geneontology / go-ontology

Source ontology files for the Gene Ontology
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Merge: 15-cis-phytoene synthase activity & geranylgeranyl-diphosphate geranylgeranyltransferase activity #29285

Open sjm41 opened 6 hours ago

sjm41 commented 6 hours ago

There was previously some discussion of these 2 terms in https://github.com/geneontology/go-ontology/issues/21165, but according to current GO guidelines and looking at the current situation in RHEA, these two terms should be merged since they correspond to a single EC comprising 2 subreactions:

id: GO:0046905 name: 15-cis-phytoene synthase activity namespace: molecular_function def: "Catalysis of the reaction: 2 geranylgeranyl diphosphate -> 15-cis-phytoene + 2 diphosphate." [GOC:ai, PMID:12641468, RHEA:34479] comment: Note that this should not be confused with 'geranylgeranyl-diphosphate geranylgeranyltransferase activity ; GO:0016767', EC:2.5.1.32. This activity is the second part of the formation of phytoene from geranylgeranyl-diphosphate, the first stage of which is catalyzed by EC:2.5.1.32. synonym: "phytoene synthase activity" BROAD [] xref: RHEA:34479 is_a: GO:0016462 ! pyrophosphatase activity relationship: part_of GO:0016120 ! carotene biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21165" xsd:anyURI

id: GO:0016767 name: geranylgeranyl-diphosphate geranylgeranyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: 2 geranylgeranyl diphosphate = diphosphate + prephytoene diphosphate." [EC:2.5.1.32] synonym: "geranylgeranyl-diphosphate:geranylgeranyl-diphosphate geranylgeranyltransferase activity" RELATED [EC:2.5.1.32] synonym: "phytoene synthetase activity" RELATED [EC:2.5.1.32] synonym: "prephytoene-diphosphate synthase activity" RELATED [EC:2.5.1.32] synonym: "PSase activity" RELATED [EC:2.5.1.32] xref: EC:2.5.1.32 xref: MetaCyc:2.5.1.32-RXN xref: RHEA:22296 is_a: GO:0004659 ! prenyltransferase activity


Here's the corresponding EC entry and RHEA xref:

EC 2.5.1.32 Name: 15-cis-phytoene synthase Alternative Name(s) inc: geranylgeranyl-diphosphate geranylgeranyltransferase Reaction catalysed: 2 (2E,6E,10E)-geranylgeranyl diphosphate = 15-cis-phytoene + 2 diphosphate Comment(s): The enzyme condenses two molecules of geranylgeranyl diphosphate to give prephytoene diphosphate, followed by rearrangement of the cyclopropylcarbinyl intermediate to 15-cis-phytoene.

RHEA xref = RHEA:34475 2 (2E,6E,10E)-geranylgeranyl diphosphate = 15-cis-phytoene + 2 diphosphate Comments: Multi-step reaction: RHEA:22296 and RHEA:34479


I think the final single entry should look like this (particularly note changes in bold):

id: GO:0046905 name: 15-cis-phytoene synthase activity namespace: molecular_function alt_id: GO: 0016767 def: "Catalysis of the reaction: 2 geranylgeranyl diphosphate -> 15-cis-phytoene + 2 diphosphate." [PMID:12641468, RHEA: 34475] synonym: "phytoene synthase activity" EXACT [] synonym: "geranylgeranyl-diphosphate:geranylgeranyl-diphosphate geranylgeranyltransferase (15-cis-phytoene-forming) activity" EXACT [EC:2.5.1.32] synonym: "phytoene synthetase activity" EXACT [EC:2.5.1.32] synonym: "prephytoene-diphosphate synthase activity" EXACT [EC:2.5.1.32] synonym: "PSase activity" EXACT [EC:2.5.1.32] synonym: "geranylgeranyl-diphosphate geranylgeranyltransferase activity" EXACT [EC:2.5.1.32] xref: EC:2.5.1.32 xref: MetaCyc:RXN-13323 xref: RHEA:34475 is_a: GO:0004659 ! prenyltransferase activity

Do you agree @pgaudet ?