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Review annotations to GO:0016401 palmitoyl-CoA oxidase activity and GO:0016402 pristanoyl-CoA oxidase activity #5426

Open pgaudet opened 2 months ago

pgaudet commented 2 months ago

Dear all,

The proposal has been made to obsolete

GO:0016401 palmitoyl-CoA oxidase activity (no xrefs)- 4 EXP (rat Acox1, rat Acaa1a, mouse Acadl, human ACAA1) GO:0016402 pristanoyl-CoA oxidase activity (RHEA:40459)

because they represent specific substrates.

deustp01 commented 2 months ago

Hmm. The parent term, GO:0003997 acyl-CoA oxidase activity, which I guess is the intended replacement for GO:0016401 and 2, now has three children: GO:0044535 very-long-chain fatty acyl-CoA oxidase activity GO:0016401 palmitoyl-CoA oxidase activity GO:0016402 pristanoyl-CoA oxidase activity

If the very-long-chain fatty acyl-CoA oxidase activity term is OK (seems OK to me), then as part of this clean-up, should it get some siblings for long-chain ~, medium-chain ~, short-chain ~, branched-chain ~, and so forth? @sjm41 ?

deustp01 commented 2 months ago

because they represent specific substrates.

Here's another case where a problem is a mismatch between the enymes' names (which are narrow, as noted) and their true substrate specificities, which are much broader as demonstrated for the rat enzymes (from which the human annotations were inferred):

Short chain mono (hexanoyl-) and dicarboxylyl (glutaryl-)-CoAs and prostaglandin E2-CoA were oxidized exclusively by palmitoyl-CoA oxidase. Long chain mono (palmitoyl-) and dicarboxylyl (hexadecanedioyl-)-CoAs were oxidized by palmitoyl-CoA oxidase and pristanoyl-CoA oxidase, the former enzyme catalyzing approximately 70% of the total eluate activity. ...

PMID: 1400324

sjm41 commented 2 months ago

If the very-long-chain fatty acyl-CoA oxidase activity term is OK (seems OK to me), then as part of this clean-up, should it get some siblings for long-chain ~, medium-chain ~, short-chain ~, branched-chain ~, and so forth? @sjm41 ?

Right, that's basically what I proposed in https://github.com/geneontology/go-ontology/issues/28733:

GO:0003997 acyl-CoA oxidase activity (EC:1.3.3.6, RHEA:38959)
   |_GO:0044535 very-long-chain fatty acyl-CoA oxidase activity (RHEA:78847)
   |_NTR short-chain fatty acyl-CoA oxidase activity [RHEA:78859]
   |_NTR medium-chain fatty acyl-CoA oxidase activity [RHEA:78855]
   |_NTR long-chain-chain fatty acyl-CoA oxidase activity [RHEA:78851]