activity similar to that of the E. coli PurE. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the ATP-grasp domain (InterPro:IPR011761, InterPro:IPR013815). ADE2 has an ATP-grasp ligase domain that consumes ATP in its reaction; correct but subsidiary to the catalytic activity. Supporting Evidence: PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: HDA from the Huh et al. 2003 GFP localization survey: ADE2-GFP cytoplasmic. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (SGD_PWY:DENOVOPURINE2-PWY) compartment for the ADE2 step. Consistent with the cytoplasmic localization of ADE2; de novo purine synthesis is cytosolic in yeast. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (SGD_PWY:DENOVOPURINE3-PWY) compartment for the ADE2 step. Consistent with the cytoplasmic localization of ADE2; de novo purine synthesis is cytosolic in yeast. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (SGD_PWY:PRPP-PWY-1) compartment for the ADE2 step. Consistent with the cytoplasmic localization of ADE2; de novo purine synthesis is cytosolic in yeast. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (SGD_PWY:PWY-6123-1) compartment for the ADE2 step. Consistent with the cytoplasmic localization of ADE2; de novo purine synthesis is cytosolic in yeast. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (SGD_PWY:PWY3O-285) compartment for the ADE2 step. Consistent with the cytoplasmic localization of ADE2; de novo purine synthesis is cytosolic in yeast. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories |
| GO:0006144 purine nucleobase metabolic process | IBA GO_REF:0000033 | MODIFY | Summary: IBA (PANTHER:PTN000549205) purine nucleobase metabolic process. Historically the 'adenine pathway' was annotated to nucleobase terms, but ADE2 acts on ribonucleotide intermediates of de novo IMP synthesis; no free purine base is made. The de novo IMP biosynthetic process term is correct. Reason: Pathway intermediates and product are ribonucleotides, not nucleobases. Proposed replacements: 'de novo' IMP biosynthetic process Supporting Evidence: file:yeast/ADE2/ADE2-uniprot.txt PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; 5- |
| GO:0006144 purine nucleobase metabolic process | IEA GO_REF:0000117 | MODIFY | Summary: IEA (ARBA:ARBA00084209) purine nucleobase metabolic process. Historically the 'adenine pathway' was annotated to nucleobase terms, but ADE2 acts on ribonucleotide intermediates of de novo IMP synthesis; no free purine base is made. The de novo IMP biosynthetic process term is correct. Reason: Pathway intermediates and product are ribonucleotides, not nucleobases. Proposed replacements: 'de novo' IMP biosynthetic process Supporting Evidence: file:yeast/ADE2/ADE2-uniprot.txt PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; 5- |
| GO:0006144 purine nucleobase metabolic process | IMP PMID:8939809 The red/white colony color assay in the yeast Saccharomyces ... | MODIFY | Summary: IMP (PMID:8939809) purine nucleobase metabolic process. Historically the 'adenine pathway' was annotated to nucleobase terms, but ADE2 acts on ribonucleotide intermediates of de novo IMP synthesis; no free purine base is made. The de novo IMP biosynthetic process term is correct. Reason: Pathway intermediates and product are ribonucleotides, not nucleobases. Proposed replacements: 'de novo' IMP biosynthetic process Supporting Evidence: PMID:8939809 In the yeast Saccharomyces cerevisiae the ade2, and/or the ade1, mutation in the adenine biosynthetic pathway leads to the accumulation of a cell-limited red pigment file:yeast/ADE2/ADE2-uniprot.txt PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; 5- |
| GO:0006164 purine nucleotide biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (SGD_PWY:DENOVOPURINE2-PWY, superpathway of purine nucleotides de novo biosynthesis II). Correct general process for ADE2. Supporting Evidence: file:yeast/ADE2/ADE2-uniprot.txt PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; 5- |
| GO:0006164 purine nucleotide biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (SGD_PWY:DENOVOPURINE3-PWY, de novo biosynthesis of purine nucleotides). Correct general process for ADE2. Supporting Evidence: file:yeast/ADE2/ADE2-uniprot.txt PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; 5- |
| GO:0006189 'de novo' IMP biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: IEA (InterPro:IPR000031, InterPro:IPR005875, InterPro:IPR016301, UniPathway:UPA00074) de novo IMP biosynthesis. Correct pathway for ADE2. Supporting Evidence: file:yeast/ADE2/ADE2-uniprot.txt PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; 5- |
| GO:0009152 purine ribonucleotide biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: RCA (SGD_PWY:PWY-6123-1) purine ribonucleotide biosynthetic process. True but general for ADE2, which acts in de novo purine ribonucleotide (IMP/AMP) synthesis. Supporting Evidence: file:yeast/ADE2/ADE2-uniprot.txt PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; 5- |
| GO:0009165 nucleotide biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: RCA (SGD_PWY:PRPP-PWY-1) nucleotide biosynthetic process. True but general for ADE2, which acts in de novo purine ribonucleotide (IMP/AMP) synthesis; the umbrella term comes from the histidine/purine/pyrimidine superpathway. Supporting Evidence: file:yeast/ADE2/ADE2-uniprot.txt PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; 5- |
| GO:0043101 purine-containing compound salvage | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA (SGD_PWY:PWY3O-285, superpathway of purine biosynthesis and salvage pathways) inherited from a superpathway combining de novo synthesis and salvage. ADE2 catalyses only a de novo step (fungal-type bifunctional AIR carboxylase (PurK-like N5-CAIR synthetase + class I PurE N5-CAIR mutase), step 6 of de novo IMP synthesis) and has no role in nucleobase/nucleoside salvage. Supporting Evidence: file:yeast/ADE2/ADE2-uniprot.txt PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; 5- |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO (ATP-grasp domain IPR011761) metal ion binding. ATP-grasp enzymes generally use Mg(2+)-ATP, but no metal binding has been characterised for Ade2; uninformative. Supporting Evidence: PMID:9500840 The N-terminal domain is related to E. coli PurK and a series of kinetic experiments show that the ADE2-PurK activity uses AIR, ATP, and HCO3- as substrates. |
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Download this section (compressed HTML)Q: Should YeastPathways and the PAINT/EC mappings represent fungal Ade2 as the two-step PurK (EC 6.3.4.18) + class I PurE (EC 5.4.99.18) route rather than the class II EC 4.1.1.21 direct carboxylation?
Q: Has the N5-CAIR intermediate been demonstrated directly for S. cerevisiae Ade2, as it has for the Cryptococcus neoformans ortholog?
Experiment: Purify recombinant Ade2 and its isolated N- and C-terminal domains; assay AIR + ATP + HCO3- turnover and detect N5-CAIR by NMR; test complementation of E. coli purK and purE mutants by each domain.
Hypothesis: S. cerevisiae Ade2 forms N5-CAIR from AIR, ATP and bicarbonate and converts it to CAIR, like the Cryptococcus ortholog.
Phosphoribosylaminoimidazole carboxylase; catalyzes a step in the 'de novo' purine nucleotide biosynthetic pathway; red pigment accumulates in mutant cells deprived of adenine
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