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NTR: Xyloside xylosyltransferase activity #16869
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"The RHEA xrefs are specific for EGF repeats, but the EC is not" |
We don't want a single GO MF to point to more than one Rhea reaction. We want to be able to capture them precisely and take their definitions. @hattrill, does either of the rhea reactions fit your annotation needs? |
But would you want different MF terms for the xylosylation by the identical molecular mechanism of two different specific peroteins, or would you want oine term for the xylosylation of a protein family or generic [rotein? |
"The RHEA xrefs are specific for EGF repeats, but the EC is not" WARNING: EC:2.4.2.n3 is a preliminary EC. It is NOT an official IUBMB entry. There are 2 Rhea reactions because the enzyme can acts on 3-O-[α-D-xylosyl-(1→3)-β-D-glucosyl]-L-seryl residue or 3-O-[α-D-xylosyl-(1→3)-β-D-glucosyl]-L-threonyl residue We (SIB) are in the process to re-organize enzyme classification data. I think this preliminary EC is in @deustp01 |
It's the molecular mechanism that I want to differentiate, rather than the underlying protein backbone. ie the dixylose linkage formed and the underlying substrate protein-O-Glc-Xyl, is the interesting bit - the EGF repeat I am not so fussed about. (But, I haven't come across this dixylose-Glc-O-X modification in non-EGF repeats, but I have not looked exhaustively.) I'd just be happy with capturing the transfer of xylose from UDP-xylose to xylose-R to make xylose-α1,3-xylose-R . This particular enzyme does not catalyse the addition of more xyloses, so dixylose-R is the product. The preliminary EC, EC:2.4.2.n3 captures the Xyl-Glc-R substrate. (It would be good for us (FlyBase) to have an EC xref in the GO, as we use this xref in other pipelines.) In relation to other points - The particular enzymatic activity that I am curating results in the addition of a xyl to a Protein-Ser-O-Glc-Xyl of the EGF repeats of Notch receptor. RHEA:22820 describes this reaction. I do not need this much detail for the MF term. |
I have now looked at this pathway both in Rhea and in the IUBMB nomenclature.
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Unfortunately my entries created Nov. 15 2019 have been stuck in the EC system until now, so they will only become public after having been in review, but this will happen soon, so they should become public in ~2 months. So I will soon be able to communicate the EC numbers. |
Now I have the EC numbers. I will list them in pathway order: |
Ready ? |
If you ask about the EC numbers, they became public just before June 23, and are now also in the UniProtKB |
@hattrill this is the term you requested: +[Term] |
EC transferred to EC:2.4.1.17 However Rhea has reactions for both EC:2.4.1.17 (RHEA:21032) and EC 2.4.2.42 (RHEA:56064) I guess we also need the two reactions in GO ? I dont understand why EC:2.4.1.17 was transferred. Thanks, Pascale |
Thanks @pgaudet |
Created other 2 terms recommended by @kaxelsen +[Term] Thanks, Pascale |
I think you have looked at EC 2.4.1.42 (one) that has been transferred to EC 2.4.1.17. |
Thanks @kaxelsen !!! |
I will add 'UDP-D-xylose:beta-D-glucoside alpha-1,3-D-xylosyltransferase activity' (EC:2.4.2.42 /RHEA:56064) as a child of GO:0035252 UDP-xylosyltransferase activity, and move the reference PMID:30127001 (Two novel protein O-glucosyltransferases that modify sites distinct from POGLUT1 and affect Notch trafficking and signaling) to the new term. |
+[Term] |
Since rheas were added already I will remove tag |
Could I request:
name: xyloside xylosyltransferase activity
Def: UDP-xylose:α-xyloside α1,3-xylosyltransferase actvity, adding an xylose to an O-linked xylose-glucose acceptor (xylose-α1,3-glucoseβ1-O-Ser/Thr).
(Sorry, this is a bit weak - could do with a bit of editior input.)
Xrefs:EC:2.4.2.n3
RHEA:22820
RHEA:56600
PMID:22117070
Reaction (from EC): UDP-alpha-D-xylose + alpha-D-xylose-(1->3)-beta-D-glucosyl-R <=> UDP + alpha-D-xylose-(1->3)-alpha-D-xylose-(1->3)-beta-D-glucosyl-R
This is to annotate a xyloside xylosyltransferase that adds a second xylose to Notch Receptor EGF repeats - the RHEA xrefs are specific for EGF repeats, but the EC is not - I don't think that the nature of the underlining structure should matter for the activity (ie any glycoprotein acceptor will do).
Is_a:
UDP-xylosyltransferase activity GO:0035252
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