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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR histone phosphatase activity #23148

Closed pgaudet closed 2 years ago

pgaudet commented 2 years ago

Hello,

To rehouse some annotations due to the obsoletion of histone dephosphorlyation (see #23145), @sylvainpoux is requesting 'histone phosphatase activity'

To be consistent with other histone modification reactions, we should perhaps create the specific modifications. I found 2 annotated modifications: H2-Y142 (catalyzed by O00167 and Q99504) H2-S140 (catalyzed by P60510)

For the Tyrosine, I can put the term under 'GO:0004725 protein tyrosine phosphatase activity'; but for the Serine, we dont have a 'phosphoserine phosphatase activity' - we have either

@sylvainpoux do you know if these phosphatases are specific for phosphoserine? I would probably create a grouping term.

Thanks, Pascale

sylvainpoux commented 2 years ago

Hi Pascale, if we follow protein phosphatase specificities, we should have one for protein serine/threonine phosphatase (P60510) activity and one for protein tyrosine/serine/threonine phosphatase activity (O00167 and Q99504) Let me know when terms are created, I will curate them Thank you very much! Sylvain

pgaudet commented 2 years ago

+[Term] +id: GO:0140789 +name: histone phosphatase activity +namespace: molecular_function +def: "Catalysis of the reaction: a phosphorylated histone + H2O = a protein + phosphate." [PMID:19351884] +is_a: GO:0004721 ! phosphoprotein phosphatase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23148 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T08:08:00Z

+[Term] +id: GO:0140790 +name: histone serine/threonine phosphatase activity +namespace: molecular_function +def: "Catalysis of the reaction: histone serine phosphate + H2O = histone serine + phosphate, and histone threonine phosphate + H2O = histone threonine + phosphate." [PMID:18614045] +is_a: GO:0004722 ! protein serine/threonine phosphatase activity +is_a: GO:0140789 ! histone phosphatase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23148 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T08:16:16Z + +[Term] +id: GO:0140791 +name: histone serine phosphatase activity (H2-S140 specific) +namespace: molecular_function +def: "Catalysis of the reaction: histone H2 serine-140 phosphate + H2O = histone serine + phosphate." [PMID:18614045] +is_a: GO:0140790 ! histone serine/threonine phosphatase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23148 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T08:16:16Z + +[Term] +id: GO:0140792 +name: histone tyrosine phosphatase activity +namespace: molecular_function +def: "Catalysis of the reaction: histone tyrosine phosphate + H2O = histone tyrosine + phosphate." [PMID:19234442, PMID:19351884] +is_a: GO:0004725 ! protein tyrosine phosphatase activity +is_a: GO:0140789 ! histone phosphatase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23148 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T08:20:40Z + +[Term] +id: GO:0140793 +name: histone tyrosine phosphatase activity (H2-Y142 specific) +namespace: molecular_function +def: "Catalysis of the reaction: histone tyrosine phosphate + H2O = histone tyrosine + phosphate." [PMID:19234442, PMID:19351884] +is_a: GO:0140792 ! histone tyrosine phosphatase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23148 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T08:20:40Z +

pgaudet commented 2 years ago

This has been said elsewhere, but for the record: we will not be doing this for every protein, but we have agreed that the histone code should be captured.