Query RNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase

[pgaudet]

This is the first time I see this: RHEA has an OR in a reaction:
https://www.rhea-db.org/rhea/42396

This is an exact match to EC:2.1.1.205 tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase, but GO has 2 reactions.

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However this one here is different, and RHEA created 2 reactions:

I think we should align with EC and have both substrates in the same reaction, for each of these 2 ECs.

@sjm41 what do you think ?

Thanks, Pascale

[sjm41]

I think we should align with EC and have both substrates in the same reaction, for each of these 2 ECs.

Yes, I agree.

[raymond91125]

@sjm41 Is the following a correct summary? If so, I can implement.

what we have
GO:0106339 tRNA (cytidine(32)-2'-O)-methyltransferase activity	EC:2.1.1.200/EC:2.1.1.205	RHEA:42396/RHEA:42932
GO:0106340 tRNA (guanine(34)-2'-O)-methyltransferase activity	EC:2.1.1.205	RHEA:42396
WHAT WE WANT
merged GO:0106339/GO:016340 tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase activity	EC:2.1.1.205	RHEA:42396
NTR tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase activity	EC:2.1.1.200	RHEA:42932/RHEA:42936

[sjm41]

@raymond91125 I think that is correct, but I think we should wait for @pgaudet to confirm when she's back next week.

I realise that one potential issue with this change is what should be annotated if/when "(cytidine(32)-2'-O)-methyltransferase activity" is shown - would the curator then annotate with both the new GO terms? We should look at current annotations (and their sources) to GO:0106339 and GO:0106340 to check on this.

[pgaudet]

This looks OK to me. I checked the annotation for both existing terms, GO:0106339 and GO:0106340, and they are greatly overlapping (most correspond to PTHR10920; others are either named 'tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase' and/or annotated to Rhea 42396.

So @raymond91125 please go ahead with the plan you propose above.

Thanks, Pascale

[raymond91125]

EC:2.1.1.205 appears to be eukaryotic whereas EC:2.1.1.200 prokaryotic. Though should we create EC:2.1.1.200 tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase activity right now before there is a request?

[pgaudet]

Yes I think this is what @raymond91125 had said in the proposal above

[raymond91125]

Also moved never_in Archaea from GO:0106339 to GO:0106340.

[raymond91125]

+[Term]
+id: GO:0160206
+name: tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: cytidine(32)/uridine(32) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(32)/2'-O-methyluridine(32) in tRNA + H+ + S-adenosyl-L-homocysteine." [EC:2.1.1.200]
+synonym: "TrMet(Xm32) activity" EXACT []
+xref: EC:2.1.1.200
+xref: RHEA:42932 {source="skos:narrowMatch"}
+xref: RHEA:42936 {source="skos:narrowMatch"}
+is_a: GO:0008175 ! tRNA methyltransferase activity
+property_value: term_tracker_item "#28550" xsd:anyURI
+created_by: rynl
+creation_date: 2024-08-21T21:13:17Z