Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
YeastPathways to GO-CAM conversion
The proteome of Saccharomyces cerevisiae mitochondria.
Proteome survey reveals modularity of the yeast cell machinery.
Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics.
Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory growth in Saccharomyces cerevisiae.
The social and structural architecture of the yeast protein interactome.
Molecular genetics of yeast TCA cycle isozymes.
Genes of succinyl-CoA ligase from Saccharomyces cerevisiae.
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Mitochondrial succinyl-CoA ligase activity needs both LSC1 and LSC2.
"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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The yeast enzyme is ATP-specific.
"The yeast succinyl-CoA ligase was shown to utilize ATP but not GTP for succinyl-CoA synthesis"
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Both LSC genes are glucose-repressed and induced on nonfermentable carbon sources.
"The expression of these genes was repressed by growth on glucose and was induced threefold to sixfold during growth on nonfermentable carbon sources"
Characterization of the ATP- and GTP-specific succinyl-CoA synthetases in pigeon. The enzymes incorporate the same alpha-subunit.
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Nucleotide specificity of succinyl-CoA synthetase resides in the beta subunit.
"Because the two succinyl-CoA synthetases incorporate the same alpha-subunit, the determinants of nucleotide specificity must reside within the beta-subunit"
Genetic evidence for the expression of ATP- and GTP-specific succinyl-CoA synthetases in multicellular eucaryotes.
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The A-beta and G-beta genes are proposed to have arisen by duplication early in the evolution of multicellular eukaryotes.
"suggests that the A-beta and G-beta genes arose by duplication early in the evolution of multicellular eucaryotes"
Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.
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In pig GTP-specific succinyl-CoA synthetase, Gln20 of the beta subunit and backbone atoms contact the guanine base and provide the specificity.
"interactions of the guanine base with a glutamine residue (Gln-20beta) and with backbone atoms provide the specificity"
Biochemical and structural characterization of the GTP-preferring succinyl-CoA synthetase from Thermus aquaticus.
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Pro20 of the beta subunit does not exclude GTP use; T. aquaticus SCS has Pro20 and prefers GTP, and E. coli SCS uses both nucleotides but prefers ATP.
"This contrasts with Escherichia coli SCS, which uses GDP/GTP but prefers ADP/ATP"
Identification and characterisation of the alpha and beta subunits of succinyl CoA ligase of tomato.
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Tomato alpha- and beta-subunit cDNAs complement the yeast lsc1 and lsc2 mutants.
"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"
Citrate Regulates the Saccharomyces cerevisiae Mitochondrial GDP/GTP Carrier (Ggc1p) by Triggering Unidirectional Transport of GTP.
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Because yeast succinyl-CoA ligase makes ATP and not GTP, matrix GTP has to be imported by Ggc1p.
"Because in yeast, succinyl-CoA ligase produces ATP instead of GTP"
Disruption and phenotypic analysis of six open reading frames from chromosome VII of Saccharomyces cerevisiae reveals one essential gene.
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YGR244C (LSC2) is non-essential.
"The other five genes are non-essential, and no phenotypes could be associated to their inactivation"
Landscape of submitochondrial protein distribution.
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Yeast mitochondrial proteins were classified as soluble, peripheral or integral by sonication and carbonate extraction, and soluble proteins were assigned to the matrix or the intermembrane space by reference to outer-membrane and intermembrane-space proteomes. Lsc1 and Lsc2 are listed as soluble matrix proteins in Supplementary Data 5 (not in the cached text; read from the publisher's file).
"We used the well-established OM and IMS reference proteomes17, 31 (Methods section) to deduce the sublocalization of all mitochondrial proteins characterized above"
Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase.
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A taxonomically broad range of eukaryotes (Dictyostelium, Naegleria, Tetrahymena, an Aspergillus) have two distinct forms of the beta subunit. The paper does not date the duplication; that the two forms are older than multicellular animals is this review's inference from it and from the local trees.
"it is clear that a taxonomically broad range of eukaryotes possess two distinct forms of SCSβ"
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Blastocystis succinyl-CoA synthetase has Gln at position 20 of the beta subunit and is ATP-specific, so this residue does not by itself decide nucleotide specificity.
"suggests that Blastocystis SCS is GTP-specific, we demonstrate that it is ATP-specific"
Evolution of the succinyl-CoA synthetase subunit families (LSC1 / LSC2)
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Lsc2 is best read as the ortholog of animal SUCLA2 and a paralog of SUCLG2.
"Yeast LSC2 and S. pombe SPCC1620.08 both fall in the SUCLA2 (A-type) daughter clade, not in the SUCLG2 (G-type) clade."
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Lsc2 has Pro at position 20 of the mature subunit, the commonest residue in the family.
"Yeast LSC2 has Pro at position 20, as do human SUCLA2, E. coli SucC and most members of the family."
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Gln at position 20 is found in the characterised GTP-specific enzymes but is not confined to them or to the clade under PTN000929335, and it does not by itself decide nucleotide specificity.
"Gln at position 20 is not sufficient for GTP specificity, and is not required for GTP use or preference."
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The G-type beta gene was lost within fungi. S. cerevisiae and the other fungal genomes in the PANTHER tree have only the A-type gene, and Mortierellomycota, Basidiobolus and Rozella keep a SUCLG2-type gene. The ascomycete Saitoella complicata also has a Gln20 SUCLG2-type entry, whose origin (vertical retention, transfer or contamination) is unresolved.
"Early-diverging fungi (Mortierellomycota, Basidiobolus, Rozella) keep a SUCLG2-type beta gene with Gln at position 20, so the G-type beta gene was lost within fungi and not in the common ancestor of all fungi."
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The analysis does not show which nucleotide specificity is ancestral.
"This analysis does not show which nucleotide specificity is ancestral."
UniProt entry P53312 (LSC2)
SGD gene description for LSC2 (yeast)
OpenScientist focused report on whether Lsc2 is an ADP-specific beta subunit by descent
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An independent run concluded that Lsc2 is ADP-forming, carries Pro at the guanine-specificity position and lies outside the animal GDP-forming SUCLG2 clade.
"yeast Lsc2 falls **outside** the animal SUCLG2/GDP clade in 99% of replicates"
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The run found Gln at the specificity position only in animal SUCLG2 and Pro in every fungal, plant and SUCLA2 sequence it sampled.
"Gln-20β is present **only** in the animal GDP-forming SUCLG2 clade"
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The run could not resolve whether Lsc2 is specifically sister to animal SUCLA2 and, following PMID:9765291, treated the A-type/G-type duplication as an animal-lineage event that fungi predate.
"Distance methods only weakly support this (yeast+SUCLA2 grouping ~54%; yeast sits on a long branch)"