kgd2 (SPBC776.15c; UniProt O94681) encodes the lipoylated E2 dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61) core of the mitochondrial 2-oxoglutarate dehydrogenase complex. It transfers the succinyl group from its lipoyl arm to CoA to form succinyl-CoA in the TCA cycle. Function is assigned by orthology; it is mitochondrial in a genome-wide screen.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004149 dihydrolipoyllysine-residue succinyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: E2 dihydrolipoyllysine-residue succinyltransferase activity (PAINT). Reason: PAINT places this activity on the SucB node; kgd2 is in the NCBIfam TIGR01347 sucB family and carries the 2-oxoacid dehydrogenase acyltransferase domain. Not assayed in S. pombe; inference by family and orthology to S. cerevisiae KGD2. Supporting Evidence: file:SCHPO/kgd2/kgd2-uniprot.txt succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA; Xref=Rhea:RHEA:15213 file:SCHPO/kgd2/kgd2-uniprot.txt NCBIfam; TIGR01347; sucB; 1. |
| GO:0004149 dihydrolipoyllysine-residue succinyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: E2 dihydrolipoyllysine-residue succinyltransferase activity (EC/InterPro mapping). Reason: InterPro IPR006255 SucB / EC 2.3.1.61 / RHEA:15213 mapping (family membership); consistent with the IBA row. Not assayed in S. pombe. Supporting Evidence: file:SCHPO/kgd2/kgd2-uniprot.txt succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA; Xref=Rhea:RHEA:15213 file:SCHPO/kgd2/kgd2-uniprot.txt InterPro; IPR006255; SucB. |
| GO:0005739 mitochondrion | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: ORFeome YFP screen: mitochondrion. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of mitochondrial location; consistent with the S. pombe ORFeome localization. Reason: IBA from the mitochondrial SucB node; by similarity UniProt places the protein in mitochondria and a mitochondrial transit peptide is annotated, in agreement with the S. pombe HDA row. Supporting Evidence: file:SCHPO/kgd2/kgd2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000250}. file:SCHPO/kgd2/kgd2-uniprot.txt TRANSIT 1..? /note="Mitochondrion" |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to mitochondrion; consistent. Reason: The UniProt location is by similarity (ECO:0000250) and agrees with a mitochondrial transit peptide and the S. pombe ORFeome HDA row. Root organelle term from a mapping whose claim holds. Supporting Evidence: file:SCHPO/kgd2/kgd2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000250}. file:SCHPO/kgd2/kgd2-uniprot.txt TRANSIT 1..? /note="Mitochondrion" |
| GO:0006099 tricarboxylic acid cycle | EXP PMID:37164017 Optimization of energy production and central carbon metabol... | ACCEPT | Summary: 13C tracing in S. pombe versus S. japonicus shows that S. pombe runs a respiratory, oxidative TCA cycle (curator, full text). Supporting Evidence: PMID:37164017 Here, we use two related fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, as a comparative model system. PMID:37164017 We show that although S. japonicus does not respire oxygen, unlike S. pombe, it is capable of efficient NADH oxidation, amino acid synthesis, and ATP generation. |
| GO:0006099 tricarboxylic acid cycle | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference; the 2-oxoglutarate to succinyl-CoA step of the TCA cycle. Reason: IBA from the SucB node, where the target itself is among the descendant evidences; by similarity, the E2 is a component of the 2-oxoglutarate dehydrogenase complex, which converts 2-oxoglutarate to succinyl-CoA in the TCA cycle. Supporting Evidence: file:SCHPO/kgd2/kgd2-uniprot.txt The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity). |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro mapping; consistent. Reason: InterPro IPR006255 SucB mapping (family membership); by similarity the complex catalyses the 2-oxoglutarate to succinyl-CoA TCA step. Consistent with the IBA and EXP rows. Supporting Evidence: file:SCHPO/kgd2/kgd2-uniprot.txt The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity). file:SCHPO/kgd2/kgd2-uniprot.txt InterPro; IPR006255; SucB. |
| GO:0016746 acyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: Generic InterPro-derived parent of the specific activity, which is already annotated. Reason: Too general. The InterPro 2-oxoacid dehydrogenase acyltransferase domain is the generic signal; the SucB family assignment and the UniProt reaction (EC 2.3.1.61) give the specific succinyltransferase activity the gene already carries. Proposed replacements: dihydrolipoyllysine-residue succinyltransferase activity Supporting Evidence: file:SCHPO/kgd2/kgd2-uniprot.txt succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA; Xref=Rhea:RHEA:15213 file:SCHPO/kgd2/kgd2-uniprot.txt InterPro; IPR001078; 2-oxoacid_DH_actylTfrase. |
| GO:0042645 mitochondrial nucleoid | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Similarity transfer of mitochondrial nucleoid association from S. cerevisiae, where Kgd2p crosslinks to mtDNA in organello. Not shown in S. pombe. Reason: By similarity to S. cerevisiae Kgd2p (P19262), identified among proteins formaldehyde-crosslinked to mtDNA in purified yeast mitochondria. No S. pombe evidence; nucleoid association is a secondary, moonlighting location of a TCA enzyme, so non-core. Supporting Evidence: PMID:10869431 we identified other mtDNA-associated proteins that were not anticipated, such as the molecular chaperone Hsp60p and a Krebs cycle protein, Kgd2p. |
| GO:0045252 oxoglutarate dehydrogenase complex | IEA GO_REF:0000002 | ACCEPT | Summary: E2 core of the 2-oxoglutarate dehydrogenase complex. Reason: InterPro IPR006255 SucB mapping (family membership); by similarity UniProt describes the complex as E1, E2 (dihydrolipoamide succinyltransferase) and E3. Not purified from S. pombe. Supporting Evidence: file:SCHPO/kgd2/kgd2-uniprot.txt The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity). file:SCHPO/kgd2/kgd2-uniprot.txt NCBIfam; TIGR01347; sucB; 1. |
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