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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR - metabolism: [branched-chain alpha-ketoacid dehydrogenase phosphatase activity] #26158

Closed nnouspikel closed 1 year ago

nnouspikel commented 1 year ago

Dear GO curators,

Could you please consider creating a new term:

[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] phosphatase activity child of GO:0004722

Catalysis of the reaction: Reaction=H2O + O-phospho-L-seryl-[3-methyl-2-oxobutanoate dehydrogenase] = L-seryl-[3-methyl-2-oxobutanoate dehydrogenase] + phosphate [Rhea:77247] Evidence: PubMed=17336929; PubMed=22589535; PubMed=19411760 https://enzyme.expasy.org/EC/3.1.3.52

Rhea:77247 is approved but not public yet.

The new term can be used to annotate PPM1K https://www.uniprot.org/uniprotkb/Q8N3J5/entry and orthologues. PPM1K forms a functional kinase and phosphatase pair with BCKDK https://enzyme.expasy.org/EC/2.7.11.4; GO:0047323

Many thanks for your help, Nevila Hyka-Nouspikel

pgaudet commented 1 year ago

Hi @nnouspikel

We do not create terms for specific substrates for protein kinases and protein phosphatases. For GO this corresponds to https://www.rhea-db.org/rhea/20629

I thought this was also the scope of RHEA (ie chemically, it is the same reaction); but it seems this is no longer the case?

Thanks, Pascale

deustp01 commented 1 year ago

I thought this was also the scope of RHEA

Is the fact that the substrate is a specific protein (rather than a hydroxyl group of a specific amino acid residue of a generic protein) an issue for RHEA? @kaxelsen ?

kaxelsen commented 1 year ago

Rhea creates reactions for specific proteins as little as possible. One case were we do create such reactinos is when there is an EC number linked to the reaction because IUBMB does create reactions for specific proteins. In the specific case of protein kinases it is the only way to make nonidentical reactions for different kinases.