search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
220 stars 40 forks source link

NTR - metabolism: [proposed new label] #28920

Open sylvainpoux opened 6 days ago

sylvainpoux commented 6 days ago

Hi GO,

I would need a bunch of terms for protein lysine delactylase activity. Please note that 2 different enzymes and reactions can mediate protein delactylation, I therefore propose to rename the existing activity to avoid any confusion.

I also realized that I wrongly associated protein delactylase and depropionylase activities as a child of protein acetylation, while lactylation and propionylation represent acyl groups. I therefore propose to create a new term for deacylase activity.

Thanks

Sylvain

Name: protein lysine delactylase activity Definition: Catalysis of the reaction: H2O + N6-lactoyl-L-lysyl-[protein] = (S)-lactate + L-lysyl-[protein] PMID:35044827 child of GO:xxxxxxxx deacylase activity RHEA:81387

Name: deacylase activity Definition: Catalysis of the hydrolysis of an acyl group or groups from a substrate molecule. parent of GO:0019213 deacetylase activity child of GO:0016787 hydrolase activity

RENAME: FROM: GO:0141208 protein lysine delactylase activity TO: GO:0141208 NAD-dependent protein lysine delactylase activity Please change hierachy as child of GO:xxxxxxxx deacylase activity

RENAME: FROM: GO:0106231 protein-propionyllysine depropionylase activity TO: GO:0141208 NAD-dependent protein-lysine depropionylase activity Please change hierachy as child of GO:xxxxxxxx deacylase activity

raymond91125 commented 2 days ago

@sylvainpoux Shouldn't GO:0141208 NAD-dependent protein lysine delactylase activity be a subclass of "protein lysine delactylase activity" or perhaps this new term should be named "NAD-independent protein lysine delactylase activity" or "zinc-dependent protein lysine delactylase activity"?

raymond91125 commented 2 days ago

+[Term] +id: GO:0160215 +name: deacylase activity +namespace: molecular_function +def: "Catalysis of the reaction: R-CO-X + H2O = R-COOH + HX, hydrolysis of an acyl group or groups from a substrate molecule." [PMID:2760018, PMID:29637793, PMID:38355760] +is_a: GO:0016787 ! hydrolase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28920" xsd:anyURI +created_by: rynl +creation_date: 2024-09-16T23:45:30Z + +[Term] +id: GO:0160216 +name: protein lysine delactylase activity +namespace: molecular_function +def: "Catalysis of the reaction: H2O + N6-lactoyl-L-lysyl-[protein] = (S)-lactate + L-lysyl-[protein]." [PMID:35044827] +xref: RHEA:81387 +is_a: GO:0160215 ! deacylase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28920" xsd:anyURI +created_by: rynl +creation_date: 2024-09-17T00:03:19Z

pgaudet commented 2 days ago

Hi @raymond91125 Before merging this could you please

  1. Add EC:3.1.5.- xref as broadMatch to GO:0160215 deacylase activity
  2. See if other children need to be moved there

Thanks, Pascale

raymond91125 commented 1 day ago

3.1.5.-: Triphosphoric monoester hydrolases Is this correct?

raymond91125 commented 1 day ago

On second thought, deacylase is a rather broad class that is not an EC classification. Perhaps we shouldn't have it in GO.

pgaudet commented 1 day ago

3.1.5.-: Triphosphoric monoester hydrolases Is this correct?

Sorry I meant https://enzyme.expasy.org/EC/3.5.1.- !!

raymond91125 commented 15 hours ago

Added some children but I cannot be sure if that's complete.