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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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GO:0006467 protein thiol-disulfide exchange #10026

Closed gocentral closed 9 years ago

gocentral commented 11 years ago

Hi,

GO:0006467 looks like a function but is in the BP ontology. Is this correct?

Thanks, Antonia.

Reported by: antonialock

Original Ticket: geneontology/ontology-requests/9822

gocentral commented 11 years ago

Original comment by: antonialock

gocentral commented 11 years ago

You're right - looks like it's the same as: GO:0015035 protein disulfide oxidoreductase activity. I'll just check that that's correct and if so I'll merge.

Original comment by: jl242

gocentral commented 11 years ago

Original comment by: jl242

gocentral commented 11 years ago

Original comment by: jl242

gocentral commented 11 years ago

I'm not an expert either on disulfide isomerase or on the boundary in GO between molecular functions and single-step biological processes, but the two terms look the same to me. I also can't tell them apart from GO:0003756 protein disulfide isomerase activity, and I see that UniProt P07237 Protein disulfide-isomerase (human) has both GO:0003756 and GO:0015035 as direct annotations. Perhaps one of these terms could be an is_a child of the other?

Original comment by: deustp01

gocentral commented 11 years ago

Thanks Peter.

From further headbanging, I've gleaned that protein disulfide isomerase and protein thiol-disulfide exchange shift around disulphide bonds within a protein, so the overall number of bonds does not change. Protein disulfide oxidoreductase, conversely, changes the overall number of disulphide bonds in a protein by oxidising or reducing bonds.

So I think it's okay to have separate terms for protein disulfide isomerase activity (GO:0003756) and protein disulfide oxidoreductase activity (GO:0015035).

But maybe we need to merge protein thiol-disulfide exchange (GO:0006467) into protein disulfide isomerase activity (GO:0003756)?

Original comment by: jl242

gocentral commented 11 years ago

[From our editors meeting]

disulphide bond enzymes

Is it okay to merge a process into a function? See [3]

Should be ok, won't break anything. People will 'lose' a process annotation. Jane will look for a process parent (protein folding) to make the function/process link for that function. Reexamine protein modification parentage.

Original comment by: jl242

gocentral commented 11 years ago

Merged protein cysteine-thiol oxidation GO:0006467 into protein disulfide isomerase activity GO:0003756

Copied protein disulfide isomerase activity (GO:0003756) (as part_of), to protein folding (GO:0006457)

Deleted protein disulfide isomerase activity (GO:0003756) from cellular protein modification process (GO:0006464) with OBO_REL:is_a

Original comment by: jl242

gocentral commented 11 years ago

Original comment by: jl242