pda1 (SPAC26F1.03; UniProt Q10489) encodes the E1 alpha subunit of the mitochondrial pyruvate dehydrogenase complex. With pdb1 (E1 beta), it forms the thiamine diphosphate-dependent pyruvate decarboxylase/dehydrogenase (EC 1.2.4.1) that makes acetyl-CoA from pyruvate, linking glycolysis to the TCA cycle. Function is assigned by orthology; it is mitochondrial in a genome-wide screen.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004739 pyruvate dehydrogenase (acetyl-transferring) activity | IBA GO_REF:0000033 | ACCEPT | Summary: E1 alpha subunit; contributes to PDH E1 activity (PAINT/EC). Reason: No experimental data on S. pombe pda1 itself. Support is the curated UniProt function, reaction (EC 1.2.4.1) and thiamine diphosphate cofactor (cofactor by similarity to human PDHA1, P08559), plus membership of the NCBIfam TIGR03182 pyruvate dehydrogenase E1 alpha subfamily, whose members are characterised E1 alpha subunits (S. cerevisiae PDA1, rat/human PDHA1 among the PAINT donors). E1 activity is carried by the alpha2beta2 tetramer with pdb1, so pda1 contributes to rather than alone enables the activity. Supporting Evidence: file:SCHPO/pda1/pda1-uniprot.txt The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) file:SCHPO/pda1/pda1-uniprot.txt Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937; file:SCHPO/pda1/pda1-uniprot.txt TIGR03182; PDH_E1_alph_y file:SCHPO/pda1/pda1-uniprot.txt SUBUNIT: Tetramer of 2 alpha and 2 beta subunits. |
| GO:0004739 pyruvate dehydrogenase (acetyl-transferring) activity | IEA GO_REF:0000120 | ACCEPT | Summary: E1 alpha subunit; contributes to PDH E1 activity (PAINT/EC). Reason: No experimental data on S. pombe pda1 itself. Support is the curated UniProt function, reaction (EC 1.2.4.1) and thiamine diphosphate cofactor (cofactor by similarity to human PDHA1, P08559), plus membership of the NCBIfam TIGR03182 pyruvate dehydrogenase E1 alpha subfamily, whose members are characterised E1 alpha subunits (S. cerevisiae PDA1, rat/human PDHA1 among the PAINT donors). E1 activity is carried by the alpha2beta2 tetramer with pdb1, so pda1 contributes to rather than alone enables the activity. Supporting Evidence: file:SCHPO/pda1/pda1-uniprot.txt The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) file:SCHPO/pda1/pda1-uniprot.txt Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937; file:SCHPO/pda1/pda1-uniprot.txt TIGR03182; PDH_E1_alph_y file:SCHPO/pda1/pda1-uniprot.txt SUBUNIT: Tetramer of 2 alpha and 2 beta subunits. |
| 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:0005759 mitochondrial matrix | IBA GO_REF:0000033 | ACCEPT | Summary: Matrix location of this TCA enzyme (inference or mapping); consistent. Reason: The UniProt location is by similarity (ECO:0000250), and the record has a predicted mitochondrial transit peptide (FT TRANSIT, ECO:0000255). A matrix location is also what the E1 function requires, since the PDH complex acts in the matrix. The genome-wide YFP screen (PMID:16823372, a separate HDA row) resolves only mitochondrion, not the sub-compartment. Supporting Evidence: file:SCHPO/pda1/pda1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | IC GO_REF:0000111 | ACCEPT | Summary: Matrix location of this TCA enzyme (inference or mapping); consistent. Reason: The UniProt location is by similarity (ECO:0000250), and the record has a predicted mitochondrial transit peptide (FT TRANSIT, ECO:0000255). A matrix location is also what the E1 function requires, since the PDH complex acts in the matrix. The genome-wide YFP screen (PMID:16823372, a separate HDA row) resolves only mitochondrion, not the sub-compartment. Supporting Evidence: file:SCHPO/pda1/pda1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | Summary: Matrix location of this TCA enzyme (inference or mapping); consistent. Reason: The UniProt location is by similarity (ECO:0000250), and the record has a predicted mitochondrial transit peptide (FT TRANSIT, ECO:0000255). A matrix location is also what the E1 function requires, since the PDH complex acts in the matrix. The genome-wide YFP screen (PMID:16823372, a separate HDA row) resolves only mitochondrion, not the sub-compartment. Supporting Evidence: file:SCHPO/pda1/pda1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0006086 pyruvate decarboxylation to acetyl-CoA | IBA GO_REF:0000033 | ACCEPT | Summary: Oxidative decarboxylation of pyruvate to acetyl-CoA by PDH. Reason: Supported by the curated UniProt function statement for the PDH complex and by family membership (NCBIfam TIGR03182 E1 alpha subfamily); the evidence is by orthology to characterised E1 alpha subunits (S. cerevisiae PDA1, mammalian PDHA1), not from S. pombe experiments. Supporting Evidence: file:SCHPO/pda1/pda1-uniprot.txt The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) file:SCHPO/pda1/pda1-uniprot.txt TIGR03182; PDH_E1_alph_y |
| GO:0006086 pyruvate decarboxylation to acetyl-CoA | IEA GO_REF:0000002 | ACCEPT | Summary: Oxidative decarboxylation of pyruvate to acetyl-CoA by PDH. Reason: Supported by the curated UniProt function statement for the PDH complex and by family membership (NCBIfam TIGR03182 E1 alpha subfamily); the evidence is by orthology to characterised E1 alpha subunits (S. cerevisiae PDA1, mammalian PDHA1), not from S. pombe experiments. Supporting Evidence: file:SCHPO/pda1/pda1-uniprot.txt The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) file:SCHPO/pda1/pda1-uniprot.txt TIGR03182; PDH_E1_alph_y |
| GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: Generic InterPro-derived parent of the specific pyruvate dehydrogenase (acetyl-transferring) activity, which is already annotated. Reason: Correct but too general. pda1 carries the E1 dehydrogenase domain (InterPro IPR001017, behind this row) and is in the PDH E1 alpha subfamily (NCBIfam TIGR03182); UniProt curates the E1 reaction (EC 1.2.4.1), the reductive acetylation of the lipoyl-lysine disulfide of E2 by pyruvate. The specific descendant GO:0004739, which the gene already carries, is the supported term. Family and by-similarity evidence, not an S. pombe enzyme assay. Proposed replacements: pyruvate dehydrogenase (acetyl-transferring) activity Supporting Evidence: file:SCHPO/pda1/pda1-uniprot.txt Reaction=N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2 file:SCHPO/pda1/pda1-uniprot.txt TIGR03182; PDH_E1_alph_y |
| GO:0045254 pyruvate dehydrogenase complex | IBA GO_REF:0000033 | ACCEPT | Summary: Component of the mitochondrial pyruvate dehydrogenase complex. Reason: UniProt describes the complex composition and the E1 alpha2beta2 tetramer (SUBUNIT by similarity, ECO:0000250); membership rests on orthology to S. cerevisiae PDA1 and mammalian PDHA1, which are experimentally established PDH complex subunits. Supporting Evidence: file:SCHPO/pda1/pda1-uniprot.txt It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1) file:SCHPO/pda1/pda1-uniprot.txt SUBUNIT: Tetramer of 2 alpha and 2 beta subunits. |
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