IEA with 2.7.11.13 calcium dependent/independent protein kinase C

[ValWood]

P36582 GO:0004698 | calcium-dependent protein kinase C activity | IEA with 2.7.11.13

P36582 is

GO:0004699 | calcium-independent protein kinase C activity

not sure who to assign to?

[pgaudet]

We have 3 terms mapped to EC:2.7.11.13:

'calcium-dependent protein kinase C activity' http://purl.obolibrary.org/obo/GO_0004698 'calcium-independent protein kinase C activity' http://purl.obolibrary.org/obo/GO_0004699 'protein kinase C activity' http://purl.obolibrary.org/obo/GO_0004697

While it seems desirable to align GO with external resources, I dont know if we want to merge all those terms together ?

Interestingly P36582 has 2 only EC2GO mappings:

UniProtKB:P36582	pck1	enables	GO:0004698 calcium-dependent protein kinase C activity	ECO:0000501 IEA	GO_REF:0000003	EC:2.7.11.13	284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843)	UniProt
UniProtKB:P36582	pck1	enables	GO:0004697 protein kinase C activity	ECO:0000501 IEA	GO_REF:0000003	EC:2.7.11.13	284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843)	UniProt

The solution may be different types of xrefs, and not map 'BROAD' xrefs; however how can we do this without loosing all mappings ?

Thanks, Pascale

[ValWood]

I think it's OK but UniProt need to remove 2.7.11.13 from P36582 Assign to @sylvainpoux ?

[sylvainpoux]

Hi Val, we can modify the entry to remove the complete EC

Could you indicate which paper shows that pkc1 is calcium-independent? We could curate it

Thanks

Sylvain

[pgaudet]

2.7.11.13 is OK for this entry tough.

I think what would be OK would be to keep the mapping in the parent GO:0004697 protein kinase C activity and maybe consider merging

• GO:0004698 calcium-dependent protein kinase C activity - 10 EXP
• GO:0004699 calcium-independent protein kinase C activity - 3 EXP

That would also take care of the EC mapping.

[pgaudet]

The specific protein kinases activities represented in EC (and pretty much mirrored in GO) are anyway a strange sample:

https://enzyme.expasy.org/EC/2.7.11.-

[ValWood]

From this paper https://www.pombase.org/reference/PMID:8463273 based on assay and homology to mammalian calcium-independent PKC's

[ValWood]

It's old though.....maybe this is overturned and Ca is required physiologically?

[sylvainpoux]

Hi Val,

honestly, I am not really convinced by this paper.

An option might be to leave the electronic annotation from 2.7.11.13 as it is and supply this annotation with experimental evidence with a NOT qualifier. I think it would be more relevant to say that it is predicted to be Calcium-dependent but that a previous paper showed that it is not the case.

Thanks

Sylvain

[pgaudet]

@sylvainpoux Do you agree that I merge

• GO:0004698 calcium-dependent protein kinase C activity - 10 EXP
• GO:0004699 calcium-independent protein kinase C activity - 3 EXP

into GO:0004697 protein kinase C activity ? That would make the mapping correct. (Or I can remove the mapping to the specific children).

[sylvainpoux]

Hi Pascale,

I think it is something to discuss with Kristian (@kaxelsen) as it affects some EC to GO mapping

Thanks

Sylvain

[ValWood]

OK, I agree, when I looked again. I had assumed that it was an accepted piece of information and a subset of pkc's were calcium independent. I don't think it does any harm to have both annotation in this case. Unless the decision is not to have this specificity. I'm OK either way.

[kaxelsen]

I am not an expert on protein kinases. In the comment of the EC 2.7.11.13 entry (https://enzyme.expasy.org/EC/2.7.11.13) it reads: "They can be activated by calcium but have a requirement for the second messenger diacylglycerol." I understand that as saying that some are calcium-dependent others not.

[pgaudet]

@vanaukenk @ukemi From a GO-CAM perspective, are those 2 terms useful ? Or is the calcium-dependency expected to be be captured differently ?

[ValWood]

closing since calcium-independent protein kinase C activity is now diacylglycerol-dependent, calcium-independent serine/threonine kinase activity