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This repository hosts the tracker for issues pertaining to GO annotations.
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GO:0000030 | mannosyltransferase activity , PTN002003922 #5293

Open ValWood opened 2 weeks ago

ValWood commented 2 weeks ago

GO:0000030 | mannosyltransferase activity | IBA with S000000557 , PTN002003922 | contributes_to | GO_REF:0000033

https://www.pombase.org/gene/SPCC1919.02 pbn1/ PIG-X https://www.yeastgenome.org/locus/S000000557 Pbn1

Annotation

@edwong57

ValWood commented 2 weeks ago

sorry the details:

UniProt Human PIG-M concurs Mannosyltransferase involved in glycosylphosphatidylinositol-anchor biosynthesis. Transfers the first alpha-1,4-mannose to GlcN-acyl-PI during GPI precursor assembly. PMID: 11226175

PIG-M (gpi14) and PIG-X (Pbn1)

are the 2 members of GO:1990529 glycosylphosphatidylinositol-mannosyltransferase I complex

PIG-X appears to be the regulatory protein https://www.ebi.ac.uk/interpro/entry/InterPro/IPR013233/

see https://github.com/geneontology/go-ontology/issues/28214

edwong57 commented 1 week ago

@ValWood What do you think is an appropriate replacement for 'mannosyltransferase activity' for PBN1? GO:0005198 structural molecule activity?

ValWood commented 1 week ago

I was thinking GO:0030234 enzyme regulator activity Molecular Function Definition (GO:0030234 GONUTS page) Binds to and modulates the activity of an enzyme.

but I'm not sure if this is correct if it has only been shown to affect stability? it seems more like a "scaffold" and we don't have such a term (it is conflated with adaptor...I have issue with this https://docs.google.com/document/d/1Qakmsk19Sr4H_2cDpzMU0bi8duD7Rbye5aJ_Rne-7ZE/edit?usp=sharing because not all scaffold proteins are adaptors

GO:0060090 molecular adaptor activity Has related synonyms protein complex scaffold activity And protein-containing complex scaffold activity

but this could be an example of a scaffold that isn't an adaptor.

@pgaudet what do you think?

marcfeuermann commented 1 week ago

I would indeed rather use GO:0060090 molecular adaptor activity. At the PAINT level, annotation has been removed. Feel free to further discuss or close this ticket.

ValWood commented 1 week ago

The problem with adaptor is that it implies a connection of A to B, via C and that does not seem to be the case here. This is an ontology issue though...

ValWood commented 1 week ago

Although quite a few of these so called regulatory subunits are actually membrane adaptors for the catalytic subunt... I will see if I can find info about this for this one...

ValWood commented 1 week ago

still not clear from the 2 most recent papers I could find https://pubmed.ncbi.nlm.nih.gov/35420475/ Leishmania donovani Ortholog 2022 https://pubmed.ncbi.nlm.nih.gov/34875117/ T. brucei 2022

edwong57 commented 1 week ago

Yeah, I'm kind of getting hung up on the definition of 'molecular adaptor activity' stating "The binding activity of a molecule that brings together two or more molecules..." In these cases, that doesn't seem to be happening.

ValWood commented 1 week ago

Perhaps enzyme regulator is best?

This does not even seem to localize gpi14 to the membrane because GPI14 is a multimenbrane-spanning protein. We know it is absolutely required for the activity, but we don't know the precise mechanism @pgaudet is it OK to use enzyme regulator activity in these cases? It doesn't have catalytic activity, and it doesn't appear to be an adaptor - there isn't really any information on how it affects/contributes to the activity of gpi14