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Source ontology files for the Gene Ontology
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(3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity & children #28163

Closed sjm41 closed 4 months ago

sjm41 commented 4 months ago

Looking at this set of terms (with the number of EXP annotations given in parentheses):

(3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity (GO:0019171, EC:4.2.1.59, RHEA:13097)
           |__(3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity  (1 EXP)
           |__(3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity (2 EXP)
           |__(3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity (0 EXP)
           |__(3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (2 EXP)
           |__(3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (0 EXP)

Only the parent term has an EC xref (EC:4.2.1.59), while the rest are substrate-specific terms that have a RHEA and sometimes a KEGG/MetaCyc xref.

There are additional substrate-specific reactions we could add here - RHEA:13097 lists the following as specific forms: RHEA:41924 (3R)-hydroxyoctadecanoyl-[ACP] = (2E)-octadecenoyl-[ACP] + H2O RHEA:41908 (3R)-hydroxyhexadecanoyl-[ACP] = (2E)-hexadecenoyl-[ACP] + H2O RHEA:41892 (3R)-hydroxytetradecanoyl-[ACP] = (2E)-tetradecenoyl-[ACP] + H2O RHEA:41876 (3R)-hydroxydodecanoyl-[ACP] = (2E)-dodecenoyl-[ACP] + H2O RHEA:41860 (3R)-hydroxydecanoyl-[ACP] = (2E)-decenoyl-[ACP] + H2O RHEA:41844 (3R)-hydroxyoctanoyl-[ACP] = (2E)-octenoyl-[ACP] + H2O RHEA:41828 (3R)-hydroxyhexanoyl-[ACP] = (2E)-hexenoyl-[ACP] + H2O RHEA:41808 (3R)-hydroxybutanoyl-[ACP] = (2E)-butenoyl-[ACP] + H2O

MetaCyc lists many more - https://biocyc.org/META/NEW-IMAGE?type=EC-NUMBER&object=EC-4.2.1.59

But I think we should:

All terms are listed below FYI:

id: GO:0019171 name: (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity namespace: molecular_function def: "Catalysis of the reaction: a (3R)-hydroxyacyl-[acyl-carrier-protein] = a (2E)-enoyl-[acyl-carrier-protein] + H2O." [RHEA:13097] synonym: "(3R)-3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity" RELATED [] synonym: "3-hydroxyacyl-[acyl-carrier protein] dehydratase activity" EXACT [] synonym: "3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity" BROAD [] synonym: "3-hydroxyacyl-ACP dehydratase activity" EXACT [] xref: EC:4.2.1.59 xref: MetaCyc:4.2.1.59-RXN xref: RHEA:13097 is_a: GO:0016836 ! hydro-lyase activity

===

id: GO:0047450 (1 EXP annotation to At2g22230) name: (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity namespace: molecular_function alt_id: GO:0080063 def: "Catalysis of the reaction: (3R)-hydroxybutanoyl-[acyl-carrier-protein] = (2E)-butenoyl-[acyl-carrier-protein] + H2O." [RHEA:41808] synonym: "(3R)-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity" EXACT [] synonym: "3-hydroxybutyryl acyl carrier protein dehydratase activity" EXACT [] synonym: "beta-hydroxybutyryl acyl carrier protein (ACP) dehydrase activity" EXACT [] synonym: "crotonoyl-[acyl-carrier protein] hydratase activity" EXACT [] synonym: "crotonoyl-[acyl-carrier-protein] hydratase activity" EXACT [] synonym: "crotonoyl-ACP hydratase activity" EXACT [] synonym: "crotonoyl-acyl-carrier-protein hydratase activity" EXACT [] synonym: "crotonyl acyl carrier protein hydratase activity" EXACT [] xref: KEGG_REACTION:R04428 xref: RHEA:41808 is_a: GO:0019171 ! (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity

id: GO:0047451 (2 EXP annotations to fabA and fabZ) name: (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity namespace: molecular_function def: "Catalysis of the reaction: (3R)-3-hydroxyoctanoyl-[acyl-carrier protein] = H2O + (2E)-octenoyl-[acyl-carrier protein]." [PMID:8910376, RHEA:41844] synonym: "(3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase activity" RELATED [] synonym: "3-hydroxyoctanoyl-[acyl-carrier protein] dehydratase activity" EXACT [] synonym: "3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity" BROAD [] synonym: "3-hydroxyoctanoyl-ACP dehydratase activity" EXACT [] xref: KEGG_REACTION:R04537 xref: MetaCyc:4.2.1.59-RXN xref: RHEA:41844 is_a: GO:0019171 ! (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity

id: GO:0004317 (0 EXP annotations) name: (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity namespace: molecular_function def: "Catalysis of the reaction: (3R)-hydroxypalmitoyl-[acyl-carrier protein] = 2-hexadecenoyl-[acyl-carrier protein] + H2O." [PMID:8088535, RHEA:41908] synonym: "(3R)-3-hydroxypalmitoyl-acyl-carrier-protein hydro-lyase (hexadec-2-enoyl-acyl-carrier protein-forming)" EXACT [] synonym: "(3R)-3-hydroxypalmitoyl-acyl-carrier-protein hydro-lyase activity" EXACT [] synonym: "(3R)-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity" EXACT [] synonym: "3-hydroxypalmitoyl-[acyl-carrier protein] dehydratase activity" EXACT [] synonym: "3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity" EXACT [] synonym: "3-hydroxypalmitoyl-ACP dehydratase activity" EXACT [] synonym: "3-hydroxypalmitoyl-acyl-carrier-protein dehydratase activity" EXACT [] xref: KEGG_REACTION:R04462 xref: RHEA:41908 is_a: GO:0019171 ! (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity

id: GO:0008659 (0 EXP annotations) name: (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity namespace: molecular_function def: "Catalysis of the reaction: (3R)-3-hydroxytetradecanoyl-[acyl-carrier protein] = tetradecenoyl-[acyl-carrier protein] + H2O." [GOC:ai, PMID:12368867, RHEA:41892] synonym: "(3R)-hydroxymyristoyl-[acyl-carrier protein] dehydratase activity" EXACT [] synonym: "(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity" EXACT [] synonym: "(3R)-hydroxymyristoyl-ACP dehydratase activity" EXACT [] xref: RHEA:41892 is_a: GO:0019171 ! (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity

id: GO:0008693 (2 EXP annotations) name: (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity namespace: molecular_function def: "Catalysis of the reaction: (3R)-3-hydroxydecanoyl-[acyl-carrier protein] = 2,3-decenoyl-[acyl-carrier protein] or 3,4-decenoyl-[acyl-carrier protein] + H2O." [PMID:8910376, RHEA:41860] synonym: "(3R)-3-hydroxydecanoyl-acyl-carrier-protein hydro-lyase activity" EXACT [] synonym: "3-hydroxydecanoyl-[acyl-carrier protein] dehydratase activity" EXACT [] synonym: "3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity" EXACT [] synonym: "3-hydroxydecanoyl-ACP dehydratase activity" EXACT [] synonym: "3-hydroxydecanoyl-acyl carrier protein dehydrase activity" EXACT [] synonym: "3-hydroxydecanoyl-acyl carrier protein dehydratase activity" EXACT [] synonym: "3-hydroxydecanoyl-acyl-carrier-protein dehydratase activity" EXACT [] synonym: "beta-hydroxyacyl-ACP dehydrase activity" EXACT [] synonym: "beta-hydroxyacyl-acyl carrier protein dehydratase activity" EXACT [] synonym: "beta-hydroxydecanoate dehydrase activity" EXACT [] synonym: "beta-hydroxydecanoyl thioester dehydrase activity" EXACT [] xref: MetaCyc:3-HYDROXYDECANOYL-ACP-DEHYDR-RXN xref: RHEA:41860 is_a: GO:0019171 ! (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity

pgaudet commented 4 months ago

Dear all,

The proposal has been made to obsolete GO:0047450 (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity >> 1 EXP GO:0008693 (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity >> 2 EXP GO:0008659 (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity >> 0 EXP GO:0047451 (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity >> 2 EXP GO:0004317 (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity >> 0 EXP

& replace by parent GO:0019171 (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity. The reason for obsoletion is that these represent specific substrates of GO:0019171 (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity; the enzyme is not selective for the length of the chain (see comments in https://enzyme.expasy.org/EC/4.2.1.59):

Different forms of the enzyme may have preferences for substrates with different chain length. Despite the differences both forms can catalyze all steps leading to the synthesis of palmitate (C16:0).

Annotations are here: https://github.com/geneontology/go-annotation/issues/5307

Thanks, Pascale