Pgam2 review notes

Evidence summary

• [UniProtKB:P16290] UniProt describes Pgam2 as catalyzing interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as primer.
• PMID:15720133 The fetched GOA file uses this publication for phosphoglycerate mutase activity and gluconeogenesis.

Curation decisions

• Core function: phosphoglycerate mutase 2 (phosphoglycerate mutase activity, GO:0004619).
• Specific catalytic activities and direct metabolic processes were accepted.
• Broad parent, localization, binding, and stimulus-response annotations were modified, kept non-core, or marked over-annotated according to support.

Re-review 2026-10-10

• GOA refresh added three rows; none retired. Two ISO rows (GO_REF:0000121) are donor-splits from human PGAM2 (UniProtKB:P15259): GO:0004619 phosphoglycerate mutase activity and GO:0006096 (now labelled "glycolysis" in GO). Both ACCEPT, matching the mouse-donor (MGI:1933118) siblings [UniProtKB:P16290 "Catalyzes the interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction."].
• New GO:1990917 ooplasm IEA (ARBA:ARBA00093730): MARK_AS_OVER_ANNOTATED, consistent with the IDA ooplasm row. The cited localization study is on skeletal muscle PMID:2158448; GO defines ooplasm as "The cytoplasm of an ovum" (QuickGO). The ARBA rule most likely propagates the RGD IDA row.
• Replaced two stale UniProt quotes (DR GO line for GO:0004082 IEA:UniProtKB-EC no longer present) with the FUNCTION CC text.
• Description stripped of review/curation commentary.
• Open question: was the RGD ooplasm IDA (PMID:2158448) intended as sarcoplasm (GO:0016528)? If so, the IDA row and the ARBA rule derived from it should be corrected at source.

Review follow-up 2026-10-17: escalated the two ooplasm rows in response to review. GO:1990917 ooplasm is "The cytoplasm of an ovum" (QuickGO), while the title and abstract of PMID:2158448 state that the study is on rat skeletal muscle PMID:2158448. The ARBA:ARBA00093730 IEA row is now REMOVE: the electronic transfer does not apply, not merely over-general. The RGD IDA row is now MODIFY to GO:0005829 cytosol, the compartment the abstract names; GO:0016528 sarcoplasm is noted in the reason as an acceptable tissue-specific alternative. The nuclear pool stays on the separate nucleus IDA row. Also replaced the 17 UniProt DR GO; cross-reference quotes with biological text. Function, process and the two muscle-contraction/Notch rows now quote the CC FUNCTION text, identical protein binding quotes CC SUBUNIT ("Homodimer. Interacts with ENO1."), and the cytosol rows quote PMID:2158448, because the entry has no SUBCELLULAR LOCATION comment.