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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Add EC xref to protein adenylyltransferase activity (GO:0070733) #17854

Closed sjm41 closed 5 years ago

sjm41 commented 5 years ago

[Term] id: GO:0070733 name: protein adenylyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + protein = diphosphate + adenylyl-protein; mediates the addition of an adenylyl (adenosine 5'-monophosphate; AMP group) to specific residues of target proteins." [GOC:mah, PMID:19039103, PMID:19362538]

Matches EC 2.7.7.n1: https://enzyme.expasy.org/EC/2.7.7.n1

hdrabkin commented 5 years ago

A while ago some at EC has told me EC 2.7.7.n1: is not an official number. It just indicates that someone has made a request. I was told NOT to use any .n1, etc. as an Xref. However, I need to contact them on this one because it has two reactions associated with it.

hdrabkin commented 5 years ago

What is interesting is that RHEA actually has this and makes separate reactions RHEA:54292 (APPROVED) ATP + L-threonyl-[protein] = 3-O-(5'-adenylyl)-L-threonyl-[protein] + diphosphate RHEA:54288 (APPROVED) ATP + L-tyrosyl-[protein] = diphosphate + O-(5'-adenylyl)-L-tyrosyl-[protein]

So I suppose I should make the two children to this term with the appropriate amino acid target, and then have annotations moved depending upon the substrate used.

sjm41 commented 5 years ago

Re. not using the 'unofficial' EC refs, I see two cases where these are already used - should they be removed?

id: GO:0052849 name: NADPH-dependent curcumin reductase activity xref: EC:1.3.1.n3

id: GO:0090409 name: malonyl-CoA synthetase activity xref: EC:6.2.1.n3

hdrabkin commented 5 years ago

Once I get confirmation from EC I would do that. What took me by surprise is RHEA using them. I need to inquire on the status of the x.x.x.n's

hdrabkin commented 5 years ago

And I have NO idea what makes an 'n1' vs 'n3" in these naming schemes.

hdrabkin commented 5 years ago

Fired off the questions; I found the old email and I was told "These letters cannot be used. They are only internal place holders until the entries go to review." My asking about them might get them fast-tracked though.

sjm41 commented 5 years ago

OK, thanks. We will see.... I'm also unclear what the turnaround time might be in changing an internal ID to an official one. (Actually, if they really are 'internal', why are they available on the public website at all...?)

hdrabkin commented 5 years ago

Lol; I have the exact same questions!

hdrabkin commented 5 years ago

So today: "EC numbers including an 'n' as part of the serial digit are preliminary EC numbers, i.e. EC numbers describing well characterized enzymes that SIB have corrected while waiting for them to be integrated in the EC list. We did that during a period when we (I) was not involved in the IUBMB nomenclature work, and where waiting times for new EC numbers were even longer than they are now.

  1. Yes, these preliminary EC numbers are stable
  2. RHEA can use
  3. They stay with the 'n' until (if ever) they are included in the EC list and thus a complete EC number is created for them. At that point they will be transferred in our list (the ENZYME database) so they will not simply disappear.
  4. The only difference between an n1 and an n3 is that they are separate enzymes. "

So, we can use; so will do this for you and close

sjm41 commented 5 years ago

OK, that's a clear reply. Thanks for adding.