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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Remove obsolete EC:1.11.1.15 from peroxiredoxin activity (GO:0051920 name) def #22598

Closed sjm41 closed 2 years ago

sjm41 commented 2 years ago

Please remove the obsolete EC:1.11.1.15 (or replace it with EC:1.11.1.24) in the attribution of the def on this term:

id: GO:0051920 name: peroxiredoxin activity def: "Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH." [EC:1.11.1.15, RHEA:10008] comment: Includes redox chemistry as part of the catalytic reaction (2 R'-SH = R'-S-S-R'), where R' refers to peroxiredoxin itself). Not to be confused with GO:0004601 (peroxidase activity, EC:1.11.1.7), which has a different reaction mechanism. xref: EC:1.11.1.24 xref: RHEA:10008

See https://enzyme.expasy.org/EC/1.11.1.15

sjm41 commented 2 years ago

Hi @pgaudet Can you do this quick one? Just need to remove EC:1.11.1.15 as a ref in the definition line.

pgaudet commented 2 years ago

It seems the entire branch represents the same activity?

'peroxiredoxin activity' -> and children: 'peroxynitrite reductase activity' -> 2 ISO, original evidence missing 'thioredoxin peroxidase activity' -> 44EXP 'tryparedoxin peroxidase activity' -> 1 EXP to a paper characterizing a 'peroxiredoxin'

I think they all catalyze the same reaction?

see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509974/

sjm41 commented 2 years ago

Are you considering merging those 3 children into the parent?

'thioredoxin peroxidase activity' at least has a specific RHEA xref (RHEA:63528), which is different to the RHEA xref on the parent term 'peroxiredoxin activity' (RHEA:10008), so there must be some difference there.

There are some other issues associated with this term, documented in https://github.com/geneontology/go-ontology/issues/23121

Main point here though was just to get rid of the obsolete EC number in the GO:0051920 definition.... :-)

pgaudet commented 2 years ago

yeah sorry I cant' help but to look at the branch...

pgaudet commented 2 years ago

Thanks, Pascale

sjm41 commented 2 years ago

Thanks Pascale.

But I don't think EC:1.11.1.24 should be an xref to thioredoxin peroxidase activity (GO:0008379) - that GO term has xref of RHEA:63528 (which has no EC association), whereas RHEA:62620 has the EC:1.11.1.24 xref.

RHEA:63528: [thioredoxin]-dithiol + a H2O2 = [thioredoxin]-disulfide + 2 H20

RHEA:62620 (EC:1.11.1.24): [thioredoxin]-dithiol + a hydro peroxide = [thioredoxin]-disulfide + an alcohol + H20

This also means EC:1.11.1.24 should also be removed from the general term peroxiredoxin activity (GO:0051920).

I think we need to add a new GO term for RHEA:62620/EC:1.11.1.24 (if we want it)

pgaudet commented 2 years ago

But I don't think EC:1.11.1.24 should be an xref to thioredoxin peroxidase activity (GO:0008379) -

I wondered about that, but EC describes both thioredoxin peroxidase activity (GO:0008379) AND ~thioredoxin peroxidase activity (GO:0008379)~ peroxiredoxin activity (GO:0051920): while the label is 'Thioredoxin-dependent peroxiredoxin', the description is clearly general for peroxidins.

@kaxelsen how should we interpret the EC definition? just the reaction? I do usually take the comments into account.

Thanks, Pascale

kaxelsen commented 2 years ago

The transfer note at expasy is unfortunately not completely covering the IUBMB information. This is because the curator tool I have been until now could only handle one-to-one transfers of EC numbers. At IUBMB the transfer note reads:

https://www.enzyme-database.org/query.php?ec=1.11.1.15 peroxiredoxin. Now described by EC 1.11.1.24, thioredoxin-dependent peroxiredoxin; EC 1.11.1.25, glutaredoxin-dependent peroxiredoxin; EC 1.11.1.26, NADH-dependent peroxiredoxin; EC 1.11.1.27, glutathione-dependent peroxiredoxin; EC 1.11.1.28, lipoyl-dependent peroxiredoxin; and EC 1.11.1.29, mycoredoxin-dependent peroxiredoxin.

So, there are actually 6 different types of peroxiredoxins, each with their own EC number and each using a different oxidant.

EC 1.11.1.24; RHEA:62620 [thioredoxin]-dithiol + a hydroperoxide = [thioredoxin]-disulfide + an alcohol + H2O EC 1.11.1.25; RHEA:62624 [glutaredoxin]-dithiol + a hydroperoxide = [glutaredoxin]-disulfide + an alcohol + H2O EC 1.11.1.26; RHEA:62628 a hydroperoxide + H+ + NADH = an alcohol + H2O + NAD+ EC 1.11.1.27; RHEA:62632 a hydroperoxide + 2 glutathione = an alcohol + glutathione disulfide + H2O EC 1.11.1.28; RHEA:62636 (R)-N6-dihydrolipoyl-L-lysyl-[lipoyl-carrier protein] + a hydroperoxide = (R)-N6-lipoyl-L-lysyl-[lipoyl-carrier protein] + an alcohol + H2O EC 1.11.1.29; RHEA:62640 [mycoredoxin]-L-dithiol + a hydroperoxide = [mycoredoxin]-L-disulfide + an alcohol + H2O

pgaudet commented 2 years ago

Thanks for your input @kaxelsen this is very useful!

@sjm41 I removed EC:1.11.1.24 from GO:0008379 thioredoxin peroxidase activity

I'm not sure what to do about the other reactions - should we wait to create them until there is a request?

Also, GO has 2 other siblings,

I dont how how/whether these relate to the list from @kaxelsen above. Looks like they dont and probably could be obsoleted?

sjm41 commented 2 years ago

@pgaudet I commented on those sibling cases in #23121 - both should be moved to being children of "peroxidase activity" rather than "peroxiredoxin activity" IMO.

Yes, I wouldn't bother adding the other reactions Kristian mentions until there's a request for them.

Shall we close this ticket, and try to finish off the remaining edits in #23121?

pgaudet commented 2 years ago

yes! thanks