NTR: mRNA 5'-phosphatase activity

[sjm41]

Please provide as much information as you can:

• Suggested term label: mRNA 5'-phosphatase activity

• Definition (free text) A 5'-triphospho-[mRNA] + H(2)O <=> a 5'-diphospho-[mRNA] + H+ + phosphate

• Reference, in format PMID:####### PMID: 9473487

• Gene product name and ID to be annotated to this term human RNGTT (O60942) fly mRNA-cap (FBgn0030556/Q9VY44)

• Parent term(s) polynucleotide 5'-phosphatase activity (GO:0004651)

• Synonyms (please specify, EXACT, BROAD, NARROW or RELATED) 5'-polynucleotidase.[BROAD] Polynucleotide 5'-triphosphatase.[BROAD] mRNA capping enzyme [EXACT]

• Cross-references EC 3.6.1.74 RHEA:67004

[pgaudet]

+[Term] +id: GO:0140818 +name: mRNA 5'-phosphatase activity +namespace: molecular_function +def: "A 5'-end triphospho-[mRNA] + H(2)O = a 5'-end diphospho-[mRNA] + H+ + phosphate." [PMID:9473487] +synonym: "mRNA 5'-triphosphate monophosphatase activity" EXACT [] +xref: EC:3.6.1.74 +xref: RHEA:67004 +is_a: GO:0004651 ! polynucleotide 5'-phosphatase activity +is_a: GO:0140098 ! catalytic activity, acting on RNA +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23319 xsd:anyURI +created_by: pg +creation_date: 2022-05-16T06:01:07Z

[sjm41]

Thanks.

[sjm41]

Sorry @pgaudet , but it looks like I got the parent wrong for this one....

According to EC classification, the parent of the new term mRNA 5'-phosphatase activity (= EC:3.6.1.74) should be GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" (= EC:3.6.1.-)

So can you change is_a: GO:0004651 ! polynucleotide 5'-phosphatase activity to is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides

[pgaudet]

Good catch!

I suggest we obsolete the grouping class 'GO:0098518 polynucleotide phosphatase activity' (no EC, no annotations), because it's confusing not to have mRNA 5'-phosphatase activity under there.

What do you think ?

Thanks, Pascale

[pgaudet]

Dear all,

The proposal has been made to obsolete GO:0098518 polynucleotide phosphatase activity'. The reason for obsoletion is that this represents an unnecessary grouping class. There are no annotations to this term. This term is not present in any subset.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/23319

Thanks, Pascale

[sjm41]

@pgaudet Given this change, I suppose we ought to add a third parent term to GO:0140818 mRNA 5'-phosphatase activity: is_a: GO:0016791 ! phosphatase activity

?

[pgaudet]

Phosphatase activity has xref 3.1.3.- so that would be inconsistent with GO:0140818's classification as a 3.6.-.-.

[sjm41]

Hmmm, interesting....

EC has lots of "phosphatases" under 3.6.1.- in addition to those under 3.1.3.- (as well as some under 3.1.7.-, 3.1.8.-, 3.7.1.-, 3.9.1.-)

See https://enzyme.expasy.org/EC/3.6.1.-

@kaxelsen Should EC:3.6.1.- enzymes be classified as "phosphatases" or not?

Currently we have: id: GO:0016791 name: phosphatase activity def: "Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate." [GOC:curators, GOC:pg] xref: EC:3.1.3.- (= Phosphoric monoester hydrolases)

id: GO:0016818 name: hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides def: "Catalysis of the hydrolysis of any acid anhydride which contains phosphorus." [GOC:jl] xref: EC:3.6.1.- (= Hydrolases, Acting on acid anhydrides, In phosphorus-containing anhydrides)

[kaxelsen]

The sub-subclass EC 3.6.1 covers hydrolases (EC 3) acting on acid anhydrides (EC 3.6) In phosphorus-containing anhydrides (EC 3.6.1).

So this sub-subclass covers di- and triphosphatases and acylphosphatases were the hydrolysis produces a carboxylate and a phosphate (see EC 3.6.1.7, RHEA:14965), so yes, they are phosphatases.

[pgaudet]

So is the problem that GO:0016791 phosphatase activity is linked to the wrong EC? Or phosphatases act by 2 mechanisms?

[sjm41]

OK, thanks.

From the hierarchy and definition, "GO:0016791 phosphatase activity" is meant to group the 3.1.3.- phosphatases only: I'll check the existing children to see if this is really the case and report back Maybe we want to tweak the term name to be more precise? Change from 'phosphatase activity' to 'phosphoric monoester phosphatase activity' or similar??

[pgaudet]

That probably makes sense - although it's an exact synonym but in this case it would help to be more precise.

Do we want a general 'phosphatases' grouping class?

[kaxelsen]

The difference is the chemical nature of the substrate. EC 3.1.3 enzymes produce a hydroxy group and a phosphate, EC 3.6.1 enzymes produce a carboxy or phosphate group and a phosphate.

[pgaudet]

The more general issues will be fixed in #23401