E1 component (Kgd1p, YIL125W; alpha-ketoglutarate dehydrogenase, KE1) of the mitochondrial 2-oxoglutarate dehydrogenase complex (KGDH). Using thiamine diphosphate, Kgd1 decarboxylates 2-oxoglutarate and transfers the succinyl group to the lipoyl arm of the E2 core (Kgd2), which forms succinyl-CoA; the E3 Lpd1 reoxidises the dihydrolipoamide with NAD+. Kgd1 binds the 24-meric Kgd2 core, and the small subunit Kgd4 bridges the Kgd1-Kgd2 core to Lpd1. KGDH catalyses the irreversible 2-oxoglutarate to succinyl-CoA step of the TCA cycle in the mitochondrial matrix; kgd1 mutants are respiratory-deficient. Part of the complex associates with mitochondrial nucleoids. KGD1 is glucose-repressed and activated by the HAP complex.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PANTHER PTN000568360 (E1o clade; donors include human OGDH, mouse Ogdh, fly and E. coli SucA). Kgd1 is the E1 (2-oxoglutarate decarboxylase/dehydrogenase) component of the yeast complex; the activity is inherited and supported by yeast genetics. Supporting Evidence: file:yeast/KGD1/KGD1-uniprot.txt Reaction=N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = PMID:2072900 mutations in KGD1 and KGD2, the structural genes for alpha-ketoglutarate dehydrogenase (KE1) and dihydrolipoyl transsuccinylase (KE2) components, respectively |
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from Rhea RHEA:12188 / EC 1.2.4.2 mapping. Correct: Kgd1 is the thiamine-diphosphate-dependent E1 subunit that decarboxylates 2-oxoglutarate and transfers the succinyl group to the lipoyl arm of Kgd2. Supporting Evidence: file:yeast/KGD1/KGD1-uniprot.txt Reaction=N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = |
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways TCA-EUK-PWY (overall 2-oxoglutarate + CoA + NAD+ -> succinyl-CoA reaction) with contributes_to. GO uses GO:0004591 for the complex reaction (the overall NAD+ term is obsolete); Kgd1 contributes the E1 step. Supporting Evidence: PMID:2072900 The reconstitution of enzymatic activity correlates with binding of KE1 to the KE2-E3 particle to form a complex with the same sedimentation properties as wild-type KGDC |
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways PWY-5084 (2-oxoglutarate decarboxylation to succinyl-CoA), E1 reaction EC 1.2.4.2. Correct for Kgd1. Supporting Evidence: file:yeast/KGD1/KGD1-uniprot.txt Reaction=N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = PMID:2072900 mutations in KGD1 and KGD2, the structural genes for alpha-ketoglutarate dehydrogenase (KE1) and dihydrolipoyl transsuccinylase (KE2) components, respectively |
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | TAS PMID:9175438 Molecular genetics of yeast TCA cycle isozymes. | ACCEPT | Summary: TAS from the McAlister-Henn & Small 1997 review of yeast TCA-cycle enzymes; KGD1 encodes the E1 2-oxoglutarate dehydrogenase component. Supporting Evidence: PMID:9175438 Molecular genetics of yeast TCA cycle isozymes. PMID:2072900 mutations in KGD1 and KGD2, the structural genes for alpha-ketoglutarate dehydrogenase (KE1) and dihydrolipoyl transsuccinylase (KE2) components, respectively |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: IPI Kgd1-Kgd2 from the Krogan et al. 2006 TAP-MS survey. The interaction is genuine (both are subunits of the 2-oxoglutarate dehydrogenase complex) and removal does not mean it is false; 'protein binding' carries no functional information and the relationship is captured by part_of oxoglutarate dehydrogenase complex (GO:0045252). Supporting Evidence: PMID:16429126 Proteome survey reveals modularity of the yeast cell machinery. PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: IPI Kgd1-Kgd4 (Ymr31) from the Krogan et al. 2006 TAP-MS survey. The interaction is genuine (both are subunits of the 2-oxoglutarate dehydrogenase complex) and removal does not mean it is false; 'protein binding' carries no functional information and the relationship is captured by part_of oxoglutarate dehydrogenase complex (GO:0045252). Supporting Evidence: PMID:16429126 Proteome survey reveals modularity of the yeast cell machinery. PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH |
| GO:0005515 protein binding | IPI PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | REMOVE | Summary: IPI Kgd1-Kgd2 from Heublein et al. 2014 affinity purification of Kgd1-His7. The interaction is genuine (both are subunits of the 2-oxoglutarate dehydrogenase complex) and removal does not mean it is false; 'protein binding' carries no functional information and the relationship is captured by part_of oxoglutarate dehydrogenase complex (GO:0045252). Supporting Evidence: PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH |
| GO:0005515 protein binding | IPI PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | REMOVE | Summary: IPI Kgd1-Kgd4 (Ymr31) from Heublein et al. 2014: Kgd4 binds the Kgd1-Kgd2 core (most likely Kgd1) and recruits E3. Real and informative biology, but 'protein binding' adds no functional content; the relationship is captured by part_of oxoglutarate dehydrogenase complex (GO:0045252). Removal does not mean the interaction is false. Supporting Evidence: PMID:25165143 these data show that Kgd4 interacts with the Kgd1-Kgd2 complex and not with Kgd2 |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: IPI Kgd1-Kgd2 from the Michaelis et al. 2023 interactome. The interaction is genuine (both are subunits of the 2-oxoglutarate dehydrogenase complex) and removal does not mean it is false; 'protein binding' carries no functional information and the relationship is captured by part_of oxoglutarate dehydrogenase complex (GO:0045252). Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome. PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: IPI Kgd1-Kgd4 (Ymr31) from the Michaelis et al. 2023 interactome. The interaction is genuine (both are subunits of the 2-oxoglutarate dehydrogenase complex) and removal does not mean it is false; 'protein binding' carries no functional information and the relationship is captured by part_of oxoglutarate dehydrogenase complex (GO:0045252). Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome. PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: HDA from a mitochondrial proteomics study detecting Kgd1. Consistent with the matrix localisation of the 2-oxoglutarate dehydrogenase complex. Supporting Evidence: PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. PMID:25165143 Mitochondrial KGDH was purified using a C-terminal His7-tag on Kgd1 |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: HDA from a mitochondrial proteomics study detecting Kgd1. Consistent with the matrix localisation of the 2-oxoglutarate dehydrogenase complex. Supporting Evidence: PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. PMID:25165143 Mitochondrial KGDH was purified using a C-terminal His7-tag on Kgd1 |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: HDA from a mitochondrial proteomics study detecting Kgd1. Consistent with the matrix localisation of the 2-oxoglutarate dehydrogenase complex. Supporting Evidence: PMID:24769239 Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory growth in Saccharomyces cerevisiae. PMID:25165143 Mitochondrial KGDH was purified using a C-terminal His7-tag on Kgd1 |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PANTHER PTN000568260 (eukaryotic E1o; donors include human OGDH and OGDHL, fly, trypanosome and yeast Kgd1). Mitochondrial location is inherited and confirmed experimentally for Kgd1. Supporting Evidence: PMID:25165143 Mitochondrial KGDH was purified using a C-terminal His7-tag on Kgd1 |
| GO:0005739 mitochondrion | IDA PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: IDA from Heublein et al. 2014: KGDH was purified from isolated mitochondria via His-tagged Kgd1. Supporting Evidence: PMID:25165143 Mitochondrial KGDH was purified using a C-terminal His7-tag on Kgd1 PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: IEA from UniProt subcellular location (SL-0173). Correct. Supporting Evidence: file:yeast/KGD1/KGD1-uniprot.txt Mitochondrion matrix. Mitochondrion matrix, mitochondrion nucleoid. |
| GO:0005739 mitochondrion | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways PWY-5084, mitochondrial placement of the E1 reaction. Correct. Supporting Evidence: PMID:25165143 Mitochondrial KGDH was purified using a C-terminal His7-tag on Kgd1 |
| GO:0005739 mitochondrion | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways TCA-EUK-PWY, mitochondrial placement of the 2-oxoglutarate dehydrogenase step. Correct. Supporting Evidence: PMID:25165143 Mitochondrial KGDH was purified using a C-terminal His7-tag on Kgd1 |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | Summary: IEA from UniProt subcellular location (SL-0170, Mitochondrion matrix). Correct; KGDH is a soluble matrix complex (free Lpd1 is also in the matrix). Supporting Evidence: file:yeast/KGD1/KGD1-uniprot.txt Mitochondrion matrix. Mitochondrion matrix, mitochondrion nucleoid. PMID:11926067 These results suggested that a part of KGDC in the mitochondrial matrix is associated with mt-nucleoids in vivo |
| GO:0006099 tricarboxylic acid cycle | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PANTHER PTN000568360 (E1o clade incl. human OGDH, E. coli SucA, M. tuberculosis). TCA-cycle participation is the conserved role of E1o; Kgd1 mutants are respiratory-deficient (pet). Supporting Evidence: PMID:2072900 mutations in KGD1 and KGD2, the structural genes for alpha-ketoglutarate dehydrogenase (KE1) and dihydrolipoyl transsuccinylase (KE2) components, respectively |
| GO:0006099 tricarboxylic acid cycle | NAS PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: NAS from Heublein et al. 2014, which frames KGDH as the TCA-cycle enzyme. Correct statement of function. Supporting Evidence: PMID:25165143 The mitochondrial citric acid cycle is a central hub of cellular metabolism PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH |
| GO:0006099 tricarboxylic acid cycle | TAS PMID:9175438 Molecular genetics of yeast TCA cycle isozymes. | ACCEPT | Summary: TAS from the McAlister-Henn & Small 1997 review of yeast TCA-cycle enzymes. Correct. Supporting Evidence: PMID:9175438 Molecular genetics of yeast TCA cycle isozymes. |
| GO:0006103 2-oxoglutarate metabolic process | IDA PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: IDA from Heublein et al. 2014: KGDH activity (2-oxoglutarate oxidation) measured in mitochondrial lysates of the complex purified via Kgd1. Supporting Evidence: PMID:25165143 Robust KGDH activity was observed in lysates from wild-type cells PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH |
| GO:0006103 2-oxoglutarate metabolic process | TAS PMID:9175438 Molecular genetics of yeast TCA cycle isozymes. | ACCEPT | Summary: TAS from the McAlister-Henn & Small 1997 review. Kgd1 decarboxylates 2-oxoglutarate. Supporting Evidence: PMID:9175438 Molecular genetics of yeast TCA cycle isozymes. file:yeast/KGD1/KGD1-uniprot.txt Reaction=N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = |
| GO:0009060 aerobic respiration | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways TCA-EUK-PWY. The TCA cycle is part of aerobic respiration; kgd1 mutants were isolated as respiratory-deficient pet mutants. Supporting Evidence: PMID:2072900 mutations in KGD1 and KGD2, the structural genes for alpha-ketoglutarate dehydrogenase (KE1) and dihydrolipoyl transsuccinylase (KE2) components, respectively |
| GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: IEA from InterPro IPR001017/IPR011603 (2-oxoacid dehydrogenase E1 / 2-oxoglutarate dehydrogenase E1). The broad parent 'oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor' is correct but uninformative; the specific activity is GO:0004591. Proposed replacements: oxoglutarate dehydrogenase (succinyl-transferring) activity Supporting Evidence: file:yeast/KGD1/KGD1-uniprot.txt Reaction=N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = |
| GO:0030976 thiamine pyrophosphate binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: IEA from InterPro IPR011603 (2-oxoglutarate dehydrogenase E1). Thiamine diphosphate is the obligate E1 cofactor; cofactor binding is subsidiary to the catalytic activity. Supporting Evidence: file:yeast/KGD1/KGD1-uniprot.txt Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937; |
| GO:0042645 mitochondrial nucleoid | IDA PMID:11926067 Identification of the YMN-1 antigen protein and biochemical ... | KEEP AS NON CORE | Summary: IDA from Sato et al. 2002: KE1 (Kgd1) detected in the mt-nucleoid fraction together with KE2 and E3. A real association but peripheral to Kgd1's catalytic role in the matrix. Supporting Evidence: PMID:11926067 alpha-Ketoglutarate dehydrogenase (KE1) and dihydrolipoyl dehydrogenase (E3), which are other subunits of KGDC, were also detected in the mt-nucleoid fraction PMID:11926067 These results suggested that a part of KGDC in the mitochondrial matrix is associated with mt-nucleoids in vivo |
| GO:0042645 mitochondrial nucleoid | IDA PMID:15692048 Aconitase couples metabolic regulation to mitochondrial DNA ... | KEEP AS NON CORE | Summary: IDA from Chen et al. 2005 survey of mtDNA-associated proteins (abstract-only in cache; Kgd1 not named in the abstract). Deferring to the curator; consistent with Sato et al. 2002. Non-core to the TCA function. Supporting Evidence: PMID:15692048 We have identified 22 mtDNA-associated proteins in yeast, among which is mitochondrial aconitase (Aco1p) PMID:11926067 alpha-Ketoglutarate dehydrogenase (KE1) and dihydrolipoyl dehydrogenase (E3), which are other subunits of KGDC, were also detected in the mt-nucleoid fraction |
| GO:0042645 mitochondrial nucleoid | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: IEA from UniProt subcellular location (SL-0269, mitochondrion nucleoid), derived from the nucleoid studies. Non-core. Supporting Evidence: file:yeast/KGD1/KGD1-uniprot.txt Mitochondrion matrix. Mitochondrion matrix, mitochondrion nucleoid. |
| GO:0045252 oxoglutarate dehydrogenase complex | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PANTHER PTN000568360 (donors include human/mouse/rat OGDH, E. coli SucA, yeast Kgd1). E1 membership of the OGDH complex is conserved. Supporting Evidence: PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH |
| GO:0045252 oxoglutarate dehydrogenase complex | IDA PMID:2072900 In vivo assembly of yeast mitochondrial alpha-ketoglutarate ... | ACCEPT | Summary: IDA from Repetto & Tzagoloff 1991: KE1 binds the KE2-E3 particle to reconstitute KGDC; kgd1 mutants form only partial complexes. Supporting Evidence: PMID:2072900 The reconstitution of enzymatic activity correlates with binding of KE1 to the KE2-E3 particle to form a complex with the same sedimentation properties as wild-type KGDC PMID:2072900 Thus mutants lacking KE1 assemble a high-molecular-weight subcomplex consisting of a KE2 core particle with bound dihydrolipoyl dehydrogenase (E3) |
| GO:0045252 oxoglutarate dehydrogenase complex | IPI PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: IPI from Heublein et al. 2014: Kgd2, Lpd1 and Kgd4 copurify with His-tagged Kgd1. Supporting Evidence: PMID:25165143 This led to the identification of four proteins that specifically copurified: Kgd1, Kgd2, and Lpd1, the catalytic subunits of KGDH PMID:25165143 In lysates from wild-type mitochondria, Kgd1, Kgd2, Lpd1, and Kgd4 comigrated |
| GO:0045333 cellular respiration | RCA GO_REF:0000123 | TOO GENERAL | Summary: RCA from YeastPathways PWY-5084. Correct but general; Kgd1 is required for respiratory growth. Supporting Evidence: PMID:2072900 mutations in KGD1 and KGD2, the structural genes for alpha-ketoglutarate dehydrogenase (KE1) and dihydrolipoyl transsuccinylase (KE2) components, respectively |
| GO:0045333 cellular respiration | TAS PMID:9175438 Molecular genetics of yeast TCA cycle isozymes. | TOO GENERAL | Summary: TAS from the McAlister-Henn & Small 1997 review. Correct but general. Supporting Evidence: PMID:9175438 Molecular genetics of yeast TCA cycle isozymes. |
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Download this section (compressed HTML)Subunit of the mitochondrial alpha-ketoglutarate dehydrogenase complex; catalyzes a key step in the tricarboxylic acid (TCA) cycle, the oxidative decarboxylation of alpha-ketoglutarate to form succinyl-CoA
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