Major 2-isopropylmalate synthase (alpha-isopropylmalate synthase, alpha-IPMS, EC 2.3.3.13) of Saccharomyces cerevisiae, catalysing the first committed step of leucine biosynthesis: condensation of acetyl-CoA with 3-methyl-2-oxobutanoate (alpha-ketoisovalerate) to give 2-isopropylmalate. LEU4 encodes two forms by alternative translation initiation: a long form imported into mitochondria, which provides most cellular alpha-IPMS activity, and a short cytosolic form that is also functional. 2-Isopropylmalate made in mitochondria is exported to the cytosol by the Oac1 carrier, where it is converted by Leu1 and Leu2 and also acts as the coactivator of the transcription factor Leu3. Leu4 homodimers are feedback-inhibited by leucine, whereas its paralog Leu9 is leucine-resistant; Leu4-Leu9 heterodimers form in vivo with intermediate regulation. leu4 deletion leaves ~20% residual activity from Leu9, and leu4 leu9 double mutants are leucine auxotrophs.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: Root catalytic activity from InterPro (HMGL-like TIM barrel). True but uninformative. Reason: Replace with the specific activity. Proposed replacements: 2-isopropylmalate synthase activity Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. PMID:25841022 Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. |
| GO:0003852 2-isopropylmalate synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (seeded by Leu4 and Leu9); family-defining activity. Core. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. PMID:25841022 Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. |
| GO:0003852 2-isopropylmalate synthase activity | IDA PMID:25841022 Diversification of Paralogous Ξ±-Isopropylmalate Synthases by... | ACCEPT | Summary: Purified Leu4 homodimer has alpha-IPMS activity and is leucine sensitive. Core. Supporting Evidence: PMID:25841022 Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. |
| GO:0003852 2-isopropylmalate synthase activity | IDA PMID:3275644 Yeast LEU4 encodes mitochondrial and nonmitochondrial forms ... | ACCEPT | Summary: Activity of LEU4-encoded long and short forms directly measured. Core. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. PMID:3275644 the short form is functional in leucine biosynthesis, is inhibited by leucine with an apparent inhibitor constant of approximately 0.4 mM, and exists as a cytoplasmic dimer |
| GO:0003852 2-isopropylmalate synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic EC/RHEA mapping (EC 2.3.3.13). Core. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. PMID:25841022 Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. |
| GO:0003852 2-isopropylmalate synthase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways BCAA superpathway assignment. Core. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. PMID:25841022 Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. |
| GO:0003852 2-isopropylmalate synthase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways leucine biosynthesis assignment. Core. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. PMID:25841022 Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | MODIFY | Summary: High-throughput detection of Leu4-Leu9 interaction. The interaction is real (confirmed by BiFC and co-purification) but protein binding is uninformative. Reason: The interaction partner is the paralogous alpha-IPMS (Leu4/Leu9); Lopez et al. 2015 showed these form heterodimeric isozymes in vivo, so the informative term is protein heterodimerization activity. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:16429126 Proteome survey reveals modularity of the yeast cell machinery. PMID:25841022 Bimolecular fluorescent complementation analysis showed that Leu4-Leu9 heterodimeric isozymes are formed in vivo. |
| GO:0005515 protein binding | IPI PMID:18719252 High-quality binary protein interaction map of the yeast int... | MODIFY | Summary: Yeast two-hybrid detection of Leu4-Leu9 interaction; real but uninformative term. Reason: The interaction partner is the paralogous alpha-IPMS (Leu4/Leu9); Lopez et al. 2015 showed these form heterodimeric isozymes in vivo, so the informative term is protein heterodimerization activity. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:18719252 demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information PMID:25841022 Bimolecular fluorescent complementation analysis showed that Leu4-Leu9 heterodimeric isozymes are formed in vivo. |
| GO:0005515 protein binding | IPI PMID:25841022 Diversification of Paralogous Ξ±-Isopropylmalate Synthases by... | MODIFY | Summary: Direct demonstration that Leu4 and Leu9 form heterodimeric alpha-IPMS isozymes in vivo, with distinct leucine sensitivity. More informatively captured as protein heterodimerization activity. Reason: Replace generic protein binding with the specific heteromeric association documented. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:25841022 Bimolecular fluorescent complementation analysis showed that Leu4-Leu9 heterodimeric isozymes are formed in vivo. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | MODIFY | Summary: High-throughput interactome detection of Leu4-Leu9; real but uninformative term. Reason: The interaction partner is the paralogous alpha-IPMS (Leu4/Leu9); Lopez et al. 2015 showed these form heterodimeric isozymes in vivo, so the informative term is protein heterodimerization activity. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome. PMID:25841022 Bimolecular fluorescent complementation analysis showed that Leu4-Leu9 heterodimeric isozymes are formed in vivo. |
| GO:0005737 cytoplasm | HDA PMID:11914276 Subcellular localization of the yeast proteome. | ACCEPT | Summary: Global localization HDA; consistent with the cytosolic short form of Leu4. Supporting Evidence: PMID:11914276 Subcellular localization of the yeast proteome. PMID:3275644 the short form is functional in leucine biosynthesis, is inhibited by leucine with an apparent inhibitor constant of approximately 0.4 mM, and exists as a cytoplasmic dimer |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: GFP localization HDA; consistent with the cytosolic short form of Leu4. Supporting Evidence: PMID:14562095 Global analysis of protein localization in budding yeast. PMID:3275644 the short form is functional in leucine biosynthesis, is inhibited by leucine with an apparent inhibitor constant of approximately 0.4 mM, and exists as a cytoplasmic dimer |
| GO:0005737 cytoplasm | IDA PMID:3275644 Yeast LEU4 encodes mitochondrial and nonmitochondrial forms ... | ACCEPT | Summary: Short (second-AUG) form of Leu4 is a functional cytoplasmic dimer. Supporting Evidence: PMID:3275644 indicate that two forms of hybrid protein are produced and that only the larger form is targeted to the mitochondria PMID:3275644 the short form is functional in leucine biosynthesis, is inhibited by leucine with an apparent inhibitor constant of approximately 0.4 mM, and exists as a cytoplasmic dimer |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location (cytoplasmic isoform). Supporting Evidence: PMID:3275644 the short form is functional in leucine biosynthesis, is inhibited by leucine with an apparent inhibitor constant of approximately 0.4 mM, and exists as a cytoplasmic dimer |
| GO:0005739 mitochondrion | HDA PMID:11914276 Subcellular localization of the yeast proteome. | ACCEPT | Summary: Global localization HDA; mitochondrial long form. Supporting Evidence: PMID:11914276 Subcellular localization of the yeast proteome. PMID:3275644 indicate that two forms of hybrid protein are produced and that only the larger form is targeted to the mitochondria |
| GO:0005739 mitochondrion | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: GFP localization HDA; mitochondrial long form. Supporting Evidence: PMID:14562095 Global analysis of protein localization in budding yeast. PMID:3275644 indicate that two forms of hybrid protein are produced and that only the larger form is targeted to the mitochondria |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | ACCEPT | Summary: Mitochondrial proteome HDA. Supporting Evidence: PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. PMID:3275644 indicate that two forms of hybrid protein are produced and that only the larger form is targeted to the mitochondria |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Mitochondrial proteome HDA. Supporting Evidence: PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. PMID:3275644 indicate that two forms of hybrid protein are produced and that only the larger form is targeted to the mitochondria |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: Mitochondrial proteome HDA. Supporting Evidence: PMID:24769239 Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory growth in Saccharomyces cerevisiae. PMID:3275644 indicate that two forms of hybrid protein are produced and that only the larger form is targeted to the mitochondria |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (is_active_in mitochondrion); the main site of alpha-IPM synthesis. Core location. Supporting Evidence: PMID:25841022 Subcellular localization analysis showed that Leu4 and Leu9 are localized in the mitochondria PMID:25841022 Ξ±-IPM is then transported from the mitochondria to the cytosol by the yeast oxaloacetate/sulfate carrier Oac1 |
| GO:0005739 mitochondrion | IDA PMID:25841022 Diversification of Paralogous Ξ±-Isopropylmalate Synthases by... | ACCEPT | Summary: Direct localization of Leu4 to mitochondria. Core location. Supporting Evidence: PMID:25841022 Subcellular localization analysis showed that Leu4 and Leu9 are localized in the mitochondria PMID:25841022 Ξ±-IPM is then transported from the mitochondria to the cytosol by the yeast oxaloacetate/sulfate carrier Oac1 |
| GO:0005739 mitochondrion | IDA PMID:3275644 Yeast LEU4 encodes mitochondrial and nonmitochondrial forms ... | ACCEPT | Summary: Long form of Leu4 is imported into mitochondria. Core location. Supporting Evidence: PMID:3275644 indicate that two forms of hybrid protein are produced and that only the larger form is targeted to the mitochondria |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic mitochondrion annotation; correct for the long form. Supporting Evidence: PMID:3275644 indicate that two forms of hybrid protein are produced and that only the larger form is targeted to the mitochondria |
| GO:0005829 cytosol | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: YeastPathways places the alpha-IPMS step in the cytosol. This is correct only for the minor short form of Leu4; the bulk of activity and the physiological reaction (on alpha-ketoisovalerate made in mitochondria) is mitochondrial. Reason: Valid for the cytosolic short isoform, but the predominant activity is mitochondrial; the YeastPathways compartment assignment for this step is incomplete. Supporting Evidence: PMID:3275644 the short form is functional in leucine biosynthesis, is inhibited by leucine with an apparent inhibitor constant of approximately 0.4 mM, and exists as a cytoplasmic dimer PMID:25841022 Ξ±-IPM is then transported from the mitochondria to the cytosol by the yeast oxaloacetate/sulfate carrier Oac1 |
| GO:0005829 cytosol | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: As above; cytosolic activity reflects only the short Leu4 form. Reason: Valid for the cytosolic short isoform only. Supporting Evidence: PMID:3275644 the short form is functional in leucine biosynthesis, is inhibited by leucine with an apparent inhibitor constant of approximately 0.4 mM, and exists as a cytoplasmic dimer |
| GO:0008270 zinc ion binding | RCA PMID:30358795 The cellular economy of the Saccharomyces cerevisiae zinc pr... | KEEP AS NON CORE | Summary: Zinc binding inferred in a computational zinc-proteome survey. Reason: The zinc assignment is from a bioinformatic zinc-proteome survey; LeuA-family synthases bind a catalytic divalent metal, but the physiological metal of the yeast enzyme has not been established. Kept as a plausible non-core cofactor annotation. Supporting Evidence: PMID:30358795 The yeast zinc proteome of 582 known or potential zinc-binding proteins was identified using a bioinformatics analysis that combined global domain searches with local motif searches. |
| GO:0009082 branched-chain amino acid biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: Correct parent of leucine biosynthesis. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. |
| GO:0009098 L-leucine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA. Core. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. PMID:10790691 A mutant in which both ORF YOR108w and LEU4 gene have been deleted proved to be leucine auxotrophic and alpha-isopropylmalate synthase (alpha-IPMS)-negative. |
| GO:0009098 L-leucine biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation consistent with experimental data. Core. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. |
| GO:0009098 L-leucine biosynthetic process | IGI PMID:10790691 Identification by functional analysis of the gene encoding a... | ACCEPT | Summary: leu4 leu9 double deletion is a leucine auxotroph lacking alpha-IPMS activity, showing redundant participation of both paralogs. Core. Supporting Evidence: PMID:10790691 A mutant in which both ORF YOR108w and LEU4 gene have been deleted proved to be leucine auxotrophic and alpha-isopropylmalate synthase (alpha-IPMS)-negative. |
| GO:0009098 L-leucine biosynthetic process | IMP PMID:25841022 Diversification of Paralogous Ξ±-Isopropylmalate Synthases by... | ACCEPT | Summary: leu4 deletion alters leucine pools and growth, rescued by LEU4. Core. Supporting Evidence: PMID:25841022 The leu4Ξ mutant, which expresses only the feedback-resistant Leu9 homodimer, grows slowly with either glucose or ethanol and accumulates elevated pools of leucine |
| GO:0009098 L-leucine biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways leucine biosynthesis. Core. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. |
| GO:0046912 acyltransferase activity, acyl groups converted into alkyl on transfer | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro-based parent class of 2-isopropylmalate synthase activity; correct but less specific. Reason: Redundant with the specific activity term. Supporting Evidence: PMID:3275644 The LEU4 gene of Saccharomyces cerevisiae is the major structural gene involved in the production of alpha-isopropylmalate synthase. |
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