search

geneontology / go-ontology

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

NTR histone citrullination MF #23152

Closed pgaudet closed 2 years ago

pgaudet commented 2 years ago

Hello,

As part of the project of removing single step BPs from the ontology (and moving them to MFs as appropriate), the proposal has been made to obsolete GO:0018101 protein citrullination & children. We do have a MF for the generic protein citrullination reaction (GO:0004668 protein-arginine deiminase activity), but not for the histones.

We want to create all major histone modifications to represent the histone code in the ontology. Based on data shown in PMID:15339660 I will create the following MF reactions, children of GO:0004668 protein-arginine deiminase activity:

Thanks, Pascale

pgaudet commented 2 years ago

+[Term] +id: GO:0140794 +name: histone-arginine deiminase activity +def: "Catalysis of the reaction: H2O + histone 3 L-arginyl = histone 3 L-citrullyl + NH4+, resulting in histone citrullination." [PMID:15339660] +is_a: GO:0004668 ! protein-arginine deiminase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23152 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T13:07:02Z

+[Term] +id: GO:0140795 +name: histone-arginine deiminase activity (H3-R2 specific) +namespace: molecular_function +def: "Catalysis of the reaction: H2O + histone 3 L-arginyl (position 2)= histone 3 L-citrullyl (position 2) + NH4+, resulting in histone H3 citrullination at position 2." [PMID:15339660] +is_a: GO:0140794 ! histone-arginine deiminase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23152 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T13:10:24Z + +[Term] +id: GO:0140796 +name: histone-arginine deiminase activity (H3-R8 specific) +namespace: molecular_function +def: "Catalysis of the reaction: H2O + histone 3 L-arginyl (position 8)= histone 3 L-citrullyl (position 8) + NH4+, resulting in histone H3 citrullination at position 8." [PMID:15339660] +is_a: GO:0140794 ! histone-arginine deiminase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23152 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T13:11:13Z + +[Term] +id: GO:0140797 +name: histone-arginine deiminase activity (H3-R17 specific) +namespace: molecular_function +def: "Catalysis of the reaction: H2O + histone 3 L-arginyl (position 17)= histone 3 L-citrullyl (position 17) + NH4+, resulting in histone H3 citrullination at position 17." [PMID:15339660] +is_a: GO:0140794 ! histone-arginine deiminase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23152 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T13:12:15Z + +[Term] +id: GO:0140798 +name: histone-arginine deiminase activity (H3-R26 specific) +namespace: molecular_function +def: "Catalysis of the reaction: H2O + histone 3 L-arginyl (position 26)= histone 3 L-citrullyl (position 26) + NH4+, resulting in histone H3 citrullination at position 26." [PMID:15339660] +is_a: GO:0140794 ! histone-arginine deiminase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23152 xsd:anyURI +created_by: pg +creation_date: 2022-04-06T13:12:51Z

pgaudet commented 2 years ago

Create H4-R3 PMID: 16567635

pgaudet commented 2 years ago

H1-R54 PMID:24463520

pgaudet commented 2 years ago

+[Term] +id: GO:0140809 +name: histone-arginine deiminase activity (H4-R3 specific) +namespace: molecular_function +def: "Catalysis of the reaction: H2O + histone 4 L-arginyl (position 3)= histone 4 L-citrullyl (position 3) + NH4+, resulting in histone H3 citrullination at position 3." [PMID:16567635] +synonym: "H4-R3 citrullination" EXACT [] +is_a: GO:0140794 ! histone-arginine deiminase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23152 xsd:anyURI +created_by: pg +creation_date: 2022-05-11T10:07:04Z + +[Term] +id: GO:0140810 +name: histone-arginine deiminase activity (H1-R54 specific) +namespace: molecular_function +def: "Catalysis of the reaction: H2O + histone 1 L-arginyl (position 54)= histone 1 L-citrullyl (position 54) + NH4+, resulting in histone H1 citrullination at position 54." [PMID:24463520] +synonym: "H1-R54 citrullination" EXACT [] +is_a: GO:0140794 ! histone-arginine deiminase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23152 xsd:anyURI +created_by: pg +creation_date: 2022-05-11T10:11:08Z

pgaudet commented 2 years ago

Added comment to all terms: "The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635)."

pgaudet commented 2 years ago

+[Term] +id: GO:0140811 +name: histone-arginine deiminase activity (H2A-R3 specific) +namespace: molecular_function +def: "Catalysis of the reaction: H2O + histone 2A L-arginyl (position 3)= histone 2A L-citrullyl (position 3) + NH4+, resulting in histone H2A citrullination at position 3." [PMID:15823041] +comment: The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635). +synonym: "H2A-R3 citrullination" EXACT [] +is_a: GO:0140794 ! histone-arginine deiminase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23152 xsd:anyURI +created_by: pg +creation_date: 2022-05-11T10:07:04Z