Summary: IEA from InterPro (succinyl-CoA synthetase signatures) to the root MF 'catalytic activity'. Correct but uninformative; Lsc1 is the alpha subunit, which binds CoA and phosphate and carries the phosphohistidine intermediate of ATP-specific succinyl-CoA synthetase.

Reason: True but uninformative: GO:0004775 succinate-CoA ligase (ADP-forming) activity, accepted in this review, entails it.

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 alpha subunit of the obligate heterodimer.

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; Lsc1 contributes as the alpha subunit, which binds CoA and phosphate and carries the phosphohistidine intermediate.

Summary: IMP (contributes_to) from Przybyla-Zawislak et al. 1998: deletion of Lsc1 abolishes mitochondrial succinyl-CoA ligase activity.

Summary: RCA from YeastPathways TCA-EUK-PWY (succinate + ATP + CoA <-> succinyl-CoA + ADP + Pi, EC 6.2.1.5) with contributes_to. Correct.

Summary: IBA from PANTHER PTN000122012, the LUCA node of the alpha-subunit family, seeded by animal and Dictyostelium alpha subunits and by E. coli and P. aeruginosa SucD. The term is true of those seeds but not of Lsc1, whose only partner is the A-type beta subunit Lsc2 and whose enzyme used ATP but not GTP when assayed.

Reason: Whether an alpha subunit takes part in GDP-forming activity is decided by its beta partner, not by the alpha subunit. The seeds fall in two groups. The animal and Dictyostelium alpha subunits come from genomes that encode a G-type beta subunit (SUCLG2 lineage), and the enzyme purified from Dictyostelium uses GTP; the E. coli and P. aeruginosa enzymes have a single beta subunit that accepts both nucleotides. Neither holds in S. cerevisiae, which encodes one alpha subunit (Lsc1) and one beta subunit (Lsc2), of the A-type (SUCLA2) lineage. The 15 fungal genomes in the PANTHER tree (14 Dikarya and one chytrid) have no G-type beta gene. This is not a property of all fungi. Mortierellomycota, Basidiobolus and Rozella keep a SUCLG2-type gene, so the G-type gene was lost within fungi. Within Dikarya one Taphrinomycotina species, Saitoella complicata, also has a Gln20 SUCLG2-type entry (A0A0E9NQG5); it groups with the Mortierellomycota genes only weakly, so vertical retention, transfer and contamination are not distinguished and its origin is unresolved. In isolated mitochondria the yeast enzyme used ATP but not GTP for succinyl-CoA synthesis; the result is qualitative and known here from the abstract only, so a low residual GTP activity is not excluded by the assay alone, and the removal rests on the assay together with the genome (one beta gene, of the A-type lineage whose assayed animal member also excludes GTP). The node placement is defensible for the family, but the term does not hold for the fungal genomes under PTN000874203 and needs pruning there; this is an argument about the node, not about the number of donors. S. pombe SPAC16E8.17c inherits the same row and, lacking a direct assay, is marked as over-annotated. An OpenScientist run given this hypothesis read the same public evidence the same way (it calls GO:0004776 an over-annotation on yeast Lsc1) and also notes that the assay is qualitative; it is a second reading of the evidence, not independent support.

Summary: IPI Lsc1-Lsc2 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 Lsc2 is real and is recorded by the complex term GO:0009361.

Summary: IPI Lsc1-Lsc2 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 Lsc2 is real and is recorded by the complex term GO:0009361.

Summary: HDA from a mitochondrial proteomics study detecting Lsc1. Consistent with mitochondrial succinyl-CoA ligase activity.

Summary: HDA from a mitochondrial proteomics study detecting Lsc1. Consistent with mitochondrial succinyl-CoA ligase activity.

Summary: HDA from a mitochondrial proteomics study detecting Lsc1. Consistent with mitochondrial succinyl-CoA ligase activity.

Summary: IBA from PANTHER PTN000122014 (eukaryotic SCS alpha; donors include Arabidopsis, mouse Suclg1, trypanosome and yeast Lsc1). Mitochondrial location is inherited and experimentally confirmed.

Reason: The node is the eukaryotic clade, which PANTHER derives from within the bacterial alpha subunits as sister to a proteobacterial clade; the beta-subunit tree instead groups eukaryotes with Archaea, so the two trees do not settle the origin of the eukaryotic enzyme. Lsc1 appears among the seeds because its own experimental annotation helped place the node; the IBA adds that the location is inherited across eukaryotes. The term stops at the organelle because the seeds are whole-organelle assays.

Summary: IDA from Przybyla-Zawislak et al. 1998: succinyl-CoA ligase activity measured in isolated mitochondria depends on the LSC genes.

Summary: IEA from UniProt subcellular location (SL-0173). Correct.

Summary: RCA from YeastPathways TCA-EUK-PWY placing the reaction in mitochondria. Correct.

Summary: IBA from PANTHER PTN000122012 (LUCA node of the alpha-subunit family; donors include fly, mouse, rat, S. pombe and plants). TCA-cycle participation is the conserved role.

Reason: The node is the LUCA node of the family and the function is retained in fungi. Tomato alpha-subunit cDNAs complement the yeast lsc1 mutant, so the role is interchangeable between a plant and a fungal alpha subunit.

Summary: IEA from UniRule/UniPathway (UPA00223, TCA cycle). Correct.

Summary: NAS from Przybyla-Zawislak et al. 1998. Succinyl-CoA ligase catalyses the substrate-level phosphorylation step of the TCA cycle.

Summary: TAS from the McAlister-Henn & Small 1997 review of yeast TCA-cycle enzymes. Correct.

Summary: IDA from Przybyla-Zawislak et al. 1998: Lsc1-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.

Summary: RCA from YeastPathways TCA-EUK-PWY. The TCA cycle is part of aerobic respiration; lsc mutants are impaired on glycerol and pyruvate.

Summary: IBA from PANTHER PTN000122012 (E. coli SucD donor). The yeast enzyme is the ATP-specific (ADP-forming) form, so this complex term is correct for Lsc1.

Reason: A single bacterial seed is enough here. ADP use is shared by the bacterial enzymes and by the A-type beta lineage to which Lsc2 belongs, and ADP-forming activity is confirmed by assay in yeast.

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).

Summary: IDA from the Chen et al. 2005 survey of mtDNA-associated proteins (abstract only in the cache). Lsc1 is listed among the nucleoid proteins attributed to that paper in Table 1 of Miyakawa 2017 (PMID:28496055). The method is in organello formaldehyde cross-linking of proteins to mtDNA; Lsc2 is not in the set.

Reason: The location is supported for Lsc1, but it is peripheral to the TCA-cycle role. The cross-linking method also recovers other abundant matrix enzymes, the beta subunit Lsc2 was not recovered, and no function of Lsc1 at the nucleoid has been shown, so the row is kept as non-core.

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.

Summary: Proposed sub-compartment. Lsc1 is a soluble protein of the mitochondrial matrix. The root mitochondrion rows do not state the sub-compartment, and the nucleoid row covers only the mtDNA-associated fraction.

Reason: Three 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. Lsc1 (YOR142W) 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) Lsc1 has a cleavable presequence. UniProt gives a transit peptide (1-24, HAMAP rule), and the yeast mitochondrial N-proteome found Lsc1 in a processed form, as reported in PMID:26338186. (3) Lsc1 is a subunit of a soluble TCA-cycle enzyme whose substrates are matrix metabolites. The mitochondrial nucleoid (GO:0042645) is part of the matrix, and that row is kept beside this one. 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 beta subunit Lsc2 gets the same row.