GO terms with xref: EC:1.11.1 (peroxidases)

[sjm41]

EC:1.11.1 is the grouping ID for 'peroxidases': https://enzyme.expasy.org/EC/1.11.1.-

Three terms to review in the GO:

id: GO:0019806 name: bromide peroxidase activity namespace: molecular_function def: "Catalysis of the reaction: 2 R-H + 2 bromide + hydrogen peroxide = 2 R-Br + 2 H2O. Enzymes with this activity often accept other halide ions as substrates, including chloride and iodide." [EC:1.11.1.10] synonym: "bromoperoxidase activity" EXACT [] xref: EC:1.11.1

=> this EC should be replaced with EC 1.11.1.18 (https://enzyme.expasy.org/EC/1.11.1.18)

id: GO:0008379 name: thioredoxin peroxidase activity namespace: molecular_function alt_id: GO:0009031 def: "Catalysis of the reaction: thioredoxin + hydrogen peroxide = thioredoxin disulfide + H2O." [MetaCyc:RXN0-267] synonym: "thiol peroxidase activity" EXACT [] synonym: "TPx activity" EXACT [] synonym: "TrxPx activity" EXACT [] xref: EC:1.11.1

=> this one should probably be removed (I can't easily see a specific EC to replace it)

id: GO:0004601 name: peroxidase activity namespace: molecular_function alt_id: GO:0016685 alt_id: GO:0016686 alt_id: GO:0016687 alt_id: GO:0016693 def: "Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O." [EC:1.11.1.7, RHEA:56136] subset: goslim_metagenomics synonym: "bacterial catalase-peroxidase activity" NARROW [] synonym: "donor:hydrogen-peroxide oxidoreductase activity" EXACT [EC:1.11.1.7] synonym: "eosinophil peroxidase activity" NARROW [] synonym: "extensin peroxidase" NARROW [EC:1.11.1.7] synonym: "guaiacol peroxidase" NARROW [EC:1.11.1.7] synonym: "heme peroxidase" NARROW [EC:1.11.1.7] synonym: "horseradish peroxidase (HRP)" NARROW [EC:1.11.1.7] synonym: "japanese radish peroxidase" NARROW [EC:1.11.1.7] synonym: "lactoperoxidase activity" NARROW [] synonym: "MPO" RELATED [EC:1.11.1.7] synonym: "myeloperoxidase activity" NARROW [] synonym: "oxyperoxidase activity" EXACT [EC:1.11.1.7] synonym: "peroxidase reaction" EXACT [] synonym: "protoheme peroxidase" NARROW [EC:1.11.1.7] synonym: "pyrocatechol peroxidase" NARROW [EC:1.11.1.7] synonym: "scopoletin peroxidase" NARROW [EC:1.11.1.7] synonym: "secretory plant peroxidase activity" NARROW [] synonym: "thiocyanate peroxidase" NARROW [EC:1.11.1.7] synonym: "verdoperoxidase" NARROW [EC:1.11.1.7] xref: EC:1.11.1.7

=> this one has EC:1.11.1.7 as an xref, but it's the parent term for various other peroxidase terms in the GO, so I wonder whether EC:1.11.1 is more appropriate?

It's a bit odd because EC:1.11.1.7 is called 'peroxidase' in the EC, with this definition: 2 phenolic donor + H(2)O(2) <=> 2 phenoxyl radical of the donor + 2 H(2)O https://enzyme.expasy.org/EC/1.11.1.7

Compare this to the GO def for "peroxidase activity" above: "Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O."

Maybe a new grouping term is required here to resolve this discrepancy? What do you think? (if so, I can make a new ticket.)

[pgaudet]

EC:1.11.1.7 doesn't have so many synonyms

https://enzyme.expasy.org/EC/1.11.1.7

Was this split at some point ?

[hdrabkin]

Perhaps whoever made the term at the time added the synonyms. It also looks like some of the synonyms are gene or gene product names (japanese radish peroxidase). I would /will remove the EC xref from anything that EC doesn't have. I

[pgaudet]

You can probably remove some of the gene product names as synonyms - I'm not sure those are very useful.

Thanks, Pascale

[hdrabkin]

We really don't know WHAT people search for when they search GO!

[pgaudet]

Still - those are more like annotations. We can not add all gene products that apply to a term as synonym. It's not scalable and messy - dont you think ?

[hdrabkin]

NOT suggested we do;

[sjm41]

But the key question here is whether GO:0004601 (peroxidase activity) is meant to correspond to: (i) EC:1.11.1 (the grouping term for peroxidases in EC), which is suggested by its GO definition and position in the GO hierarchy/children (ii) EC:1.11.1.7 (a specific term for 'peroxidase'/'Lactoperoxidase' in EC), which is suggested by its current xref and synonyms - though the GO def doesn't seem to quite match the EC def.

It looks like GO:0004601 is currently trying to be both (i) and (ii), and I'm not sure that's right?

[hdrabkin]

The EC 1.11.1.17 maps to this 2 phenolic donor + H(2)O(2) <=> 2 phenoxyl radical of the donor + 2 H(2)O The RHEA RHEA:56136 is this RHEA:56136 (APPROVED) 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O Glad to see they agree BUt, as you note,The GO def is catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O; So do ALL peroxidases use a phenolic donor? My guess is no

@deustp01 can you lend me your thoughts

[ValWood]

These synonyms will probably be useful for searching for activities because historically they were used as proxies for specific activities. I think we should follow Rhea/Brenda here and include if they do.

[hdrabkin]

yes @ValWood , I just won't attribute them to that EC number; RHEA does not do synonyms. And EC does not do them either; they to 'alternative names' and do not make assumptions about exact/related/ etc. That is a GO thing.

[hdrabkin]

Requesting RHEA for EC:1.11.1.18; removed partial ec Requesting RHEA for thioredoxin peroxidase; removed partial ec.

[hdrabkin]

requested RHEA for EC:1.11.10 and EC:1.11.18, Chloride and Bromide respectively. RHEA ticket 183260

[hdrabkin]

Requested RHEA for GO:0008379, Rhea ticket 183264

[pgaudet]

Ready ?

[hdrabkin]

Rhea for EC:1.11.1.18 is not available.

GO:0008379, based on Metacyc xref should be EC:1.11.1.15 but no RHEA yet Tracking 183264 now.

[hdrabkin]

Found: put in wrong folder RHEA:63528 for GO:0008379 [thioredoxin]-dithiol + H2O2 = [thioredoxin]-disulfide + 2 H2O RHEA:63528 will be publicly available mid-June. FYI, according to table I of PMID:11087748, I'm going to create 2 additional reactions, one for ter-butyl hydroperoxide (CHEBI:64090) and one for cumene hydroperoxide (CHEBI:78673)

[hdrabkin]

added RHEA

[hdrabkin]

Removed EC:1.11.1.17 and RHEA to grouping term GO:0004601; removed all EC:1.11.1.17 xrefs in synonyms, etc. to this term. It is a generic grouping term for all of the other peroxidases. Searching for where these requests ended up GO:0019806, EC:1.11.18 PMID:22842973 RH + HBr + H(2)O(2) <=> RBr + 2 H(2)O

This parallels EC:1.11.1.10, PMID:8344520 GO:0016691 RH + Cl(-) + H(2)O(2) <=> RCl + 2 H(2)O

[sjm41]

@hdrabkin Did you ever get the new RHEAs you requested above (back in 2020)? If they are not forthcoming, I suggest we close this ticket (my original request has been addressed).

[hdrabkin]

EC:1.11.1.18 still does not have a RHEA. So let's close this.

[harold]

@harold checking in here - good luck with your computational biology project! 😄