Pgam2

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004619 phosphoglycerate mutase activity	IBA GO_REF:0000033	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining phosphoglycerate mutase activity as a direct annotation (IBA, GO_REF:0000033). Reason: phosphoglycerate mutase activity is a specific catalytic activity matching Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0004619; F:phosphoglycerate mutase activity; IDA:RGD. file:rat/Pgam2/Pgam2-deep-research-falcon.md PGAM2 is a glycolytic enzyme that catalyzes the reversible isomerization of 3-phosphoglycerate (3-PG) to 2-phosphoglycerate (2-PG) in the “lower” portion of glycolysis file:rat/Pgam2/Pgam2-deep-research-falcon.md The canonical PGAM-family mechanism proceeds via a phospho-histidine catalytic cycle, commonly summarized as involving an active-site histidine (often referred to as His11) and a 2,3-bisphosphoglycerate (2,3-BPG/2,3-DPG)-dependent priming/turnover mechanism
GO:0005829 cytosol	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: cytosol is retained as useful context for Pgam2, but it is not the defining core function (IBA, GO_REF:0000033). Reason: cytosol records where Pgam2 has been observed, but localization does not define the gene product's primary activity. Supporting Evidence: UniProtKB:P16290 GO; GO:0005829; C:cytosol; ISO:RGD. file:rat/Pgam2/Pgam2-deep-research-falcon.md Within the provided evidence set, PGAM2 is described as a cytosolic enzyme in an isoform table summary
GO:0061621 canonical glycolysis	IBA GO_REF:0000033	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining canonical glycolysis as a direct annotation (IBA, GO_REF:0000033). Reason: canonical glycolysis is a direct metabolic process expected from Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0061621; P:canonical glycolysis; ISO:RGD. file:rat/Pgam2/Pgam2-deep-research-falcon.md PGAM2 is a glycolytic enzyme that catalyzes the reversible isomerization of 3-phosphoglycerate (3-PG) to 2-phosphoglycerate (2-PG) in the “lower” portion of glycolysis
GO:0003824 catalytic activity	IEA GO_REF:0000002	MODIFY	Summary: catalytic activity captures part of Pgam2 biology, but a more specific replacement better represents the direct role (IEA, GO_REF:0000002). Reason: catalytic activity is directionally correct but less specific than the curated replacement term for Pgam2's role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Proposed replacements: phosphoglycerate mutase activity Supporting Evidence: UniProtKB:P16290 FUNCTION: Catalyzes the interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction.
GO:0004082 bisphosphoglycerate mutase activity	IEA GO_REF:0000120	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining bisphosphoglycerate mutase activity as a direct annotation (IEA, GO_REF:0000120). Reason: bisphosphoglycerate mutase activity is a specific catalytic activity matching Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0004082; F:bisphosphoglycerate mutase activity; IEA:UniProtKB-EC.
GO:0004619 phosphoglycerate mutase activity	IEA GO_REF:0000120	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining phosphoglycerate mutase activity as a direct annotation (IEA, GO_REF:0000120). Reason: phosphoglycerate mutase activity is a specific catalytic activity matching Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0004619; F:phosphoglycerate mutase activity; IDA:RGD.
GO:0006096 glycolytic process	IEA GO_REF:0000120	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining glycolytic process as a direct annotation (IEA, GO_REF:0000120). Reason: glycolytic process is a direct metabolic process expected from Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0006096; P:glycolytic process; ISO:RGD.
GO:0016868 intramolecular phosphotransferase activity	IEA GO_REF:0000002	MODIFY	Summary: intramolecular phosphotransferase activity captures part of Pgam2 biology, but a more specific replacement better represents the direct role (IEA, GO_REF:0000002). Reason: intramolecular phosphotransferase activity is directionally correct but less specific than the curated replacement term for Pgam2's role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Proposed replacements: phosphoglycerate mutase activity Supporting Evidence: UniProtKB:P16290 FUNCTION: Catalyzes the interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction.
GO:0005654 nucleoplasm	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: nucleoplasm is retained as useful context for Pgam2, but it is not the defining core function (IEA, GO_REF:0000107). The supporting evidence for a nuclear pool of PGAM is the immunocytochemical and biochemical study PMID:2158448, which found the enzyme in both cytosol and nucleus of rat skeletal muscle and confirmed the nuclear localization biochemically. Reason: nucleoplasm is biologically compatible with Pgam2 (a nuclear pool of PGAM was demonstrated in rat skeletal muscle), but it is contextual rather than the direct catalytic core function in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: PMID:2158448 With the aid of highly affinity-purified anti-phosphoglycerate mutase antibodies, the enzyme was found in both cytosol and nucleus of rat skeletal muscle. PMID:2158448 Activity measurements from nuclear extracts showed that 25% of total specific activity is found in the nuclei.
GO:0005829 cytosol	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: cytosol is retained as useful context for Pgam2, but it is not the defining core function (IEA, GO_REF:0000107). Reason: cytosol records where Pgam2 has been observed, but localization does not define the gene product's primary activity. Supporting Evidence: UniProtKB:P16290 GO; GO:0005829; C:cytosol; ISO:RGD.
GO:0006941 striated muscle contraction	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: striated muscle contraction is treated as over-annotation because it reflects context or consequence rather than Pgam2's direct role (IEA, GO_REF:0000107). Reason: striated muscle contraction reflects exposure, expression, phenotype, or downstream pathway context rather than the direct Pgam2 role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0006941; P:striated muscle contraction; ISO:RGD.
GO:0042802 identical protein binding	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: identical protein binding is retained as useful context for Pgam2, but it is not the defining core function (IEA, GO_REF:0000107). Reason: identical protein binding records substrate, cofactor, or quaternary-structure context for Pgam2, but the curated core function is phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0042802; F:identical protein binding; ISO:RGD. UniProtKB:P16290 SUBUNIT: Homodimer. Interacts with ENO1. file:rat/Pgam2/Pgam2-deep-research-falcon.md Active enzyme can occur in dimeric forms within mammalian PGAM system
GO:0061621 canonical glycolysis	IEA GO_REF:0000107	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining canonical glycolysis as a direct annotation (IEA, GO_REF:0000107). Reason: canonical glycolysis is a direct metabolic process expected from Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0061621; P:canonical glycolysis; ISO:RGD.
GO:0042802 identical protein binding	ISO GO_REF:0000121	KEEP AS NON CORE	Summary: identical protein binding is retained as useful context for Pgam2, but it is not the defining core function (ISO, GO_REF:0000121). Reason: identical protein binding records substrate, cofactor, or quaternary-structure context for Pgam2, but the curated core function is phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0042802; F:identical protein binding; ISO:RGD.
GO:0005654 nucleoplasm	ISO GO_REF:0000121	KEEP AS NON CORE	Summary: nucleoplasm is retained as useful context for Pgam2, but it is not the defining core function (ISO, GO_REF:0000121). The supporting evidence for a nuclear pool of PGAM is the immunocytochemical and biochemical study PMID:2158448, which found the enzyme in both cytosol and nucleus of rat skeletal muscle and confirmed the nuclear localization biochemically. Reason: nucleoplasm is biologically compatible with Pgam2 (a nuclear pool of PGAM was demonstrated in rat skeletal muscle), but it is contextual rather than the direct catalytic core function in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: PMID:2158448 With the aid of highly affinity-purified anti-phosphoglycerate mutase antibodies, the enzyme was found in both cytosol and nucleus of rat skeletal muscle. PMID:2158448 Activity measurements from nuclear extracts showed that 25% of total specific activity is found in the nuclei.
GO:0005634 nucleus	IDA PMID:2158448 Location of phosphoglycerate mutase in rat skeletal muscle. ...	KEEP AS NON CORE	Summary: nucleus is retained as useful context for Pgam2, but it is not the defining core function (IDA, PMID:2158448). Reason: nucleus records where Pgam2 has been observed, but localization does not define the gene product's primary activity. Supporting Evidence: PMID:2158448 The subcellular distribution of phosphoglycerate mutase was studied by immunogold techniques. With the aid of highly affinity-purified anti-phosphoglycerate mutase antibodies, the enzyme was found in both cytosol and nucleus of rat skeletal muscle.
GO:1990917 ooplasm	IDA PMID:2158448 Location of phosphoglycerate mutase in rat skeletal muscle. ...	MARK AS OVER ANNOTATED	Summary: ooplasm is an over-annotation. The cited reference (PMID:2158448) is an immunogold study of rat skeletal muscle that localized the enzyme to cytosol and nucleus; it does not provide evidence for an oocyte/ooplasm localization. Falcon deep research finds no support for non-cytosolic localization of mammalian PGAM2 beyond the intracellular carbohydrate-metabolism context. Reason: ooplasm (an oocyte cytoplasm term) is not supported by the muscle immunocytochemistry reference, and PGAM2 is a muscle/heart-enriched cytosolic glycolytic enzyme; the dominant functional context is intracellular carbohydrate metabolism. Supporting Evidence: PMID:2158448 The subcellular distribution of phosphoglycerate mutase was studied by immunogold techniques. With the aid of highly affinity-purified anti-phosphoglycerate mutase antibodies, the enzyme was found in both cytosol and nucleus of rat skeletal muscle. file:rat/Pgam2/Pgam2-deep-research-falcon.md No evidence in the retrieved texts supports stable extracellular localization for mammalian PGAM2, and the dominant functional context is intracellular carbohydrate metabolism
GO:0004082 bisphosphoglycerate mutase activity	ISS GO_REF:0000024	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining bisphosphoglycerate mutase activity as a direct annotation (ISS, GO_REF:0000024). Reason: bisphosphoglycerate mutase activity is a specific catalytic activity matching Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0004082; F:bisphosphoglycerate mutase activity; IEA:UniProtKB-EC.
GO:0004619 phosphoglycerate mutase activity	ISS GO_REF:0000024	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining phosphoglycerate mutase activity as a direct annotation (ISS, GO_REF:0000024). Reason: phosphoglycerate mutase activity is a specific catalytic activity matching Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0004619; F:phosphoglycerate mutase activity; IDA:RGD.
GO:0005829 cytosol	ISO GO_REF:0000121	KEEP AS NON CORE	Summary: cytosol is retained as useful context for Pgam2, but it is not the defining core function (ISO, GO_REF:0000121). Reason: cytosol records where Pgam2 has been observed, but localization does not define the gene product's primary activity. Supporting Evidence: UniProtKB:P16290 GO; GO:0005829; C:cytosol; ISO:RGD.
GO:0061621 canonical glycolysis	ISO GO_REF:0000121	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining canonical glycolysis as a direct annotation (ISO, GO_REF:0000121). Reason: canonical glycolysis is a direct metabolic process expected from Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0061621; P:canonical glycolysis; ISO:RGD.
GO:0007219 Notch signaling pathway	ISO GO_REF:0000121	MARK AS OVER ANNOTATED	Summary: Notch signaling pathway is treated as over-annotation because it reflects context or consequence rather than Pgam2's direct role (ISO, GO_REF:0000121). Reason: Notch signaling pathway reflects exposure, expression, phenotype, or downstream pathway context rather than the direct Pgam2 role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Propagation Review Root cause: PROPAGATION BAD Failure modes: CONTEXT OR TISSUE MISMATCH ROLE CONFLATION Sources checked: MGI:MGI:1933118 · mouse Pgam2 SUPPORTS SOURCE BUT NOT TARGET The mouse Pgam2 donor annotation places the gene in a Notch pathway context; the transfer imports that context rather than any mutase activity of rat Pgam2 within the pathway. Supporting Evidence: UniProtKB:P16290 GO; GO:0007219; P:Notch signaling pathway; ISO:RGD.
GO:0006096 glycolytic process	ISO GO_REF:0000121	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining glycolytic process as a direct annotation (ISO, GO_REF:0000121). Reason: glycolytic process is a direct metabolic process expected from Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0006096; P:glycolytic process; ISO:RGD.
GO:0004619 phosphoglycerate mutase activity	IDA PMID:15720133 Monochloroacetic acid inhibits liver gluconeogenesis by inac...	ACCEPT	Summary: phosphoglycerate mutase activity is a specific catalytic activity consistent with Pgam2's core role. Note that in PMID:15720133 (Sakai et al. 2005) phosphoglycerate mutase activity was measured as a negative control and shown NOT to be inactivated by MCA (in contrast to GAPDH); the measurement nonetheless demonstrates assayable PGAM activity, so the activity annotation is retained as a correct molecular function term. Reason: phosphoglycerate mutase activity is a specific catalytic activity matching Pgam2's documented role; PMID:15720133 directly measured this activity (as an MCA-insensitive negative control). Supporting Evidence: PMID:15720133 GAPDH was inactivated by MCA in vitro, but enolase, phosphoglycerate mutase, and phosphoglycerate kinase were not inactivated at the same or higher concentrations of MCA.
GO:0006094 gluconeogenesis	IDA PMID:15720133 Monochloroacetic acid inhibits liver gluconeogenesis by inac...	MARK AS OVER ANNOTATED	Summary: The cited reference (PMID:15720133, Sakai et al. 2005) does not provide IDA support for a direct PGAM role in gluconeogenesis. The paper concludes that MCA-induced inhibition of liver gluconeogenesis is caused by inactivation of GAPDH, and explicitly shows that phosphoglycerate mutase (along with enolase and phosphoglycerate kinase) was NOT inactivated; PGAM was measured only as a negative control. While PGAM2 catalyzes a reversible reaction and can in principle participate in gluconeogenesis, this reference actively argues that PGAM is not the operative enzyme in the studied effect, so the IDA annotation to gluconeogenesis from this paper is an over-annotation. Reason: PMID:15720133 implicates GAPDH (not PGAM) in MCA-induced inhibition of liver gluconeogenesis and shows phosphoglycerate mutase was not inactivated, so it does not support a direct IDA annotation of PGAM2 to gluconeogenesis. Supporting Evidence: PMID:15720133 GAPDH was inactivated by MCA in vitro, but enolase, phosphoglycerate mutase, and phosphoglycerate kinase were not inactivated at the same or higher concentrations of MCA.
GO:0004619 phosphoglycerate mutase activity	IDA PMID:2158448 Location of phosphoglycerate mutase in rat skeletal muscle. ...	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining phosphoglycerate mutase activity as a direct annotation (IDA, PMID:2158448). Reason: phosphoglycerate mutase activity is a specific catalytic activity matching Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: PMID:2158448 The subcellular distribution of phosphoglycerate mutase was studied by immunogold techniques. With the aid of highly affinity-purified anti-phosphoglycerate mutase antibodies, the enzyme was found in both cytosol and nucleus of rat skeletal muscle.
GO:0007283 spermatogenesis	IEP PMID:7867621 The muscle-specific phosphoglycerate mutase gene is specific...	MARK AS OVER ANNOTATED	Summary: spermatogenesis is treated as over-annotation. PMID:7867621 shows that the muscle-specific PGAM-M gene is developmentally expressed in testis during spermatogenesis, where the paper frames PGAM as "an essential glycolytic enzyme for the spermatozoa energy supply". This testis expression reflects the same core glycolytic mutase function operating in a germ-cell context (an IEP expression-pattern observation) rather than a distinct, direct involvement of PGAM2 in the spermatogenesis differentiation program itself. Reason: The evidence is an IEP expression-pattern observation; although PMID:7867621 frames PGAM-M as essential for spermatozoa energy supply, this is the same glycolytic mutase activity deployed in germ cells, not a direct PGAM2 role in the spermatogenesis developmental process, so annotating Pgam2 to spermatogenesis over-states its function. Supporting Evidence: PMID:7867621 we have investigated the expression during spermatogenesis of the genes that encode phosphoglycerate mutase, an essential glycolytic enzyme for the spermatozoa energy supply
GO:0046689 response to mercury ion	IMP PMID:2850701 Inactivation of type MM phosphoglycerate mutase by sulfhydry...	MARK AS OVER ANNOTATED	Summary: response to mercury ion is treated as over-annotation because it reflects context or consequence rather than Pgam2's direct role (IMP, PMID:2850701). Reason: response to mercury ion reflects exposure, expression, phenotype, or downstream pathway context rather than the direct Pgam2 role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: PMID:2850701 Type MM phosphoglycerate mutase from free dissected mandibular processes from embryonic rats was reversibly inactivated by tetrathionate, p-chloromercuribenzoate, and Hg2+.
GO:0004619 phosphoglycerate mutase activity	ISO GO_REF:0000121	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining phosphoglycerate mutase activity as a direct annotation (ISO, GO_REF:0000121). Reason: phosphoglycerate mutase activity is a specific catalytic activity matching Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: UniProtKB:P16290 GO; GO:0004619; F:phosphoglycerate mutase activity; IDA:RGD.
GO:0006941 striated muscle contraction	ISO GO_REF:0000121	MARK AS OVER ANNOTATED	Summary: striated muscle contraction is treated as over-annotation because it reflects context or consequence rather than Pgam2's direct role (ISO, GO_REF:0000121). Reason: striated muscle contraction reflects exposure, expression, phenotype, or downstream pathway context rather than the direct Pgam2 role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Propagation Review Root cause: PROPAGATION BAD Failure modes: CONTEXT OR TISSUE MISMATCH ROLE CONFLATION Sources checked: UniProtKB:P15259 · human PGAM2 SUPPORTS SOURCE BUT NOT TARGET The human PGAM2 muscle-contraction context reflects its muscle-restricted expression and glycogenosis phenotype; contraction itself is not a phosphoglycerate mutase function in rat. Supporting Evidence: UniProtKB:P16290 GO; GO:0006941; P:striated muscle contraction; ISO:RGD.
GO:0004619 phosphoglycerate mutase activity	IDA PMID:2850701 Inactivation of type MM phosphoglycerate mutase by sulfhydry...	ACCEPT	Summary: Pgam2's phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis supports retaining phosphoglycerate mutase activity as a direct annotation (IDA, PMID:2850701). Reason: phosphoglycerate mutase activity is a specific catalytic activity matching Pgam2's documented role in phosphoglycerate and bisphosphoglycerate mutase reactions in glycolysis. Supporting Evidence: PMID:2850701 Type MM phosphoglycerate mutase from free dissected mandibular processes from embryonic rats was reversibly inactivated by tetrathionate, p-chloromercuribenzoate, and Hg2+.

Gene Description

Existing Annotations Review

Core Functions

Pgam2 encodes rat phosphoglycerate mutase 2. FUNCTION: Catalyzes the interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction.

References

Deep Research

Falcon

📚 Additional Documentation

Notes

Pgam2 review notes

Evidence summary

Curation decisions

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