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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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6 terms with xref: EC:3.1.4 (merges/obsoletions?) #20117

Closed sjm41 closed 3 months ago

sjm41 commented 4 years ago

EC:3.1.4 is a grouping term for Phosphoric diester hydrolases https://enzyme.expasy.org/EC/3.1.4.-

But there are 6 GO terms with this xref (below) - first one is correct, second one needs changing, other four probably just need removing?

id: GO:0008081 name: phosphoric diester hydrolase activity xref: EC:3.1.4 => correct!

id: GO:0004115 name: 3',5'-cyclic-AMP phosphodiesterase activity xref: EC:3.1.4

id: GO:0004117 name: calmodulin-dependent cyclic-nucleotide phosphodiesterase activity xref: EC:3.1.4

id: GO:0004118 name: cGMP-stimulated cyclic-nucleotide phosphodiesterase activity xref: EC:3.1.4

id: GO:0004119 name: cGMP-inhibited cyclic-nucleotide phosphodiesterase activity xref: EC:3.1.4

id: GO:0004120 name: photoreceptor cyclic-nucleotide phosphodiesterase activity xref: EC:3.1.4

hdrabkin commented 4 years ago

id: GO:0004117 name: calmodulin-dependent cyclic-nucleotide phosphodiesterase activity

Activity is regulated by calmodulin. I suspect this should be obsoleted? @pgaudet what do you think?

hdrabkin commented 4 years ago

So looking at the last 4 I wonder if they should all be removed. and GO:0004120 seems to be a gene product? (ie, activity is enabled by a photoreceptor I removed 3 digit ec from them and put GOC: curators as ref for last one as temporary fix while we decide what to do with these 4

pgaudet commented 4 years ago

According to wikipedia this is just a general property of PDE: https://en.wikipedia.org/wiki/PDE1 I think you can merge into GO:0004112 | cyclic-nucleotide phosphodiesterase activity

Thanks, Pascale

pgaudet commented 4 years ago

GO:0004120 name: photoreceptor cyclic-nucleotide phosphodiesterase activity

-> no reference, no annotations; I would obsolete that one, it does sound like a substrate - see Q14028.

Thanks, Pascale

hdrabkin commented 4 years ago

@pgaudet what about the ' calmodulin-dependent cyclic-nucleotide phosphodiesterase activity'? I would think this term represents what we would put in a model now (calmodulin gp regulating gp activity of whatever is doing the activity?

pgaudet commented 4 years ago

@pgaudet what about the ' calmodulin-dependent cyclic-nucleotide phosphodiesterase activity'?

Se my comment above https://github.com/geneontology/go-ontology/issues/20117#issuecomment-707746250

I suggest a merge.

sjm41 commented 2 years ago

@pgaudet @hdrabkin Looks like there are some outstanding obsoletions/merges to do here?

sjm41 commented 3 months ago

@pgaudet I just reviewed this ticket: it was suggested previously that that 4 GO terms mentioned above should be obsoleted/merged - below is an update on each one.

id: GO:0004117 name: calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity namespace: molecular_function def: "Catalysis of the reactions: 3',5'-cyclic AMP + H2O = AMP + H+ and 3',5'-cyclic GMP + H2O = GMP + H+; this activity is activated by binding to calcium-bound calmodulin." [PMID:8557689, PMID:9419816] synonym: "calmodulin-activated cyclic-nucleotide dual specificity phosphodiesterase activity" RELATED [] synonym: "calmodulin-dependent cyclic-nucleotide phosphodiesterase activity" BROAD [] is_a: GO:0004115 ! 3',5'-cyclic-AMP phosphodiesterase activity is_a: GO:0047555 ! 3',5'-cyclic-GMP phosphodiesterase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22791" xsd:anyURI

=> this term was since discussed and updated in #22791 => it now has 8 EXP annotations, and should be retained

id: GO:0004118 name: cGMP-stimulated cyclic-nucleotide phosphodiesterase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is increased in the presence of cGMP." [GOC:mah] is_a: GO:0004114 ! 3',5'-cyclic-nucleotide phosphodiesterase activity

=> 6 EXP annotations to PDE2A, PDE11A and PDE10A, , but no reference/xref

id: GO:0047555 name: 3',5'-cyclic-GMP phosphodiesterase activity namespace: molecular_function alt_id: GO:0004116 def: "Catalysis of the reaction: 3',5'-cyclic GMP + H2O = GMP + H+." [RHEA:16957] synonym: "3',5' cyclic-GMP phosphodiesterase activity" EXACT [] synonym: "3',5'-cyclic-GMP 5'-nucleotidohydrolase activity" RELATED [EC:3.1.4.35] synonym: "cGMP phosphodiesterase activity" EXACT [] synonym: "cGMP-PDE" RELATED [EC:3.1.4.35] synonym: "cGMP-specific phosphodiesterase activity" EXACT [] synonym: "cyclic 3',5'-GMP phosphodiesterase activity" RELATED [EC:3.1.4.35] synonym: "cyclic GMP phosphodiesterase activity" EXACT [] synonym: "cyclic guanosine 3',5'-monophosphate phosphodiesterase activity" RELATED [EC:3.1.4.35] synonym: "cyclic guanosine 3',5'-phosphate phosphodiesterase activity" RELATED [EC:3.1.4.35] synonym: "guanosine cyclic 3',5'-phosphate phosphodiesterase activity" EXACT [] xref: EC:3.1.4.35 xref: MetaCyc:35-CYCLIC-GMP-PHOSPHODIESTERASE-RXN xref: RHEA:16957 is_a: GO:0004114 ! 3',5'-cyclic-nucleotide phosphodiesterase activity

id: GO:0004119 name: cGMP-inhibited cyclic-nucleotide phosphodiesterase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is decreased in the presence of cGMP." [GOC:mah] is_a: GO:0004114 ! 3',5'-cyclic-nucleotide phosphodiesterase activity

id: GO:0004120 name: photoreceptor cyclic-nucleotide phosphodiesterase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside cyclic phosphate + H2O = nucleoside phosphate. This reaction is the hydrolysis of bonds in a cyclic nucleotide." [GOC:curators] is_a: GO:0004114 ! 3',5'-cyclic-nucleotide phosphodiesterase activity

raymond91125 commented 3 months ago

Genes annotated with GO:0004118 or GO:0004119 appear to be cAMP and cGMP dual specificity according to UniProt. Thus they fit better with EC:3.1.4.17/RHEA:14653. Instead of merge into the sibling GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity, we may consider merging into the parent GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity

sjm41 commented 3 months ago

Genes annotated with GO:0004118 or GO:0004119 appear to be cAMP and cGMP dual specificity according to UniProt. Thus they fit better with EC:3.1.4.17/RHEA:14653. Instead of merge into the sibling GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity, we may consider merging into the parent GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity

Hi @raymond91125 Yes, that would also work. Thanks.

raymond91125 commented 3 months ago

@pgaudet I wonder if you can help clarify MF guideline concerning this case: cGMP-stimulated cyclic-nucleotide phosphodiesterase activity vs. cGMP-inhibited cyclic-nucleotide phosphodiesterase activity. If appears that these represent two types of PDE's (2 and 3) that carry out the same enzymatic reactions but that differ by their intrinsic regulation mechanisms (via distinct regulatory domains). I don't think EC or RHEA has separate classes for them. For GO, should we?

pgaudet commented 3 months ago

@raymond91125

@hattrill and I have reviewed this in the context of the signaling work. We agree these should be kept. I fixed the EC xrefs.

See useful review here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8880502/

Thanks, Pascale