Beta subunit (Lsc2p, YGR244C) of mitochondrial succinyl-CoA ligase (succinyl-CoA synthetase, EC 6.2.1.5), an alpha/beta heterodimer with Lsc1. The enzyme catalyses the substrate-level phosphorylation step of the TCA cycle, converting succinyl-CoA, ADP and phosphate to succinate, ATP and CoA. The beta subunit carries the ATP-grasp nucleotide site, binds succinate and Mg2+, and determines nucleotide specificity; S. cerevisiae has a single beta subunit and its enzyme uses ATP but not GTP. LSC2 is glucose-repressed and induced on non-fermentable carbon sources; its deletion abolishes mitochondrial succinyl-CoA ligase activity and impairs growth on glycerol or pyruvate. Lsc2 is a soluble protein of the mitochondrial matrix. It belongs to the A-type beta-subunit lineage, whose assayed members are ATP-specific, and is the ortholog of animal SUCLA2. Gene trees place the duplication of the eukaryotic beta subunit before the divergence of animals, fungi and amoebozoa; animals kept both copies (SUCLA2 and the GDP-specific SUCLG2), whereas S. cerevisiae, like nearly all Dikarya examined, has only the A-type copy. Some early-diverging fungi keep both.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: IEA from UniRule (HAMAP MF_03219). The beta subunit binds the Mg2+ needed for the ATP-dependent reaction; cofactor binding is subsidiary to the catalytic activity. Reason: The term is as specific as the family rule allows and is true of the beta subunit, but binding the Mg2+ cofactor is part of the ligase mechanism and not a separate function, so it is kept as non-core. Supporting Evidence: file:yeast/LSC2/LSC2-uniprot.txt Note=Binds 1 Mg(2+) ion per subunit. |
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: IEA from InterPro (succinyl-CoA synthetase signatures) to the root MF 'catalytic activity'. Correct but uninformative; Lsc2 is the beta subunit, which binds succinate and determines nucleotide (ATP) specificity of ATP-specific succinyl-CoA synthetase. Reason: True but uninformative: GO:0004775 succinate-CoA ligase (ADP-forming) activity, accepted in this review, entails it. Supporting Evidence: file:yeast/LSC2/LSC2-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate; PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | IDA PMID:9874242 Genes of succinyl-CoA ligase from Saccharomyces cerevisiae. | ACCEPT | Summary: IDA (contributes_to) from Przybyla-Zawislak et al. 1998: mitochondrial succinyl-CoA ligase activity is absent in lsc deletion strains and restored by the plasmid-borne gene; the yeast enzyme uses ATP, not GTP. contributes_to is correct for the beta subunit of the obligate heterodimer. Supporting Evidence: PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid PMID:9874242 The yeast succinyl-CoA ligase was shown to utilize ATP but not GTP for succinyl-CoA synthesis |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from Rhea RHEA:17661 / EC 6.2.1.5 / UniRule. The ATP-specific (ADP-forming) reaction is correct for yeast succinyl-CoA ligase; Lsc2 contributes as the beta subunit, which binds succinate and determines nucleotide (ATP) specificity. Supporting Evidence: file:yeast/LSC2/LSC2-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate; PMID:9874242 The yeast succinyl-CoA ligase was shown to utilize ATP but not GTP for succinyl-CoA synthesis |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | IMP PMID:9874242 Genes of succinyl-CoA ligase from Saccharomyces cerevisiae. | ACCEPT | Summary: IMP (contributes_to) from Przybyla-Zawislak et al. 1998: deletion of Lsc2 abolishes mitochondrial succinyl-CoA ligase activity. Supporting Evidence: PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways TCA-EUK-PWY (succinate + ATP + CoA <-> succinyl-CoA + ADP + Pi, EC 6.2.1.5) with contributes_to. Correct. Supporting Evidence: PMID:9874242 The yeast succinyl-CoA ligase was shown to utilize ATP but not GTP for succinyl-CoA synthesis PMID:9874242 The enzyme is composed of alpha and beta subunits that are required for catalytic activity |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: IPI Lsc2-Lsc1 from the Krogan et al. 2006 TAP-MS survey. The alpha/beta interaction is genuine (obligate heterodimer) and removal does not mean it is false; 'protein binding' adds no functional information beyond part_of succinate-CoA ligase complex (ADP-forming). Reason: Bare GO:0005515 protein binding is removed under the protein-binding policy as uninformative. The interaction with Lsc1 is real and is recorded by the complex term GO:0009361. Supporting Evidence: PMID:16429126 Proteome survey reveals modularity of the yeast cell machinery. PMID:9874242 The enzyme is composed of alpha and beta subunits that are required for catalytic activity |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: IPI Lsc2-Lsc1 from the Michaelis et al. 2023 interactome. Genuine subunit interaction captured by complex membership; 'protein binding' is uninformative. Reason: Bare GO:0005515 protein binding is removed under the protein-binding policy as uninformative. The interaction with Lsc1 is real and is recorded by the complex term GO:0009361. Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome. PMID:9874242 The enzyme is composed of alpha and beta subunits that are required for catalytic activity |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: IEA from InterPro IPR013815 (ATP-grasp) / UniRule. The beta subunit carries the ATP-grasp nucleotide site and confers ATP specificity, consistent with the yeast enzyme using ATP but not GTP. Substrate binding, subsidiary to the ligase activity. Reason: The term is true and as specific as a binding term can be for this enzyme, but ATP is a substrate of the ligase reaction, so binding it is part of GO:0004775 and not a separate function. Kept as non-core. Supporting Evidence: PMID:9874242 The yeast succinyl-CoA ligase was shown to utilize ATP but not GTP for succinyl-CoA synthesis |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | TOO GENERAL | Summary: IEA from ARBA00026971, a broad cytoplasm rule. The condition set that fires here is IPR005809 + IPR005811 + PTHR11815:SF1, the eukaryotic A-type (mitochondrial) beta subfamily, with no effective taxon restriction. GO cytoplasm includes mitochondria, so the term is true but uninformative. Reason: Changed from MARK_AS_OVER_ANNOTATED. The term is true, and GO:0005739 mitochondrion, a part_of descendant, is asserted elsewhere in this review, so the row is too general, not doubtful. This matches the action on the same row of the S. pombe ortholog SPCC1620.08. Supporting Evidence: file:yeast/LSC2/LSC2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule: PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | ACCEPT | Summary: HDA from a mitochondrial proteomics study detecting Lsc2. Consistent with mitochondrial succinyl-CoA ligase activity. Supporting Evidence: PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: HDA from a mitochondrial proteomics study detecting Lsc2. Consistent with mitochondrial succinyl-CoA ligase activity. Supporting Evidence: PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: HDA from a mitochondrial proteomics study detecting Lsc2. Consistent with mitochondrial succinyl-CoA ligase activity. Supporting Evidence: PMID:24769239 Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory growth in Saccharomyces cerevisiae. PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PANTHER PTN000212530 (eukaryotic SCS beta; donors include mouse Sucla2 and Suclg2, Arabidopsis, fly and yeast Lsc2). Correct and inherited. Reason: PTN000212530 is the duplication node at the root of the eukaryotic beta subunits, so the location was placed before the A-type and G-type lineages split and both inherit it; the seeds come from both daughter clades. Lsc2 is among the seeds because its own experimental annotation helped place the node. The term stops at the organelle because the seeds are whole-organelle assays. Supporting Evidence: file:yeast/LSC2/LSC2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule: file:yeast/LSC2/LSC2-bioinformatics/RESULTS.md PANTHER places a duplication node (PTN000212530) at the root of the eukaryotic beta subunits. |
| GO:0005739 mitochondrion | IDA PMID:9874242 Genes of succinyl-CoA ligase from Saccharomyces cerevisiae. | ACCEPT | Summary: IDA from Przybyla-Zawislak et al. 1998: succinyl-CoA ligase activity measured in isolated mitochondria depends on the LSC genes. Supporting Evidence: PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: IEA from UniProt subcellular location (SL-0173). Correct. Supporting Evidence: file:yeast/LSC2/LSC2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule: |
| GO:0005739 mitochondrion | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways TCA-EUK-PWY placing the reaction in mitochondria. Correct. Supporting Evidence: PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid |
| GO:0006099 tricarboxylic acid cycle | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PANTHER PTN000212531 (root of the beta-subunit family; donors include E. coli SucC, mouse, rat, fly, S. pombe and plants). Conserved TCA-cycle role. Reason: The node is the LUCA root of the family and the seeds span bacteria, plants, fungi and animals. Fungi retain the role, and a tomato beta-subunit cDNA complements the yeast lsc2 mutant. Supporting Evidence: PMID:9874242 This enzyme functions in the tricarboxylic acid (TCA) cycle PMID:16270230 These three cDNAs were used to complement the respective Saccharomyces cerevisiae mutants deficient in the alpha- and beta-subunit, demonstrating that they encode functionally active polypeptides |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from UniRule/UniPathway (UPA00223, TCA cycle). Correct. Supporting Evidence: PMID:9874242 This enzyme functions in the tricarboxylic acid (TCA) cycle |
| GO:0006099 tricarboxylic acid cycle | NAS PMID:9874242 Genes of succinyl-CoA ligase from Saccharomyces cerevisiae. | ACCEPT | Summary: NAS from Przybyla-Zawislak et al. 1998. Succinyl-CoA ligase catalyses the substrate-level phosphorylation step of the TCA cycle. Supporting Evidence: PMID:9874242 This enzyme functions in the tricarboxylic acid (TCA) cycle PMID:9874242 Succinyl-CoA ligase (succinyl-CoA synthetase) catalyzes the nucleotide-dependent conversion of succinyl-CoA to succinate |
| 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. PMID:9874242 This enzyme functions in the tricarboxylic acid (TCA) cycle |
| GO:0006104 succinyl-CoA metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PANTHER PTN000212531 (root of the beta-subunit family; donors include yeast Lsc2 itself, rat Sucla2 and Suclg2, and tomato). Correct. Reason: Lsc2 is one of the seeds because its own IDA for this term helped place the node; the IBA adds that the role is ancestral to the family, not specific to yeast. GO:0006104 is the is_a parent of GO:1901289 succinyl-CoA catabolic process, which is also asserted (NAS). It is kept beside that child and not marked TOO_GENERAL because the reaction is reversible, so the direction-neutral term names the process of the reaction. Supporting Evidence: PMID:9874242 Succinyl-CoA ligase (succinyl-CoA synthetase) catalyzes the nucleotide-dependent conversion of succinyl-CoA to succinate |
| GO:0006104 succinyl-CoA metabolic process | IDA PMID:9874242 Genes of succinyl-CoA ligase from Saccharomyces cerevisiae. | ACCEPT | Summary: IDA from Przybyla-Zawislak et al. 1998: Lsc2-dependent mitochondrial succinyl-CoA ligase activity converts succinyl-CoA/succinate. Correct; the term covers both directions of the reaction. Reason: GO:0006104 is the is_a parent of GO:1901289 succinyl-CoA catabolic process, which is also asserted (NAS). It is kept beside that child and not marked TOO_GENERAL because the reaction is reversible and the assay was run in the direction of succinyl-CoA synthesis, so the direction-neutral term is what the experiment shows. It is not an ancestor of GO:0006099 tricarboxylic acid cycle. Supporting Evidence: PMID:9874242 The yeast succinyl-CoA ligase was shown to utilize ATP but not GTP for succinyl-CoA synthesis PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid PMID:9874242 Succinyl-CoA ligase (succinyl-CoA synthetase) catalyzes the nucleotide-dependent conversion of succinyl-CoA to succinate |
| GO:0009060 aerobic respiration | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways TCA-EUK-PWY. The TCA cycle is part of aerobic respiration; lsc mutants are impaired on glycerol and pyruvate. Supporting Evidence: PMID:9874242 growth on glycerol or pyruvate was impaired PMID:9874242 This enzyme functions in the tricarboxylic acid (TCA) cycle |
| GO:0009361 succinate-CoA ligase complex (ADP-forming) | NAS PMID:9874242 Genes of succinyl-CoA ligase from Saccharomyces cerevisiae. | ACCEPT | Summary: NAS from Przybyla-Zawislak et al. 1998: the enzyme is an alpha/beta heteromer requiring both subunits, and the yeast enzyme is ATP-specific (ADP-forming). Supporting Evidence: PMID:9874242 The enzyme is composed of alpha and beta subunits that are required for catalytic activity PMID:9874242 The yeast succinyl-CoA ligase was shown to utilize ATP but not GTP for succinyl-CoA synthesis |
| GO:0042709 succinate-CoA ligase complex | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PANTHER PTN000212531 (root of the beta-subunit family). True of Lsc2; the yeast complex is specifically the ADP-forming form (GO:0009361), a child of this term. Reason: Changed from ACCEPT. The node placement is sound. The root of the beta family cannot carry a nucleotide-specific complex term, because its descendants include both the ADP-forming lineage and the GDP-forming SUCLG2 lineage, so PAINT correctly records the parent term there. For Lsc2 the specific child GO:0009361 succinate-CoA ligase complex (ADP-forming) is already asserted in this review (NAS) and is supported by its descent in the A-type lineage, so the parent adds nothing. The S. pombe ortholog SPCC1620.08 takes the same action on this row. Supporting Evidence: PMID:9874242 The enzyme is composed of alpha and beta subunits that are required for catalytic activity PMID:9874242 The yeast succinyl-CoA ligase was shown to utilize ATP but not GTP for succinyl-CoA synthesis file:yeast/LSC2/LSC2-bioinformatics/RESULTS.md Yeast LSC2 is therefore best read as the ortholog of animal SUCLA2 and a paralog of animal SUCLG2. |
| GO:1901289 succinyl-CoA catabolic process | NAS PMID:9874242 Genes of succinyl-CoA ligase from Saccharomyces cerevisiae. | ACCEPT | Summary: NAS from Przybyla-Zawislak et al. 1998. In the TCA-cycle direction the enzyme converts succinyl-CoA to succinate (with ATP formation), i.e. succinyl-CoA catabolism. Supporting Evidence: PMID:9874242 Succinyl-CoA ligase (succinyl-CoA synthetase) catalyzes the nucleotide-dependent conversion of succinyl-CoA to succinate |
| GO:0005759 mitochondrial matrix | IC PMID:28819139 Landscape of submitochondrial protein distribution. | NEW | Summary: Proposed sub-compartment. Lsc2 is a soluble protein of the mitochondrial matrix, and the existing rows stop at the organelle. Reason: Lsc2 has no sub-compartment row, and four lines agree. (1) Voegtle et al. 2017 fractionated yeast mitochondria by sonication and by carbonate extraction and assigned soluble proteins to the matrix by reference to outer-membrane and intermembrane-space proteomes. Lsc2 (YGR244C) is listed as soluble and as a matrix protein in their Supplementary Data 5, which is not part of the cached text and was read from the publisher's file. (2) UniProt gives a cleavable transit peptide (1-30, HAMAP rule). (3) Lsc2 is a subunit of a soluble TCA-cycle enzyme whose substrates are matrix metabolites, and the activity was measured in isolated mitochondria. (4) Its obligate partner Lsc1 has the same matrix assignment, a processed presequence and a mitochondrial nucleoid row, and the nucleoid is part of the matrix. IC is used because the matrix assignment in the proteomic study is a deduction from fractionation and not a direct assay. All GO:0005739 rows are kept. The alpha subunit Lsc1 gets the same row. Supporting Evidence: PMID:28819139 We used the well-established OM and IMS reference proteomes17, 31 (Methods section) to deduce the sublocalization of all mitochondrial proteins characterized above file:yeast/LSC2/LSC2-uniprot.txt TRANSIT 1..30 /note="Mitochondrion" PMID:9874242 This enzyme functions in the tricarboxylic acid (TCA) cycle PMID:9874242 Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid |
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Download this section (compressed HTML)Q: Is Pro at position 20 of the mature beta subunit enough to explain why yeast succinyl-CoA synthetase does not use GTP? E. coli and Thermus aquaticus enzymes also have Pro there and accept GTP, and the Blastocystis enzyme has Gln there and is ATP-specific, so other residues of the Lsc2 nucleotide site must contribute.
Q: Why was the G-type beta subunit lost in most Dikarya and several other fungal lineages, while Mortierellomycota, Basidiobolus, Rozella and the ascomycete Saitoella retain a SUCLG2-type gene, as animals, choanoflagellates and Dictyostelium do? Is the SUCLG2-type enzyme of those fungi GDP-forming, and is import of GTP by Ggc1p the compensating adaptation or a separate, older trait?
Q: What does the divergent second beta-like protein of Ustilago maydis (A0A0D1E3R8, UMAG_01904) do? It lacks the ATP-grasp domain. PANTHER places it in the SUCLG2 clade, but both sequence trees place it with prokaryotic sequences, outside both human paralogs. The neighbouring gene UMAG_01903 (A0A0D1CWH6) is a divergent alpha-like protein, so the two may form a separate enzyme.
Q: From which copy of the eukaryotic beta-subunit duplication do the plant, stramenopile and excavate subunits descend? PANTHER puts them on the SUCLG2 side and both sequence trees put the plant, stramenopile and trypanosomatid subunits on the SUCLA2 side, without strong support for plants and trypanosomatids; the Trichomonas subunits are unresolved.
Q: Do the phosphoserines of Lsc2 (Ser102, Ser263, Ser276) regulate succinyl-CoA synthetase during the shift between fermentative and respiratory growth?
Experiment: Purify recombinant Lsc1/Lsc2 and measure kcat/Km with ADP and GDP for wild type and for a Pro-to-Gln substitution at the position aligned to Pro20 of E. coli SucC; compare with the E. coli P20Q enzyme.
Hypothesis: Nucleotide specificity of yeast succinyl-CoA synthetase is set by a small number of residues in the Lsc2 ATP-grasp site, with position 20 of the mature subunit a main contributor.
Experiment: Express a mitochondrially targeted animal SUCLG2 in an lsc2 deletion strain and assay GDP-dependent succinyl-CoA synthetase activity in isolated mitochondria and growth on glycerol.
Hypothesis: The yeast alpha subunit can partner a G-type beta subunit, so the absence of GDP-forming activity in S. cerevisiae is explained by absence of the G-type beta paralog alone.
Beta subunit of succinyl-CoA ligase; succinyl-CoA ligase is a mitochondrial enzyme of the TCA cycle that catalyzes the nucleotide-dependent conversion of succinyl-CoA to succinate
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