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Source ontology files for the Gene Ontology
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Three GO terms with EC:3.2.1.169 xref #27560

Closed sjm41 closed 6 months ago

sjm41 commented 6 months ago

EC:3.2.1.169 (protein O-GlcNAcase) has two associated reactions: 3-O-(N-acetyl-beta-D-glucosaminyl)-L-seryl-[protein] + H2O <=> L-seryl-[protein] + N-acetyl-D-glucosamine 3-O-(N-acetyl-beta-D-glucosaminyl)-L-threonyl-[protein] + H2O <=> L-threonyl-[protein] + N-acetyl-D-glucosamine

And we have EC:3.2.1.169 as an xref on three related GO terms:

id: GO:0102571 name: [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity namespace: molecular_function def: "Catalysis of the reaction: H2O + an N-acetyl-alpha-D-glucosaminyl-[glycoprotein] = N-acetyl-alpha-D-glucosaminide + a [glycoprotein]-(L-serine/L-threonine)." [EC:3.2.1.169, GOC:pz] xref: EC:3.2.1.169 xref: MetaCyc:RXN-15215 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

id: GO:0102166 name: [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-threonine O-N-acetyl-alpha-D-glucosaminase activity namespace: molecular_function def: "Catalysis of the reaction: H2O + an N-acetyl-alpha-D-glucosaminyl-L-threonine-[glycoprotein] = N-acetyl-alpha-D-glucosaminide + a [protein]-L-threonine." [EC:3.2.1.169, GOC:pz] xref: EC:3.2.1.169 xref: MetaCyc:RXN-11891 xref: RHEA:48892 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

id: GO:0102167 name: [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine O-N-acetyl-alpha-D-glucosaminase activity namespace: molecular_function def: "Catalysis of the reaction: H2O + an N-acetyl-alpha-D-glucosaminyl-L-serine-[glycoprotein] = N-acetyl-alpha-D-glucosaminide + a [protein]-L-serine." [EC:3.2.1.169, GOC:pz] xref: EC:3.2.1.169 xref: MetaCyc:RXN-11892 xref: RHEA:48876 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

What's the best resolution here?:

  1. Obsolete GO:0102166 and GO:0102167, and then make RHEA and MetaCyc xrefs narrowMatch on GO:0102571?
  2. Keep GO:0102166 and GO:0102167, and make EC:3.2.1.169 a narrowMatch on them? If keeping these terms, then they should be made children of GO:0102571.

I vote for 1.

Also, the term def of GO:0102571 should be changed to: "Catalysis of the reaction: 3-O-(N-acetyl-beta-D-glucosaminyl)-L-seryl/L-threonyl-[protein] + H2O <=> L-seryl//L-threonyl-[protein] + N-acetyl-D-glucosamine."

pgaudet commented 6 months ago

I will obsolete GO:0102166 and GO:0102167.

pgaudet commented 6 months ago

@sjm41 Note that we dont use ' <=> ' in definitons. I used '='.

pgaudet commented 6 months ago

@sjm41 For RHEA we dont capture specific reactions as cross references; so for MetaCyc I dont think we should include the narrow xrefs RXN-11891 and RXN-11892. OK with you?

sjm41 commented 6 months ago

@sjm41 Note that we dont use ' <=> ' in definitons. I used '='.

Yep, I was just being lazy and just copied and pasted the reaction from the Expasy site.....

pgaudet commented 6 months ago

Dear all,

The proposal has been made to obsolete GO:0102166 name: [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-threonine O-N-acetyl-alpha-D-glucosaminase activity and GO:0102167 [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine O-N-acetyl-alpha-D-glucosaminase activity. The reason for obsoletion is that these represent specific substrates of GO:0102571 name: [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity, so they will be replaced by GO:0102571 [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity.

There are no annotations to these terms. RHEA mappings will be moved as NARROW matches on GO:0102571. These terms are not present in any subsets.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/27560

Thanks, Pascale

sjm41 commented 6 months ago

For RHEA we dont capture specific reactions as cross references; so for MetaCyc I dont think we should include the narrow xrefs RXN-11891 and RXN-11892. OK with you?

Sure. Does that mean that the final remaining term here (GO:0102571) won't have any RHEA xrefs?

sjm41 commented 6 months ago

Couple of questions about when we update an enzyme def to match the EC/RHEA reaction def:

  1. Is there a preference whether we add the EC or RHEA ID as the def xref?
  2. Is there a need/desire to preserve def xrefs like "[GOC:pz]" if the revised def is based solely on EC/RHEA?
pgaudet commented 6 months ago

Hi @sjm41

The current guidelines are here: https://wiki.geneontology.org/Guidelines_for_GO_textual_definitions

I added this to the next ontology call to get some clarification.

pgaudet commented 6 months ago

[protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity >> added is_a GO:0140096 ! catalytic activity, acting on a protein