NTR: S-adenosylmethionine-dependent O-methyltransferase activity

[ValWood]

Please provide as much information as you can:

• Suggested term label: S-adenosylmethionine-dependent O-methyltransferase activity

• Definition (free text) standard

• Reference, in format PMID:####### Pending (I will use refs from the children once I locate one)

• Gene product name and ID to be annotated to this term

• Parent term(s) GO:0008171 O-methyltransferase activity GO:0008757 S-adenosylmethionine-dependent methyltransferase activity

• Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term?

all of the terms which are children of GO:0008171 O-methyltransferase activity and mention S-adenosylmethionine-dependent in their definition.

This allows us to correclty annotate S-adenosylmethionine-dependent O-methyltransferase when we aren't sure abou the specificity

• Synonyms (please specify, EXACT, BROAD, NARROW or RELATED)

• Cross-references

• For enzymes, please provide RHEA and/or EC numbers.

• Can also provide MetaCyc, KEGG, Wikipedia, and other links.

• Any other information

[ValWood]

@pgaudet is this OK?

[ValWood]

If I add this do I need to do a logical def? or is there a design pattern? I'm not sure how this works

[ValWood]

Hi @pgaudet, can I add this?

[pgaudet]

In this case, what is the other type(s) of S-adenosylmethionine-dependent methyltransferase activity ? Is it S-adenosylmethionine-dependent N-methyltransferase activity? ie, where should others terms be classified?

Thanks, Pascale

[ValWood]

I asked about this because I had a mapping to S-adenosylmethionine-dependent methyltransferase activity which appears to be correct. I had annotated to

GO:0010340 | carboxyl-O-methyltransferase activity

I don't know if all GO:0010340 | carboxyl-O-methyltransferase activity are S-adenosylmethionine-dependent though.

but this one is. The IntrePro family is called Class I-like SAM-dependent O-methyltransferase

If there was a term, this family could be mapped to the new term and it would prevent people (function prediction) from predicting it. Of course we could also annotate to both terms too, but that's a bit suboptimal.

[ValWood]

If we can be sure that all GO:0010340 | carboxyl-O-methyltransferase activity are S-adenosylmethionine-dependent we could just move it underneath his term.

[ValWood]

In pombe all t least 15 of the GO:0010340 | carboxyl-O-methyltransferase activity appear to be S-adenosylmethionine-dependent but they are annotated inconsistently

[pgaudet]

If we can be sure that all GO:0010340 | carboxyl-O-methyltransferase activity are S-adenosylmethionine-dependent

I dont know this - @kaxelsen do you know ?

[kaxelsen]

If we can be sure that all GO:0010340 | carboxyl-O-methyltransferase activity are S-adenosylmethionine-dependent

I dont know this - @kaxelsen do you know ?

@pgaudet, asked like that, no we cannot be sure. I have seen that we have tetrahydrofolate dependent demethylases, so maybe there are also tetrahydrofolate dependent methylases.

[pgaudet]

OK thanks @kaxelsen

@ValWood If you want you can go ahead and do this, but keep in mind we wont be helped by external resources to find terms that should be classified under the new grouping.

[deustp01]

A Google search for tetrahydrofolate dependent _de_methylase turns up this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1064056/, and a search for tetrahydrofolate dependent methylase turns up this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037834/. These look like reminders that SAM can donate methyl groups, and tetrahydrofolate can donate and accept them, and that while the SAM and tetrahydrofolate pathways are interconnected, the actual methylation / demethylation reactions proceed by what look like distinct mechanisms that should have distinct EC numbers?

[kaxelsen]

They are both in EC 2.1.1.-, e.g. 2.1.1.341, vanillate/3-O-methylgallate O-demethylase