ILV5 encodes the mitochondrial ketol-acid reductoisomerase (acetohydroxyacid reductoisomerase, KARI, EC 1.1.1.86) of Saccharomyces cerevisiae, one of the most abundant mitochondrial matrix proteins. Using NADPH and Mg2+, it converts 2-acetolactate to 2,3-dihydroxyisovalerate and 2-aceto-2-hydroxybutyrate to 2,3-dihydroxy-3-methylvalerate, the second step shared by valine and isoleucine biosynthesis; ilv5 mutants require isoleucine and valine. ILV5 is regulated by general amino acid control and leucine. Ilv5 is also a bifunctional mtDNA nucleoid protein: it binds double-stranded DNA, associates with nucleoids (more so in abf2 cells), and is required for stable inheritance of rho+ mtDNA independently of its enzymatic activity, as point mutations separate the two functions and ILV5 overexpression suppresses mtDNA loss in abf2 mutants. Cytosol-targeted truncated Ilv5 is used in brewing yeast to reduce vicinal diketone (diacetyl) formation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003690 double-stranded DNA binding | IDA PMID:18023287 Maintenance and stabilization of mtDNA can be facilitated by... | ACCEPT | Summary: Macierzanka et al. showed purified Ilv5p binds dsDNA in vitro, independently of Abf2p, and that nucleoid-associated Ilv5p rises in abf2 cells. A genuine moonlighting activity that is genetically separable from catalysis. Supporting Evidence: PMID:18023287 Here we show that Ilv5p binds double-stranded DNA in vitro and is unaffected by the presence of saturating concentrations of Abf2p PMID:18023287 In cells lacking Abf2p the amount of Ilv5p associated with the nucleoid increases significantly |
| GO:0004455 ketol-acid reductoisomerase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN000483120 (seeded by E. coli IlvC P05793 and others, including Ilv5 itself). Correct, core. Supporting Evidence: PMID:3027658 which codes for the branched-chain amino acid biosynthesis enzyme acetohydroxyacid reductoisomerase file:yeast/ILV5/ILV5-uniprot.txt RecName: Full=Ketol-acid reductoisomerase, mitochondrial |
| GO:0004455 ketol-acid reductoisomerase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (IPR000506/IPR016207 KARI, RHEA:22068, EC 1.1.1.86); correct. Supporting Evidence: file:yeast/ILV5/ILV5-uniprot.txt RecName: Full=Ketol-acid reductoisomerase, mitochondrial |
| GO:0004455 ketol-acid reductoisomerase activity | IMP PMID:14124940 GENETIC AND BIOCHEMICAL ANALYSIS OF ISOLEUCINE-VALINE MUTANT... | ACCEPT | Summary: Kakar & Wagner correlated ilv5 isoleucine-valine auxotrophs with loss of reductoisomerase (title-only cache; classical gene-enzyme assignment). Defer to curator. Supporting Evidence: PMID:14124940 GENETIC AND BIOCHEMICAL ANALYSIS OF ISOLEUCINE-VALINE MUTANTS OF YEAST PMID:3027658 which codes for the branched-chain amino acid biosynthesis enzyme acetohydroxyacid reductoisomerase |
| GO:0004455 ketol-acid reductoisomerase activity | IMP PMID:3027658 The ILV5 gene of Saccharomyces cerevisiae is highly expresse... | ACCEPT | Summary: Petersen & Holmberg cloned and sequenced ILV5 as the gene for acetohydroxyacid reductoisomerase, with a gene-dosage-dependent protein band; the activity link rests on complementation of ilv5 mutants. Accept. Supporting Evidence: PMID:3027658 which codes for the branched-chain amino acid biosynthesis enzyme acetohydroxyacid reductoisomerase |
| GO:0004455 ketol-acid reductoisomerase activity | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways BRANCHED-CHAIN-AA-SYN-PWY-1 (superpathway of branched chain amino acid biosynthesis). Ilv5 catalyses step 2/4 (reductive isomerisation of 2-acetolactate / 2-aceto-2-hydroxybutanoate); MF correct. Supporting Evidence: file:yeast/ILV5/ILV5-uniprot.txt RecName: Full=Ketol-acid reductoisomerase, mitochondrial |
| GO:0004455 ketol-acid reductoisomerase activity | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways ILEUSYN-PWY-1 (L-isoleucine biosynthesis I (from threonine)). Ilv5 converts (S)-2-aceto-2-hydroxybutanoate to (2R,3R)-2,3-dihydroxy-3-methylpentanoate in the isoleucine branch; correct. Supporting Evidence: file:yeast/ILV5/ILV5-uniprot.txt RecName: Full=Ketol-acid reductoisomerase, mitochondrial |
| GO:0004455 ketol-acid reductoisomerase activity | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways VALSYN-PWY (L-valine biosynthesis). Ilv5 converts (S)-2-acetolactate to (2R)-2,3-dihydroxy-3-methylbutanoate in the valine branch; correct. Supporting Evidence: file:yeast/ILV5/ILV5-uniprot.txt RecName: Full=Ketol-acid reductoisomerase, mitochondrial |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | ACCEPT | Summary: Ilv5 detected in the mass-spectrometric proteome of highly purified mitochondria (Sickmann et al.); consistent with its N-terminal targeting and low-throughput data. Supporting Evidence: PMID:14576278 The proteins of highly pure yeast mitochondria were separated by several independent methods and analyzed by tandem MS file:yeast/ILV5/ILV5-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion. |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Ilv5 detected in the PROMITO multidimensional mitochondrial proteome; consistent with its N-terminal targeting and low-throughput data. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified file:yeast/ILV5/ILV5-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion. |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: Ilv5 detected in the quantitative proteome of isolated mitochondria under fermentative/respiratory growth; consistent with its N-terminal targeting and low-throughput data. Supporting Evidence: PMID:24769239 we performed an overall quantitative proteomic and phosphoproteomic study of isolated mitochondria file:yeast/ILV5/ILV5-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN001085749, Ilv5 as source); fungal KARIs are mitochondrial. Correct. Supporting Evidence: PMID:18193418 intermediates in isoleucine and valine biosynthesis taking place in the mitochondria |
| GO:0005739 mitochondrion | IDA PMID:18193418 Targeting of mitochondrial Saccharomyces cerevisiae Ilv5p to... | ACCEPT | Summary: Omura showed native Ilv5p is mitochondrial and that removing 46 N-terminal residues is required to make it cytosolic (GFP microscopy). Supporting Evidence: PMID:18193418 intermediates in isoleucine and valine biosynthesis taking place in the mitochondria PMID:18193418 exhibited an unequivocal localization in the cytosol judged from microscopy |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapped to GO; correct. Supporting Evidence: file:yeast/ILV5/ILV5-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion. |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA rule for mitochondrial matrix; consistent with matrix localisation of the valine/isoleucine pathway enzymes (Brat et al.) and with Ilv5 association with matrix-side mtDNA nucleoids. Supporting Evidence: PMID:22954227 The anabolic reactions are part of valine biosynthesis and are located in the mitochondrial matrix, whereas the Ehrlich pathway reactions take place in the cytosol PMID:22954227 Isobutanol production could be improved by re-locating the valine biosynthesis enzymes Ilv2, Ilv5 and Ilv3 from the mitochondrial matrix into the cytosol |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: is_active_in cytosol from YeastPathways BRANCHED-CHAIN-AA-SYN-PWY-1 (superpathway of branched chain amino acid biosynthesis). YeastPathways defaults its reactions to the cytosol; for Ilv5 this contradicts the experimental location. Ilv5 is a mitochondrial matrix protein; cytosolic Ilv5 exists only as an engineered N-terminally truncated construct. Supporting Evidence: PMID:18193418 intermediates in isoleucine and valine biosynthesis taking place in the mitochondria PMID:18193418 exhibited an unequivocal localization in the cytosol judged from microscopy |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: is_active_in cytosol from YeastPathways ILEUSYN-PWY-1 (L-isoleucine biosynthesis I (from threonine)). YeastPathways defaults its reactions to the cytosol; for Ilv5 this contradicts the experimental location. Native Ilv5 is imported into mitochondria. Supporting Evidence: PMID:18193418 intermediates in isoleucine and valine biosynthesis taking place in the mitochondria PMID:22954227 The anabolic reactions are part of valine biosynthesis and are located in the mitochondrial matrix, whereas the Ehrlich pathway reactions take place in the cytosol |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: is_active_in cytosol from YeastPathways VALSYN-PWY (L-valine biosynthesis). YeastPathways defaults its reactions to the cytosol; for Ilv5 this contradicts the experimental location. The valine branch is localised in the matrix. Supporting Evidence: PMID:22954227 The anabolic reactions are part of valine biosynthesis and are located in the mitochondrial matrix, whereas the Ehrlich pathway reactions take place in the cytosol |
| GO:0009082 branched-chain amino acid biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro KARI mapping; correct. Supporting Evidence: PMID:3027658 which codes for the branched-chain amino acid biosynthesis enzyme acetohydroxyacid reductoisomerase |
| GO:0009082 branched-chain amino acid biosynthetic process | IMP PMID:14124940 GENETIC AND BIOCHEMICAL ANALYSIS OF ISOLEUCINE-VALINE MUTANT... | ACCEPT | Summary: ilv5 mutants require isoleucine and valine (classical, title-only cache); defer to curator. Supporting Evidence: PMID:14124940 GENETIC AND BIOCHEMICAL ANALYSIS OF ISOLEUCINE-VALINE MUTANTS OF YEAST PMID:18826960 Ilv5 is required for branched chain amino acid biosynthesis and mtDNA stability. |
| GO:0009082 branched-chain amino acid biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways BRANCHED-CHAIN-AA-SYN-PWY-1 (superpathway of branched chain amino acid biosynthesis). Ilv5 catalyses the shared second step of Ile/Val synthesis. Supporting Evidence: PMID:3027658 which codes for the branched-chain amino acid biosynthesis enzyme acetohydroxyacid reductoisomerase |
| GO:0009099 L-valine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from the KARI node; correct. Supporting Evidence: PMID:3027658 which codes for the branched-chain amino acid biosynthesis enzyme acetohydroxyacid reductoisomerase |
| GO:0009099 L-valine biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway (L-valine biosynthesis step 2/4); correct. Supporting Evidence: file:yeast/ILV5/ILV5-uniprot.txt RecName: Full=Ketol-acid reductoisomerase, mitochondrial |
| GO:0009099 L-valine biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways VALSYN-PWY (L-valine biosynthesis). Correct: Ilv5 reduces 2-acetolactate en route to valine. Supporting Evidence: PMID:3027658 which codes for the branched-chain amino acid biosynthesis enzyme acetohydroxyacid reductoisomerase |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro (IPR013023 KARI domain) mapped to generic 'oxidoreductase activity'; correct but uninformative. Proposed replacements: ketol-acid reductoisomerase activity Supporting Evidence: PMID:3027658 which codes for the branched-chain amino acid biosynthesis enzyme acetohydroxyacid reductoisomerase |
| GO:0042645 mitochondrial nucleoid | IDA PMID:10869431 In organello formaldehyde crosslinking of proteins to mtDNA:... | ACCEPT | Summary: Kaufman et al. identified mtDNA-crosslinked proteins by in organello formaldehyde crosslinking; Ilv5 is a known nucleoid component (abstract does not name it, full text not cached), corroborated by later work showing Ilv5p in nucleoids. Accept. Supporting Evidence: PMID:10869431 we have developed an in organello formaldehyde crosslinking procedure to identify proteins associated with mtDNA PMID:18023287 In cells lacking Abf2p the amount of Ilv5p associated with the nucleoid increases significantly |
| GO:1901705 L-isoleucine biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways ILEUSYN-PWY-1 (L-isoleucine biosynthesis I (from threonine)). Correct: Ilv5 catalyses step 2/4 of isoleucine synthesis. Supporting Evidence: file:yeast/ILV5/ILV5-uniprot.txt RecName: Full=Ketol-acid reductoisomerase, mitochondrial |
| GO:1901859 negative regulation of mitochondrial DNA metabolic process | IGI PMID:18826960 The conserved translocase Tim17 prevents mitochondrial DNA l... | KEEP AS NON CORE | Summary: OXA1 multicopy suppression of mtDNA instability in the ilv5 W327R mutant. GO:1901859 'negative regulation of mitochondrial DNA metabolic process' records the mtDNA-stability phenotype; the former term 'mitochondrial genome maintenance' (GO:0000002) is now obsolete. The regulatory-sign framing is awkward (ilv5 loss causes mtDNA loss, i.e. Ilv5 protects/maintains mtDNA, probably as a nucleoid DNA-binding protein) but no better live GO process exists. Second, genetically separable function of Ilv5; non-core relative to catalysis. Supporting Evidence: PMID:18826960 We have identified OXA1 and TIM17 as novel multicopy suppressors of mtDNA instability in ilv5 cells PMID:18826960 Ilv5 is required for branched chain amino acid biosynthesis and mtDNA stability. |
| GO:1901859 negative regulation of mitochondrial DNA metabolic process | IGI PMID:18826960 The conserved translocase Tim17 prevents mitochondrial DNA l... | KEEP AS NON CORE | Summary: TIM17 multicopy suppression of mtDNA instability in ilv5 cells. GO:1901859 'negative regulation of mitochondrial DNA metabolic process' records the mtDNA-stability phenotype; the former term 'mitochondrial genome maintenance' (GO:0000002) is now obsolete. The regulatory-sign framing is awkward (ilv5 loss causes mtDNA loss, i.e. Ilv5 protects/maintains mtDNA, probably as a nucleoid DNA-binding protein) but no better live GO process exists. Supporting Evidence: PMID:18826960 We have identified OXA1 and TIM17 as novel multicopy suppressors of mtDNA instability in ilv5 cells |
| GO:1901859 negative regulation of mitochondrial DNA metabolic process | IMP PMID:7621838 An enzyme in yeast mitochondria that catalyzes a step in bra... | KEEP AS NON CORE | Summary: Zelenaya-Troitskaya et al.: ilv5 null cells lose rho+ mtDNA, independently of the BCAA biosynthetic block (ilv2 cells keep mtDNA), and ILV5 dosage suppresses abf2. GO:1901859 'negative regulation of mitochondrial DNA metabolic process' records the mtDNA-stability phenotype; the former term 'mitochondrial genome maintenance' (GO:0000002) is now obsolete. The regulatory-sign framing is awkward (ilv5 loss causes mtDNA loss, i.e. Ilv5 protects/maintains mtDNA, probably as a nucleoid DNA-binding protein) but no better live GO process exists. Supporting Evidence: PMID:7621838 Wild-type mtDNA is unstable in cells with an ILV5 null mutation (delta ilv5), leading to the production of mostly rho- petite mutants PMID:7621838 The instability of rho+ mtDNA in delta ilv5 cells is not simply a consequence of a block in branched-chain amino acid biosynthesis PMID:7621838 We suggest that ILV5 encodes a bifunctional protein required for branched-chain amino acid biosynthesis and for the maintenance of rho+ mtDNA |
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Download this section (compressed HTML)Q: GO:0000002 mitochondrial genome maintenance is obsolete; is GO:1901859 negative regulation of mitochondrial DNA metabolic process really the intended replacement for nucleoid proteins such as Ilv5 whose loss causes mtDNA loss?
Experiment: Compare DNA-binding (EMSA) and nucleoid association of catalytic-dead and mtDNA-defective (e.g. W327R) Ilv5 variants with rho+ maintenance in ilv5 and abf2 ilv5 strains.
Hypothesis: The mtDNA-maintenance function of Ilv5 requires its DNA binding but not catalysis.
Acetohydroxyacid reductoisomerase and mtDNA binding protein; involved in branched-chain amino acid biosynthesis and maintenance of wild-type mitochondrial DNA; found in mitochondrial nucleoids
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