enzyme

METPO:1000527 · CLASS · REVIEWED

A biological macromolecule (typically a protein, occasionally a catalytic RNA) that catalyses a specific biochemical reaction. This class is the material-entity sense of "enzyme" (the molecule itself), matching METPO:1000527's placement as a subclass of METPO:1000186 (material entity). Used as the range class for METPO enzyme-related OBJECT_PROPERTYs (shows_activity_of, enzyme_activity_analyzed, does_not_show_activity_of).

Trait evidence (2)

DOI:10.1093/nar/gku1003
ENZYME nomenclature

ENZYME / EC nomenclature provides the canonical external vocabulary for enzymes named by the catalytic reaction they perform; supports 'enzyme' as a recognised material-entity class.
PMID:21413255
enzymes

Medical Microbiology chapter uses 'enzyme' in the material-entity sense (the biocatalyst protein) throughout its physiology and metabolism discussion; consistent with this record's scope.

Provenance

Identifier source: METPO (2026-06-12)
Definition source: DOI:10.1093/nar/gku1003

Parent traits (1)

material entity METPO:1000186

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

METPO:1000527 [+0.167, -0.909, -0.249, +1.095, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

upper microbe 0.969
upper chemical entity 0.957
upper material entity 0.950
metabolism organism interacts with chemical 0.376
metabolism has quality 0.370
metabolism has phenotype 0.368
metabolism does not transport 0.364
metabolism transports 0.364

Curation history

2026-05-16T09:30:00-07:00 · CREATED_UPPER_CLASS_RECORD · claude
Created upper-ontology CLASS record for METPO:1000527 (enzyme) so that the range of un-deprecated activity-assay OBJECT_PROPERTYs (shows_activity_of, enzyme_activity_analyzed, and their negation companions) resolves to a curated TraitMech record.
2026-05-16T09:45:00-07:00 · REMOVED_NON_EQUIVALENT_XREFS_AND_TIGHTENED_DEFINITION · claude
Per Copilot review of PR #55, removed xrefs to GO:0003824 (catalytic activity) and CHEBI:23357 (catalyst). Neither is an equivalence mapping: GO:0003824 is an activity/process class and CHEBI:23357 is a role, while this record represents the enzyme material entity. The definition was rewritten to be strictly about the enzyme molecule itself, removing the earlier wording that conflated material entity with catalytic activity. No clean cross-ontology equivalent for the material-entity "enzyme" class is available (CHEBI does not have a single enzyme class; PR is too broad as "protein"), so xrefs is left empty.