Cofactor (2,3-bisphosphoglycerate)-dependent phosphoglycerate mutase (dPGM; EC 5.4.2.11) of Saccharomyces cerevisiae, a highly abundant homotetrameric enzyme of the histidine-phosphatase superfamily that reversibly interconverts 3-phosphoglycerate and 2-phosphoglycerate via a phospho-histidine (His8) intermediate, with His181 acting as general acid/base. It catalyses step 8 of glycolysis and the reverse step in gluconeogenesis and is the sole phosphoglycerate mutase supporting both pathways: gpm1 deletion mutants cannot grow on glucose and require a mixture of glycerol and ethanol. It also has very low 2,3-bisphosphoglycerate synthase and phosphatase side activities. Gpm1 is predominantly cytosolic, with a fraction associated with the mitochondrial outer surface and recovered in mitochondrial intermembrane-space preparations.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro IPR001345 (PGAM/BPGM family) mapping to the root catalytic activity term; uninformative. Reason: Replace with the specific phosphoglycerate mutase activity. Proposed replacements: phosphoglycerate mutase activity Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; |
| GO:0004619 phosphoglycerate mutase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from the dPGM node PTN002630707 (human PGAM1/2, S. pombe gpm1, Gpm1 itself). Gpm1 is the canonical BPG-dependent PGAM. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; PMID:1386023 A system has been developed to allow the convenient production, expression and purification of site-directed mutants of the enzyme phosphoglycerate mutase from Saccharomyces cerevisiae. |
| GO:0004619 phosphoglycerate mutase activity | IDA PMID:1386023 Development of a mutagenesis, expression and purification sy... | ACCEPT | Summary: White & Fothergill-Gilmore expressed and purified recombinant yeast Gpm1 and characterised the mutase kinetically, including the His181A mutant. Supporting Evidence: PMID:1386023 A system has been developed to allow the convenient production, expression and purification of site-directed mutants of the enzyme phosphoglycerate mutase from Saccharomyces cerevisiae. PMID:1386023 Kinetic analysis shows a large decrease (1.6 x 10(4)) in the catalytic efficiency |
| GO:0004619 phosphoglycerate mutase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from EC 5.4.2.11 / RHEA:15901; correct for Gpm1. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; |
| GO:0004619 phosphoglycerate mutase activity | IMP PMID:3033435 Isolation of the yeast phosphoglyceromutase gene and constru... | ACCEPT | Summary: Rodicio & Heinisch cloned GPM1 by complementation; deletion abolishes growth on glucose or on glycerol or ethanol alone, consistent with loss of the sole PGAM activity. Supporting Evidence: PMID:3033435 The deletion mutants showed that the gene is not essential for yeast growing in the presence of a combination of glycerol and ethanol. However, growth was inhibited by glucose and neither glycerol nor ethanol alone were sufficient to support growth. |
| GO:0004619 phosphoglycerate mutase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (superpathway of glucose fermentation, GLUCFERMEN-PWY); activity correct. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; |
| GO:0004619 phosphoglycerate mutase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (gluconeogenesis, GLUCONEO-PWY-1); Gpm1 catalyses the reversible step used in gluconeogenesis. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; PMID:3033435 The deletion mutants showed that the gene is not essential for yeast growing in the presence of a combination of glycerol and ethanol. However, growth was inhibited by glucose and neither glycerol nor ethanol alone were sufficient to support growth. |
| GO:0004619 phosphoglycerate mutase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (glycolysis, GLYCOLYSIS); activity correct. Note: YeastCyc also attaches EC 5.4.2.12 (cofactor-independent iPGM) to Gpm1, which is wrong for this dPGM; the GO term here is the generic mutase activity and is fine. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; |
| GO:0005737 cytoplasm | EXP PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Huh et al. GFP localisation: cytoplasmic. Supporting Evidence: PMID:14562095 Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. file:yeast/GPM1/GPM1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping (Cytoplasm); correct. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | KEEP AS NON CORE | Summary: Reinders et al. PROMITO mitochondrial proteome detected Gpm1. Reason: A fraction of Gpm1, like other glycolytic enzymes, associates with the mitochondrial surface; this is not where its core glycolytic activity is executed. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | KEEP AS NON CORE | Summary: Renvoise et al. quantitative mitochondrial proteome detected Gpm1. Reason: A fraction of Gpm1, like other glycolytic enzymes, associates with the mitochondrial surface; this is not where its core glycolytic activity is executed. Supporting Evidence: PMID:24769239 we performed an overall quantitative proteomic and phosphoproteomic study of isolated mitochondria |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA mitochondrion from node PTN008530354, whose only experimental donor is Gpm1's own mitochondrial annotation; inherits the same peripheral-association caveat. Reason: A fraction of Gpm1, like other glycolytic enzymes, associates with the mitochondrial surface; this is not where its core glycolytic activity is executed. Supporting Evidence: PMID:16962558 we show that all glycolytic enzymes are associated with mitochondria in yeast |
| GO:0005739 mitochondrion | IDA PMID:16962558 Enolase takes part in a macromolecular complex associated to... | KEEP AS NON CORE | Summary: Brandina et al. showed that all glycolytic enzymes, including PGAM, are associated with yeast mitochondria by enzymatic assay. Reason: A fraction of Gpm1, like other glycolytic enzymes, associates with the mitochondrial surface; this is not where its core glycolytic activity is executed. Supporting Evidence: PMID:16962558 we show that all glycolytic enzymes are associated with mitochondria in yeast |
| GO:0005741 mitochondrial outer membrane | EXP PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | KEEP AS NON CORE | Summary: PROMITO proteome supports peripheral association of Gpm1 with the outer mitochondrial membrane (UniProt: cytoplasmic side). Reason: A fraction of Gpm1, like other glycolytic enzymes, associates with the mitochondrial surface; this is not where its core glycolytic activity is executed. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS file:yeast/GPM1/GPM1-uniprot.txt Mitochondrion outer membrane {ECO:0000269|PubMed:16823961, |
| GO:0005741 mitochondrial outer membrane | EXP PMID:16962558 Enolase takes part in a macromolecular complex associated to... | KEEP AS NON CORE | Summary: Brandina et al. glycolytic enzymes associated with mitochondrial surface; supports outer-membrane association. Reason: A fraction of Gpm1, like other glycolytic enzymes, associates with the mitochondrial surface; this is not where its core glycolytic activity is executed. Supporting Evidence: PMID:16962558 we show that all glycolytic enzymes are associated with mitochondria in yeast file:yeast/GPM1/GPM1-uniprot.txt Mitochondrion outer membrane {ECO:0000269|PubMed:16823961, |
| GO:0005741 mitochondrial outer membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location mapping (mitochondrion outer membrane, peripheral); reflects the experimental data above. Reason: A fraction of Gpm1, like other glycolytic enzymes, associates with the mitochondrial surface; this is not where its core glycolytic activity is executed. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Mitochondrion outer membrane {ECO:0000269|PubMed:16823961, |
| GO:0005758 mitochondrial intermembrane space | IDA PMID:22984289 Intermembrane space proteome of yeast mitochondria. | KEEP AS NON CORE | Summary: Voegtle et al. IMS proteome (Bax-release) listed Gpm1 among novel IMS proteins, annotated as cytosol/mitochondria. Gpm1 has no known import signal and an IMS role is unexplained. Reason: Experimental, retained as non-core; IMS residence of a glycolytic enzyme warrants independent confirmation. Supporting Evidence: PMID:22984289 we found 20 novel intermembrane space proteins, out of which 10 had not been localized to mitochondria before file:yeast/GPM1/GPM1-uniprot.txt Mitochondrion intermembrane space {ECO:0000269|PubMed:22984289}. |
| GO:0005758 mitochondrial intermembrane space | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location mapping from the IMS proteome entry. Reason: Non-core, see IDA row. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Mitochondrion intermembrane space {ECO:0000269|PubMed:22984289}. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA cytosol from mammalian PGAM1/2 orthologs; consistent with Gpm1 localisation. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0005829 cytosol | IDA PMID:3332961 Identification of polypeptides of the carbon metabolism mach... | ACCEPT | Summary: Bataille et al. identified Gpm1 among cytoplasmic carbon-metabolism enzymes on 2D protein maps. Supporting Evidence: PMID:3332961 Ten of them were identified as corresponding to cytoplasmic enzymes of the carbon metabolism machinery |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA cytosol (GLUCFERMEN-PWY); correct compartment for the reaction. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA cytosol (GLUCONEO-PWY-1); correct. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA cytosol (GLYCOLYSIS); correct. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0006094 gluconeogenesis | IMP PMID:3033435 Isolation of the yeast phosphoglyceromutase gene and constru... | ACCEPT | Summary: gpm1 deletion mutants cannot grow on glycerol or ethanol alone, showing Gpm1 is required to run the 3PG <-> 2PG step in the gluconeogenic direction. Supporting Evidence: PMID:3033435 The deletion mutants showed that the gene is not essential for yeast growing in the presence of a combination of glycerol and ethanol. However, growth was inhibited by glucose and neither glycerol nor ethanol alone were sufficient to support growth. |
| GO:0006094 gluconeogenesis | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (gluconeogenesis I); Gpm1 catalyses the reversible mutase step. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; |
| GO:0006096 glycolysis | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from UniPathway UPA00109 (glycolysis, step 3/5 of pyruvate from G3P); correct. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt PATHWAY: Carbohydrate degradation; glycolysis; pyruvate from D- |
| GO:0006096 glycolysis | IMP PMID:11015729 Simultaneous overexpression of enzymes of the lower part of ... | ACCEPT | Summary: Smits et al. co-overexpressed lower-glycolysis enzymes including PGAM and increased fermentative capacity; glucose-negative phenotype of gpm1 deletions independently establishes the role. Supporting Evidence: PMID:11015729 indicating a higher fermentative capacity in the recombinant strain PMID:3033435 The deletion mutants showed that the gene is not essential for yeast growing in the presence of a combination of glycerol and ethanol. However, growth was inhibited by glucose and neither glycerol nor ethanol alone were sufficient to support growth. |
| GO:0016868 intramolecular phosphotransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro IPR005952 (PGAM, BPG-dependent) mapped to the parent intramolecular phosphotransferase term; correct but less specific. Reason: Replace with the specific phosphoglycerate mutase activity. Proposed replacements: phosphoglycerate mutase activity Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; |
| GO:0019658 bifid shunt | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways superpathway of glucose fermentation (GLUCFERMEN-PWY) was mapped to 'bifid shunt', the Bifidobacterium phosphoketolase pathway yielding lactate and acetate. S. cerevisiae has no bifid shunt; glucose fermentation goes to ethanol via EMP glycolysis. Reason: Erroneous pathway-to-GO mapping; not applicable to yeast. Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; |
| GO:0061620 obsolete glycolytic process through glucose-6-phosphate | RCA GO_REF:0000123 | MODIFY | Summary: RCA to the now-obsolete term 'glycolytic process through glucose-6-phosphate'; the biology (Gpm1 in EMP glycolysis) is correct, the term is retired. Reason: Update to current glycolysis term. Proposed replacements: glycolysis Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; |
| GO:0061621 obsolete canonical glycolysis | IBA GO_REF:0000033 | MODIFY | Summary: IBA to the now-obsolete 'canonical glycolysis'; biology correct, term retired. Reason: Update to current glycolysis term. Proposed replacements: glycolysis Supporting Evidence: file:yeast/GPM1/GPM1-uniprot.txt Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; PMID:3033435 The deletion mutants showed that the gene is not essential for yeast growing in the presence of a combination of glycerol and ethanol. However, growth was inhibited by glucose and neither glycerol nor ethanol alone were sufficient to support growth. |
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Tetrameric phosphoglycerate mutase; mediates the conversion of 3-phosphoglycerate to 2-phosphoglycerate during glycolysis and the reverse reaction during gluconeogenesis
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