NTR: DNA demethylases MF about go-ontology

[pgaudet]

MERGE
GO:0043734 'DNA-N1-methyladenine dioxygenase activity'

Def: oxidative demethylation of N1-methyladenine and N3-methylcytosine in DNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N1-methyladenine and N3-methylcytosine as formaldehyde.
No mappings

and GO:0035516 'oxidative DNA demethylase activity'

Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2.
EC:1.14.11.33
RHEA:30299

represent the same reaction

---

Also, change label and def of GO:0035516 oxidative DNA demethylase activity to broad specificity oxidative DNA demethylase activity

Old def: "Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2." [PMID:12594517, PMID:16482161, PMID:18775698, RHEA:30299]

New def: "Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2. Catalyzes oxidative demethylation of the DNA base lesions N1- methyladenine, N3-methylcytosine, N1-methylguanine, and N3- methylthymine. Can also act of RNA." [PMID:12594517, PMID:16482161, PMID:18775698, RHEA:30299]

[pgaudet]

5-methylcytosine dioxygenase activity
add a note: do not confuse with oxidative DNA demethylase activity
(and vice versa)

Add comment: 5-methylcytosine dioxygenase activity

This reaction removes the methyl group from position 5 of cytosine in DNA via oxidation of the 5-methylcytosine, followed by removal of the oxidated base by the base excision repair system. Do not confuse with oxidative DNA demethylase activity ; GO:0035516, which directly reverses the alkylation on the cytosine.

Add comment: oxidative DNA demethylase activity

This reaction directly reverses the alkylation on a cytosine. Do not confuse with 5-methylcytosine dioxygenase activity ; GO:0070579, which removes the methyl group from position 5 of cytosine in DNA via oxidation of the 5-methylcytosine, followed by removal of the oxidated base by the base excision repair system.

[pgaudet]

Dear all,

The proposal has been made to obsolete GO:0043734 'DNA-N1-methyladenine dioxygenase activity'. The reason for obsoletion is that is defined with two substrates ( N1-methyladenine and N3-methylcytosine in DNA), which corresponds better to another existing term, GO:0035516 'oxidative DNA demethylase activity' defined as Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2.

GO:0043734 has no mappings, while GO:0035516 is mapped to EC:1.14.11.33 and RHEA:30299

GO:0043734 'DNA-N1-methyladenine dioxygenase activity' will be replaced by GO:0035516 'oxidative DNA demethylase activity.

There are 8 Uniprot annotations, 1 EcoCyc, and 2 Reactome mappings, see geneontology/go-annotation#4880

You can comment on the ticket: #26656

Thanks, Pascale

[pgaudet]

+[Term]
+id: GO:0141131
+name: DNA N6-methyladenine demethylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: 2-oxoglutarate + an N6-methyl-2'-deoxyadenosine in DNA + O2 = a 2'-deoxyadenosine in DNA + CO2 + formaldehyde + succinate." [RHEA:49524]
+synonym: "DNA N(6)-methyladenine demethylase activity" EXACT []
+xref: EC 1.14.11.51
+xref: RHEA:49524
+is_a: GO:0035514 ! DNA demethylase activity
+property_value: term_tracker_item "#26656" xsd:anyURI
+created_by: pg
+creation_date: 2023-12-15T15:38:23Z