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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Should GO:0033842 be a child of GO:0033207? #18752

Closed sjm41 closed 8 hours ago

sjm41 commented 4 years ago

Seems like "N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity" (GO:0033842) should be a child of "beta-1,4-N-acetylgalactosaminyltransferase activity" (GO:0033207)?

== [Term] id: GO:0033842 name: N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: UDP-N-acetyl-D-galactosamine + N-acetyl-beta-D-glucosaminyl group = UDP + N-acetyl-beta-D-galactosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl group." [EC:2.4.1.244] synonym: "beta1,4-N-acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.244] synonym: "beta1,4-N-acetylgalactosaminyltransferase III activity" EXACT [EC:2.4.1.244] synonym: "beta1,4-N-acetylgalactosaminyltransferase IV activity" EXACT [EC:2.4.1.244] synonym: "beta4GalNAc-T3" RELATED [EC:2.4.1.244] synonym: "beta4GalNAc-T4" RELATED [EC:2.4.1.244] synonym: "UDP-N-acetyl-D-galactosamine:N-acetyl-D-glucosaminyl-group beta-1,4-N-acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.244] xref: EC:2.4.1.244 xref: MetaCyc:2.4.1.244-RXN xref: RHEA:20493 is_a: GO:0008376 ! acetylgalactosaminyltransferase activity is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein

== [Term] id: GO:0033207 name: beta-1,4-N-acetylgalactosaminyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of an N-acetylgalactosaminyl residue from UDP-N-acetyl-galactosamine to an acceptor molecule, forming a beta-1,4 linkage." [GOC:mah] synonym: "beta-1,4-GalNAc transferase activity" EXACT [] is_a: GO:0008376 ! acetylgalactosaminyltransferase activity

sjm41 commented 4 years ago

Hi Harold - any thoughts/insights on this?

hdrabkin commented 4 years ago

@deustp01 what do you think?

hdrabkin commented 4 years ago

I notice id: GO:0033207 really has no decent references (like many of the grouping terms)

hdrabkin commented 4 years ago

I'm inclined to agree

deustp01 commented 4 years ago

The chemistry here is way beyond my limited knowledge of glycoprotein biochemistry. Sorry!

pgaudet commented 4 years ago

Merge ? https://enzyme.expasy.org/EC/2.4.1.244

Accepted Name: N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N- acetylgalactosaminyltransferase. synonym: Beta-1,4-N-acetylgalactosaminyltransferase.

GO:0033207 name: beta-1,4-N-acetylgalactosaminyltransferase activity

Pascale

pgaudet commented 4 years ago

Some proteins are annotated to all 3

https://www.uniprot.org/uniprot/Q9VAQ8 (mapped to EC:2.4.1.244)

acetylgalactosaminyltransferase activity Source: FlyBase beta-1,4-N-acetylgalactosaminyltransferase activity Source: FlyBase N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity Source: FlyBase

sjm41 commented 4 years ago

Reviewing this again, I agree with Pascale - we should merge GO:0033842 and GO:0033207.

Looking at QuickGO, I see 470 annotations to GO:0033842 and only 39 annotations to GO:0033207. Of those 39 annotations using GO:0033207:

Looking at the three IDAs from FB (which correspond to just two genes): UniProtKB:Q7KN92 beta4GalNAcTA PMID:17498683 UniProtKB:Q86NU9 beta4GalNAcTB PMID:17498683 UniProtKB:Q9VAQ8 beta4GalNAcTB PMID:17498683 I can say that the merge of the two GO terms would be fine.

@vanaukenk - can you check out the WB annotation using GO:0033207 to Q9GUM2?

==

Some proteins are annotated to all 3 https://www.uniprot.org/uniprot/Q9VAQ8 (mapped to EC:2.4.1.244) acetylgalactosaminyltransferase activity Source: FlyBase beta-1,4-N-acetylgalactosaminyltransferase activity Source: FlyBase N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity Source: FlyBase

Yeah, that's what got me looking at the two GO terms in the first place! The first annotation (to the parent term from PMID:15563714) appears to be correct, based on the description of the assay in that paper.

sjm41 commented 4 years ago

Oh, hang on.... I see that GO:0033842, but not GO:0033207, currently has parent of "catalytic activity, acting on a glycoprotein" (GO:0140103). Consistent with that, I note that GO:0033842 and EC:2.4.1.244 specifically mention 'glycoprotein' in the term name (though not in the definition).

This may reflect why we have the two separate GO terms. Indeed, PMID:17498683 (the source of the 3 FlyBase annotations to GO:0033207) describes the 2 fly enzymes as working in glycosphingolipid synthesis (so not glycoprotein).

So....I return to my original proposal: GO:0033207 (the more generic term) should be the parent of GO:0033842 (a more specific term, in that it specifies a glycoprotein substrate).

And/or we could make a new specific term for the 2 fly enzymes (and maybe the worm enzyme??) to specify the glycolipid substrate.

Thoughts?

sjm41 commented 1 day ago

Reviewing this (yet) again:

id: GO:0033842 name: N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity def: "Catalysis of the reaction: UDP-N-acetyl-D-galactosamine + N-acetyl-beta-D-glucosaminyl group = UDP + N-acetyl-beta-D-galactosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl group." [EC:2.4.1.244] xref: EC:2.4.1.244 xref: RHEA:20493

The current EC/RHEA def for this is: an N-acetyl-beta-D-glucosaminyl derivative + UDP-N-acetyl-alpha-D-galactosamine = an N-acetyl-beta-D-galactosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + UDP + H+.

That is, it is not specific for a glycoprotein, as the current GO/EC name suggests.

So, there are now 3 tasks to be done to close this issue:

sjm41 commented 1 day ago

@pgaudet I've updated the name and def. Could you take care of the merge and obsoletion? thanks.

pgaudet commented 8 hours ago

Neither EC:2.4.1.165 nor RHEA:13569 have any genes associate, so let's obsolete.

Made a request to RHEA to obsolete RHEA:13569.