Beta subunit of mitochondrial succinyl-CoA synthetase (ADP-forming; EC 6.2.1.5), the alpha-beta heterodimer that converts succinyl-CoA to succinate with substrate-level ATP formation in the TCA cycle. The S. pombe enzyme has not been characterised biochemically; its role is inferred from the S. cerevisiae Lsc1/Lsc2 enzyme. The protein localises to mitochondria.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: Mg2+ cofactor binding by the beta subunit; subsidiary to the ligase activity. Reason: Family-level evidence: the HAMAP rule MF_03219 cofactor annotation and the HAMAP-predicted Mg2+-binding residues (228, 242) for the succinyl-CoA synthetase beta family; not tested in S. pombe. Cofactor binding is part of the catalytic mechanism, not a separate role, so it is non-core. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Note=Binds 1 Mg(2+) ion per subunit. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt BINDING 228 /ligand="Mg(2+)" |
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: Generic InterPro-derived parent of the specific activity, which is already annotated. Reason: True but uninformative: GO:0004775 succinate-CoA ligase (ADP-forming) activity, accepted in this review, entails it. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents the only step of substrate-level phosphorylation in the TCA. |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | IBA GO_REF:0000033 | ACCEPT | Summary: ADP-forming succinyl-CoA synthetase activity (PAINT); the beta subunit sets ATP/ADP specificity. Reason: PAINT places this activity on the succinyl-CoA synthetase beta-chain node; SPCC1620.08 falls in the PANTHER PTHR11815:SF1 mitochondrial ADP-forming subfamily, and the HAMAP rule (family membership) gives the ATP-linked reaction. No S. pombe enzymology; inference is by family and orthology to S. cerevisiae LSC2. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt PANTHER; PTHR11815:SF1; SUCCINATE--COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL; 1. |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | IEA GO_REF:0000120 | ACCEPT | Summary: ADP-forming succinyl-CoA synthetase activity (EC/Rhea mapping); consistent with the IBA row. Reason: EC 6.2.1.5 / RHEA:17661 mapping from the HAMAP rule MF_03219 (family membership; HAMAP MF_00558 Succ_CoA_beta). Not assayed in S. pombe; consistent with the IBA row for the same term. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt HAMAP; MF_00558; Succ_CoA_beta; 1. |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: ATP binding at the beta-subunit nucleotide site; subsidiary to the ligase activity. Reason: Family-level evidence: the HAMAP rule states that the beta subunit provides nucleotide specificity and predicts ATP-binding residues in the ATP-grasp domain. Not tested in S. pombe; nucleotide binding is part of the catalytic activity, so non-core. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt BINDING 68 /ligand="ATP" |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | TOO GENERAL | Summary: ARBA mapping to cytoplasm; the enzyme is a mitochondrial matrix TCA enzyme, annotated elsewhere in this review. Reason: Changed from KEEP_AS_NON_CORE: cytoplasm is true only in the GO sense that the mitochondrial matrix is part_of cytoplasm, and GO:0005759 mitochondrial matrix (part_of descendant) is asserted elsewhere in this review. Support for the matrix location is family-level: the HAMAP-predicted mitochondrial transit peptide, the mitochondrial location (also seen in the S. pombe ORFeome screen) and the TCA-cycle function. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt TRANSIT 1..23 /note="Mitochondrion" file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03219, ECO:0000269|PubMed:16823372}. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents the only step of substrate-level phosphorylation in the TCA. |
| 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 succinyl-CoA synthetase beta node; independently consistent with the S. pombe genome-wide YFP localization (cited in UniProt as ECO:0000269 PubMed:16823372) and a predicted N-terminal mitochondrial transit peptide. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03219, ECO:0000269|PubMed:16823372}. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt TRANSIT 1..23 /note="Mitochondrion" |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to mitochondrion; consistent. Reason: The UniProt location rests on the HAMAP rule and on the S. pombe ORFeome localization (ECO:0000269 PubMed:16823372); a predicted transit peptide agrees. Root organelle term from a mapping whose claim holds. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03219, ECO:0000269|PubMed:16823372}. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt TRANSIT 1..23 /note="Mitochondrion" |
| GO:0005759 mitochondrial matrix | IC GO_REF:0000111 | ACCEPT | Summary: Matrix location of this TCA enzyme (curator inference from the activity). Reason: Inference from two family-level lines: a cleavable mitochondrial transit peptide (HAMAP prediction) and the TCA-cycle succinyl-CoA synthetase function, which acts on matrix metabolites. No sub-mitochondrial assay in S. pombe. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt TRANSIT 1..23 /note="Mitochondrion" file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents the only step of substrate-level phosphorylation in the TCA. |
| 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 succinyl-CoA synthetase step of the TCA cycle. Reason: IBA from the succinyl-CoA synthetase beta node, where the target itself is among the descendant evidences; the HAMAP rule (family membership) places the enzyme at the succinyl-CoA to succinate step of the TCA cycle. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents the only step of substrate-level phosphorylation in the TCA. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro/UniPathway mapping; consistent. Reason: InterPro IPR005809 / UniPathway UPA00223 mapping; the HAMAP rule (family membership) places the enzyme in the TCA cycle, succinate from succinyl-CoA step. Consistent with the IBA and EXP rows. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents the only step of substrate-level phosphorylation in the TCA. |
| GO:0006104 succinyl-CoA metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Succinyl-CoA metabolism; the direct process of the reaction the enzyme catalyses. Reason: True by family-level evidence: the HAMAP-rule reaction interconverts succinyl-CoA and succinate, the reaction is reversible, and the term names the direct process of the reaction. No asserted term in this review is a descendant of succinyl-CoA metabolic process (the TCA cycle is not). Changed from KEEP_AS_NON_CORE so that the term has the same action on every reviewed subunit of the enzyme, including S. cerevisiae Lsc2, which is one of the seeds of this PAINT node. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents the only step of substrate-level phosphorylation in the TCA. |
| GO:0009361 succinate-CoA ligase complex (ADP-forming) | IC GO_REF:0000111 | ACCEPT | Summary: Subunit of the ADP-forming succinate-CoA ligase alpha-beta heterodimer. Reason: Family-level evidence (HAMAP rule MF_03219): the enzyme is an alpha-beta heterodimer and catalyses the ATP/ADP-linked reaction, so the complex is the ADP-forming one. Not purified from S. pombe. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt SUBUNIT: Heterodimer of an alpha and a beta subunit. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate |
| GO:0042709 succinate-CoA ligase complex | IBA GO_REF:0000033 | TOO GENERAL | Summary: PAINT inference of the succinate-CoA ligase complex; the more specific ADP-forming complex is annotated. Reason: Changed from ACCEPT: the PAINT node placement is not challenged (the claim is true), but GO:0009361 succinate-CoA ligase complex (ADP-forming), an is_a descendant, is asserted elsewhere in this review, so this term adds nothing. Family-level support (HAMAP rule) for the heterodimer and the ADP-forming reaction. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000212531 SUPPORTS TRANSFER The node transfers correctly; the term is entailed by the accepted ADP-forming succinate-CoA ligase complex row. Supporting Evidence: file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt SUBUNIT: Heterodimer of an alpha and a beta subunit. file:SCHPO/SPCC1620.08/SPCC1620.08-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate |
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