pgaudet
commented
2 years ago yes we'll harmonize both branches.
Closed sjm41 closed 3 years ago
pgaudet
commented
2 years ago yes we'll harmonize both branches.
I've just been reviewing the branch shown below (with current EC/RHEA xrefs):
Looks like several improvements should be made to:
Some specific suggestions below (indicated by '=>') - note I've omitted the synonyms/Reactome xrefs for brevity:
[Term] id: GO:0032452 name: histone demethylase activity namespace: molecular_function def: "Catalysis of the removal of a methyl group from a histone." [GOC:mah] is_a: GO:0140457 ! protein demethylase activity
[Term] id: GO:0033746 name: histone demethylase activity (H3-R2 specific) namespace: molecular_function def: "Catalysis of the removal of a methyl group from arginine at position 2 of the histone H3 protein." [GOC:mah] is_a: GO:0032452 ! histone demethylase activity => (can't find EC/RHEA for this)
[Term] id: GO:0033749 name: histone demethylase activity (H4-R3 specific) namespace: molecular_function def: "Catalysis of the removal of a methyl group from arginine at position 3 of the histone H4 protein." [GOC:mah] is_a: GO:0032452 ! histone demethylase activity => (can't find EC/RHEA for this)
[Term] id: GO:0032453 name: histone demethylase activity (H3-K4 specific) namespace: molecular_function def: "Catalysis of the removal of a methyl group from lysine at position 4 of the histone H3 protein." [GOC:mah] is_a: GO:0032452 ! histone demethylase activity => add additional child term for RHEA:60212 (2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl4-[histone H3] + O2 = CO2 + formaldehyde + N6,N6-dimethyl-L-lysyl4-[histone H3] + succinate)
[Term] id: GO:0034649 name: histone demethylase activity (H3-monomethyl-K4 specific) namespace: molecular_function def: "Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 4) + O2 + FAD + H2O = histone H3 L-lysine (position 4) + H2O2 + formaldehyde + FADH2. This reaction is the removal of a methyl group from monomethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:16223729] is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen is_a: GO:0032453 ! histone demethylase activity (H3-K4 specific) => add RHEA:60220 (2-oxoglutarate + N6-methyl-L-lysyl4-[histone H3] + O2 = CO2 + formaldehyde + L-lysyl4-[histone H3] + succinate)
[Term] id: GO:0034648 name: histone demethylase activity (H3-dimethyl-K4 specific) namespace: molecular_function def: "Catalysis of the removal of a methyl group from dimethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:17550896] is_a: GO:0032453 ! histone demethylase activity (H3-K4 specific)
[Term] id: GO:0034647 name: histone demethylase activity (H3-trimethyl-K4 specific) namespace: molecular_function def: "Catalysis of the removal of a methyl group from trimethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:17550896] xref: EC:1.14.11.67 is_a: GO:0032453 ! histone demethylase activity (H3-K4 specific) => add RHEA:60208 (3 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl4-[histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl4-[histone H3] + 3 succinate)
[Term] id: GO:0032454 name: histone demethylase activity (H3-K9 specific) namespace: molecular_function def: "Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein." [PMID:16362057] xref: EC:1.14.11.65 xref: EC:1.14.11.66 is_a: GO:0032452 ! histone demethylase activity => make 5 child terms and move EC numbers to first two: 1) RHEA:60188 2 2-oxoglutarate + N6,N6-dimethyl-L-lysyl9-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl9-[histone H3] + 2 succinate (EC:1.14.11.65) 2) RHEA:60200 2 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N6-methyl-L-lysyl9-[histone H3] + 2 succinate (EC:1.14.11.66) 3) RHEA:60192 2-oxoglutarate + N6,N6-dimethyl-L-lysyl9-[histone H3] + O2 = CO2 + formaldehyde + N6-methyl-L-lysyl9-[histone H3] + succinate
4) RHEA:60196 2-oxoglutarate + N6-methyl-L-lysyl9-[histone H3] + O2 = CO2 + formaldehyde + L-lysyl9-[histone H3] + succinate 5) RHEA:60204 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + O2 = CO2 + formaldehyde + N6,N6-dimethyl-L-lysyl9-[histone H3] + succinate
[Term] id: GO:0035575 name: histone demethylase activity (H4-K20 specific) namespace: molecular_function def: "Catalysis of the reaction: histone H4 N6-methyl-L-lysine (position 20) + 2-oxoglutarate + O2 = histone H4 L-lysine (position 20) + succinate + formaldehyde + CO2. This reaction is the removal of a methyl group from lysine at position 20 of the histone H4 protein." [PMID:20622853] is_a: GO:0032452 ! histone demethylase activity => (can't find EC/RHEA for this)
[Term] id: GO:0071558 name: histone demethylase activity (H3-K27 specific) namespace: molecular_function def: "Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein." [GOC:sp, PMID:20622853] xref: EC:1.14.11.68 is_a: GO:0032452 ! histone demethylase activity => make 3 child terms corresponding to these RHEAs and move EC xref to first one
[Term] id: GO:0051864 name: histone demethylase activity (H3-K36 specific) namespace: molecular_function def: "Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein." [PMID:16362057] xref: EC:1.14.11.27 xref: MetaCyc:RXN-8660 xref: MetaCyc:RXN-8661 xref: RHEA:42032 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity is_a: GO:0032452 ! histone demethylase activity