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NTR: Xyloside xylosyltransferase activity #16869

Closed hattrill closed 3 years ago

hattrill commented 5 years ago

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

deustp01 commented 5 years ago

"The RHEA xrefs are specific for EGF repeats, but the EC is not" In a case like this where the reaction chemistry itself is the same for both protein participants, would it be possible to ask Rhea to broaden their reaction annotation to use a generic protein? Getting grandiose, could Rhea be proactive and, where it's clear that the reaction to be annotated could proceed with any of a variety of specific proteins as inputs, create the Rhea reaction with a generic protein input in the first place? @ukemi @amorgat

ukemi commented 5 years ago

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?

deustp01 commented 5 years ago

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?

amorgat commented 5 years ago

"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 is a warning in the IntEnz page (https://www.ebi.ac.uk/intenz/query?cmd=SearchID&id=19969) but not in the enzyme@ExPASy page (https://enzyme.expasy.org/EC/2.4.2.n3) "This is a preliminary EC number. The content has not yet been validated and included in the official IUBMB Enzyme list."

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 Kristian's to-do list. @kaxelsen, please would you comment on EC:2.4.2.n3?

@deustp01 "Getting grandiose, could Rhea be proactive and, where it's clear that the reaction to be annotated could proceed with any of a variety of specific proteins as inputs, create the Rhea reaction with a generic protein input in the first place?" Yes, this is definitely the direction we want to go! Will be discussed during our Rhea meeting this week.

hattrill commented 5 years ago

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.

kaxelsen commented 4 years ago

I have now looked at this pathway both in Rhea and in the IUBMB nomenclature.

  1. I have updated EC 2.4.2.42 at IUBMB (covering GXYLT1 and GXYLT2). The reaction described was actually more specific than the one in Rhea, as it was described for "-EGF-like domain of bovine factor IX(45-87)". I have now changed it to "EGF domain containing protein" using the agreed nomenclature for the carbohydrate part of the reaction. I have realised RHEA:56564 is wrong, as the glycosylation only takes place on serine amino acids in the CXSXPC motif of the EGF domains, and not on threonine residues as described in RHEA:56564.
  2. I have created a new EC number at IUBMB covering the preliminary EC 2.4.2.n3. This covers the activity of XXYLT1. For this entry, RHEA:56600 is wrong (threonyl residue).
  3. I have created two EC numbers covering the activity of POGLUT1 (or rumi in fruit flies) that catalyzes the first step in the pathway, and in addition has xylosyltransferase activity. The two EC numbers will be in classes: EC 2.4.2. (xylosyltransferase activity) and EC 2.4.1 (glucosyltransferase activity). The corresponding Rhea reactions are: RHEA:62016 and RHEA:58116, respectively.
hdrabkin commented 4 years ago

@hattrill and @kaxelsen was waiting for the RHEAs to become public but now I"ve totally lost the point of this thread. Is the request term xyloside xylosyltransferase activity suppose to be assigned to EC:2.4.2.42? What RHEA should I use?

kaxelsen commented 4 years ago

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.

kaxelsen commented 4 years ago

Now I have the EC numbers. I will list them in pathway order: POGLUT1 EC 2.4.2.63 RHEA:62016 L-seryl-[EGF-like domain protein] + UDP-α-D-xylose = 3-O-(β-D-xylosyl)-L-seryl-[EGF-like domain protein] + H+ + UDP POGLUT1 EC 2.4.1.376 RHEA:58116 L-seryl-[EGF-like domain protein] + UDP-α-D-glucose = 3-O-(β-D-glucosyl)-L-seryl-[EGF-like domain protein] + H+ + UDP GXYLT2 EC 2.4.2.42 RHEA:56064 3-O-(β-D-glucosyl)-L-seryl-[EGF-like domain protein] + UDP-α-D-xylose = 3-O-[α-D-xylosyl-(1→3)-β-D-glucosyl]-L-seryl-[EGF-like domain protein] + H+ + UDP XXYLT1 EC 2.4.2.62 RHEA:22820 3-O-[α-D-xylosyl-(1→3)-β-D-glucosyl]-L-seryl-[EGF-like domain protein] + UDP-α-D-xylose = 3-O-[α-D-xylosyl-(1→3)-α-D-xylosyl-(1→3)-β-D-glucosyl]-L-seryl-[EGF-like domain protein] + H+ + UDP

pgaudet commented 3 years ago

Ready ?

kaxelsen commented 3 years ago

If you ask about the EC numbers, they became public just before June 23, and are now also in the UniProtKB

pgaudet commented 3 years ago

@hattrill  this is the term you requested:

+[Term] +id: GO:0140560 +name: xylosyl alpha-1,3-xylosyltransferase activity +namespace: molecular_function +def: "Catalyzes the reaction: UDP-alpha-D-xylose + [protein with EGF-like domain]-3-O-(alpha-D-xylosyl-(1->3)-beta-D-glucosyl)-L-serine <=> UDP + [protein with EGF-like domain]-3-O-(alpha-D-xylosyl-(1->3)-alpha-D-xylosyl-(1->3)-beta-D-glucosyl)-L-serine. The enzyme, found in animals and insects, is involved in the biosynthesis of the alpha-D-xylosyl-(1->3)-alpha-D-xylosyl-(1->3)- beta-D-glucosyl trisaccharide on epidermal growth factor-like (EGF- like) domains." [PMID:22117070, PMID:8982869, RHEA:22820] +xref: EC:2.4.2.62 +xref: RHEA:22820 +is_a: GO:0016757 ! transferase activity, transferring glycosyl groups +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/16869 xsd:anyURI +created_by: pg +creation_date: 2020-11-25T13:45:18Z

pgaudet commented 3 years ago

@amorgat @kaxelsen

GXYLT2 EC:2.4.2.42 RHEA:56064

EC transferred to EC:2.4.1.17 GO already exists: GO:0015020 glucuronosyltransferase activity :)

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

hattrill commented 3 years ago

Thanks @pgaudet

pgaudet commented 3 years ago

Created other 2 terms recommended by @kaxelsen

+[Term] +id: GO:0140561 +name: EGF-domain serine glucosyltransferase activity +namespace: molecular_function +def: "Catalysis of the reaction: UDP-alpha-D-glucose + [protein with EGF-like domain]-L-serine <=> UDP + [protein with EGF-like domain]-3-O-(beta-D-glucosyl)-L-serine." [RHEA:58116] +xref: EC:2.4.1.376 +xref: RHEA:58116 +is_a: GO:0035251 ! UDP-glucosyltransferase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/16869 xsd:anyURI +created_by: pg +creation_date: 2020-11-25T14:19:23Z + +[Term] +id: GO:0140562 +name: EGF-domain serine xylosyltransferase activity +namespace: molecular_function +def: "Catalyses the reaction: UDP-alpha-D-xylose + [protein with EGF-like domain]-L-serine <=> UDP + [protein with EGF-like domain]-3-O-(beta-D-xylosyl)-L-serine." [RHEA:62016] +xref: EC 2.4.2.63 +xref: RHEA:62016 +is_a: GO:0035252 ! UDP-xylosyltransferase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/16869 xsd:anyURI +created_by: pg +creation_date: 2020-11-25T14:30:56Z

Thanks, Pascale

kaxelsen commented 3 years ago

@amorgat @kaxelsen

GXYLT2 EC:2.4.2.42 RHEA:56064

EC transferred to EC:2.4.1.17 GO already exists: GO:0015020 glucuronosyltransferase activity :)

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

I think you have looked at EC 2.4.1.42 (one) that has been transferred to EC 2.4.1.17. EC 2.4.2.42 (two) is active and will remain so. EC 2.4.1.17 has not been transferred.

pgaudet commented 3 years ago

Thanks @kaxelsen !!!

pgaudet commented 3 years ago

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.

pgaudet commented 3 years ago

+[Term] +id: GO:0140563 +name: UDP-D-xylose:beta-D-glucoside alpha-1,3-D-xylosyltransferase activity +namespace: molecular_function +def: "Catalyzes the reaction: UDP-alpha-D-xylose + [protein with EGF-like domain]-3-O-(beta-D-glucosyl)-L-serine <=> UDP + [protein with EGF-like domain]-3-O-(alpha-D-xylosyl-(1->3)-beta-D-glucosyl)-L-serine." [EC:2.4.2.42, PMID:30127001, RHEA:56064] +xref: EC:2.4.2.42 +xref: RHEA:56064 +is_a: GO:0035252 ! UDP-xylosyltransferase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/16869 xsd:anyURI +created_by: pg +creation_date: 2020-11-25T16:07:58Z +

hdrabkin commented 3 years ago

Since rheas were added already I will remove tag