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carboxylic ester hydrolase activity (GO:0052689) / EC:3.1.1.- & EC:3.1.1.1 xrefs #21843

Closed sjm41 closed 2 years ago

sjm41 commented 3 years ago

@balhoff @hdrabkin

Looks like the EC xref on carboxylic ester hydrolase activity (GO:0052689) recently got changed from EC:3.1.1.- to EC:3.1.1.1 (maybe as part of #21287 ?).

https://enzyme.expasy.org/EC/3.1.1.- is the grouping term for "Carboxylic ester hydrolases" whereas https://enzyme.expasy.org/EC/3.1.1.1 is the specific term for "Carboxylesterase" (def:A carboxylic ester + H(2)O <=> an alcohol + a carboxylate) - which maps to RHEA:21164.

I'm not entirely sure of the practical difference between EC:3.1.1.- and EC:3.1.1.1, but since GO:0052689 is the equivalent grouping term to EC:3.1.1.-, it seems it should have the EC:3.1.1.- xref??

sjm41 commented 3 years ago

Looks like these other terms with xrefs to EC:3.1.1.1 or EC:3.1.1.- may also need reviewing?: .... most of these are misuse of the xref. in each case I guess the term is a child of the xref. In most cases this is not needed for these terms. I will remove.

sjm41 commented 3 years ago

@kaxelsen Can we also get your take on this one? Thanks.

kaxelsen commented 3 years ago

EC 3.1.1 is the sub-subclass of "Carboxylic ester hydrolases" that covers all the specific enzymes described in EC 3.1.1.1-3.1.1.117. EC 3.1.1.1 only covers the specific enzyme carboxylesterase (in this case an enzyme with a very broad substrate specificity). So if GO:0052689 is a 'grouping term', I would link it to EC 3.1.1.-.

Regarding the list: id: GO:0080030: I would use EC 3.1.1.-. As a note I can add that there is no reaction in Rhea that corresponds MetaCyc:RXN-10711, All the other GO terms use EC 3.1.1.- correctly except for GO:0052768 that belongs to EC 3.2.1.-

sjm41 commented 3 years ago

Thanks @kaxelsen

Good that we agree that the xref on GO:0052689 should be reverted to EC:3.1.1.-.

Wrt the list in my second comment, my understanding is that the GO should only have 'grouping type' EC numbers as xrefs on 'grouping type' GO terms (so EC:3.1.1.- on GO:0052689 is correct). If there's a more specific GO child term that lacks an equivalent EC number, then that GO term should have no EC xref rather than having the grouping EC xref. That's right, isn't it @hdrabkin ?

hdrabkin commented 3 years ago

The 3 digit ECs should only be used for the GO terms that correspond to that EC. We have many records still left from the plant /metacyc requests where they were uploaded in bulk before seeing that the EC was uses as a def ref.

As for this example (which did not come from the above project)

xref: id: GO:0052767 name: mannosyl-oligosaccharide 1,6-alpha-mannosidase activity def: "Catalysis of the hydrolysis of the alpha-(1->6) bonds of alpha-D-mannose residues in mannosyl-oligosaccharide." [GOC:mengo_curators, PMID:1849817, PMID:2338081] xref: EC:3.1.1.- <<<<<< no; this is an enzyme class ( Hydrolases Acting on ester bonds. Carboxylic ester hydrolases. ) and the GO term for that could be used as a parent (GO:0052767 is a type of EC:3.1.1.- I can't seem to find EC:3.1.1.- as a grouping term in GO at the moment.

sjm41 commented 3 years ago

I can't seem to find EC:3.1.1.- as a grouping term in GO at the moment.

Right, EC:3.1.1.- used to be the xref on carboxylic ester hydrolase activity (GO:0052689), but it recently got changed from EC:3.1.1.- to EC:3.1.1.1 The change should be reverted!

hdrabkin commented 3 years ago

Ah, this seems to be a problem with nomenclature? EC:3.1.1.1 refers specifically to the enzyme ' carboxylesterase'.
In this case, the actual enzyme has a 'specificity' as broad as it's parent 3.1.1.- If the term is used in annotations, it may be referring specifically to that enzyme There are 1080 exp annotations to GO:0052689, and looking quickly, yes they catalyze the hydrolysis of a carboxyl-ester.

sjm41 commented 3 years ago

Ah, so you're saying that while the EC differentiates between the EC:3.1.1.- grouping class and the the specific EC:3.1.1.1 enzyme, the GO just has GO:0052689 - which is used as BOTH a grouping term and to annotate specific activities (1080 exp annotations).

OK, I see the issue better now.

Given that GO:0052689 is used as BOTH a grouping term and a specific activity term, should it have both EC:3.1.1.- and EC:3.1.1.1 as xrefs?

hdrabkin commented 3 years ago

OR, a new grouping term to correspond to EC:3.1.1.- which would be a parent of GO:0052689 ; The grouping term should have a specific 'do not annotate' flay, the GO:0052689 would get a comment of some sort to indicate that it should be used specifically to annotate a enzyme with very broad specificity. RHEA:21164 is also very genetic too. really ANY kind of carboxylic ester ; RHEA has 130 reactions using EC:3.1.1.n (note, not -) including EC:3.1.1.1 I'm more inclined to make a separate grouping term (that does not get a rhea).

sjm41 commented 3 years ago

I'm more inclined to make a separate grouping term (that does not get a rhea). That works for me! If you did that, I guess all current children of GO:0052689 would get moved to be children of the new grouping term?

hdrabkin commented 3 years ago

There's a lot of them!

kaxelsen commented 3 years ago

Regarding: _id: GO:0080030 name: methyl indole-3-acetate esterase activity def: "Catalysis of the reaction: methyl indole-3-acetate + H2O = indole-3-acetate + methanol + H+." [MetaCyc:RXN-10711, PMID:18467465] xref: EC:3.1.1.1 xref: MetaCyc:RXN-10711 isa: GO:0052689 ! carboxylic ester hydrolase activity

I have now created RHEA:32919, PMID:18467465 H2O + methyl (indol-3-yl)acetate => (indol-3-yl)acetate + H+ + methanol

Based on the same paper, I have also created RHEA:33611, PMID:18467465, 15668381 H2O + methyl salicylate = H+ + methanol + salicylate

and RHEA:55372, PMID:18467465, 26934101 H2O + methyl (−)-jasmonate = H+ + jasmonate + methanol

They will become public with release 2021_05 scheduled for November 24

alanbridge commented 3 years ago

Hi Kristian, noticed a typo in first ID, should be RHEA:32919. All the best, Alan

kaxelsen commented 3 years ago

Thank you very much, it has been corrected!

hdrabkin commented 2 years ago

the EC: def for 3.1.1.1 is 'a carboxylic ester + H2O <=> a carboxylate + an alcohol + H(+)" which pretty much sounds like a grouping term. EC: 3.1.1.- is 'Catalysis of the hydrolysis of a carboxylic ester bond, or 'Hydrolases Acting on ester bonds and Carboxylic ester hydrolases I wonder if what is needed is to make a new term as a chld of GO:0052689 for EC:3.1.1.1 and tighten up the definition somehow. However, the EC comment about 'Wide specificity; also hydrolyzes vitamin A esters. The enzymes from microsomes also catalyze the reactions of EC 3.1.1.2, EC 3.1.1.5, EC 3.1.1.6, EC 3.1.1.23, EC 3.1.1.28, EC 3.1.2.2, EC 3.5.1.4 and EC 3.5.1.13.' really muddies up the hope of fixing the def.

BUT If I made a new grouping term for ec 3.1.1.-, I could remove 3.1.1.- from GO:0052689 , and make it a direct child of the new grouping term (keeping it's current def) and everything that was under GO:0052689 would become sibs of GO:0052689 .

hdrabkin commented 2 years ago

After editors discussion, I will make new term for 3.1.1.1, and remove 3.1.1.1 and RHEA from GO:0052689 ; transfer the synonyms where we are sure; remove other synonyms from GO:0052689 . Then look at annotations to GO:0052689 to see which ones can be transferred to the new term (annotation ticket?).

hdrabkin commented 2 years ago

NTR id: GO:0106435 name: carboxylesterase activity def: Catalysis of the reaction: a carboxylic ester + H2O = a carboxylate + an alcohol + H(+). is_a: GO:0052689

Clean up: should goslim annotation to GO:0052689 be transferred to new term? (@sjm4) Disposition of all REACTOME xefs in GO:0052689 (@deustp01

sjm41 commented 2 years ago

Hi @hdrabkin Thanks for returning to this issue. The fix looks good to me.

Clean up: should goslim annotation to GO:0052689 be transferred to new term? (@SJM4) Not sure... But my feeling is it would be safer (and still accurate) to keep it on the parent term.

hdrabkin commented 2 years ago

Finished