Merge children of 'prenol kinase activity'?

[sjm41]

id: GO:0052671 name: geranylgeraniol kinase activity xref: EC:2.7.1.B19

The EC xref either needs to be removed or perhaps replaced with a partial EC:2.7.1.-

[sjm41]

Hmmm, just noticed in the change log that the partial EC:2.7.1 was deleted and the new EC:2.7.1.B19 was added very recently, on 2018-07-15. So I guess there was a reason for this change - but I don't see that new EC number at https://enzyme.expasy.org/

[sjm41]

@hdrabkin - this dead xref is still on GO:0052671. Its a grouping term in GO that seems to have no equivalent in the current EC. Can you just remove it and then we can close this ticket.

[pgaudet]

I removed the xref but I think the 3 terms should be merged:

• GO:0052671 geranylgeraniol kinase activity -> MetcCyc: https://biocyc.org/META/NEW-IMAGE?type=NIL&object=RXN-11629; no Rhea
• GO:0102243 ATP:geranylgeraniol phosphotransferase activity -> Rhea https://www.rhea-db.org/rhea/61660
• GO:0052672 CTP:geranylgeraniol kinase activity -> MetcCyc: https://biocyc.org/META/NEW-IMAGE?type=NIL&object=RXN-11629; same as GO:0052671; no Rhea

probably into 'GO:0052672 CTP:geranylgeraniol kinase activity '; see description in EC (https://enzyme.expasy.org/EC/2.7.1.216) and UniProt Q67ZM7 "Substrate preferrence is farnesol > geraniol > geranylgeraniol, but has no activity with farnesyl phosphate. Can use CTP > ATP > GTP = UTP as phosphoryl donor"

and maybe also

• GO:0052668 farnesol kinase activity: MetaCyc: https://biocyc.org/META/NEW-IMAGE?type=NIL&object=RXN-11625; EC:2.7.1.216; no Rhea
• GO:0052669 CTP:2-trans,-6-trans-farnesol kinase activity: Same MetaCyc: https://biocyc.org/META/NEW-IMAGE?type=NIL&object=RXN-11625; EC:2.7.1.216; Rhea:51680

It looks like the reaction is 'GO:0052669 CTP:2-trans,-6-trans-farnesol kinase activity, but that the enzyme can also act on geranylgeraniol and use other nucleotides.

What's our policy for those cases ? Are they not all the same activity?

Thanks, Pascale

[hdrabkin]

Note there are 4 rheas associated with EC:EC:2.7.1.216; They are mechanistically related but have diferent substrates/products

RHEA:51680 | (2E,6E)-farnesol + CTP = (2E,6E)-farnesyl phosphate + CDP + H+ RHEA:61656 | (2E,6E)-farnesol + ATP = (2E,6E)-farnesyl phosphate + ADP + H+ RHEA:61660 | ATP + geraniol = (2E)-geranyl phosphate + ADP + H+ and RHEA:61664 | (2E,6E,10E)-geranylgeraniol + ATP = (2E,6E,10E)-geranylgeranyl phosphate + ADP + H+ Different substrates. Note CTP vs ATP, and farnesol vs geranoil

[pgaudet]

@amorgat Any thoughts on that one? It looks like RHEA:51680 | (2E,6E)-farnesol + CTP = (2E,6E)-farnesyl phosphate + CDP + H+ is the only reaction meaningful biologically?

Thanks, Pascale

[sjm41]

@amorgat @pgaudet @hdrabkin Just reviewing this old ticket.... The original xref issue has been fixed (removed), but the question Pascale raised about merging the related entries still exists. Good news: looks like GO:0052669 has already been merged into GO:0052668, so there are now only four terms from the above to consider. Bad news: I think there are an additional three terms to consider (other children of 'prenol kinase activity'), so a total of seven to consider. All shown below - current thoughts?

id: GO:0052671 name: geranylgeraniol kinase activity def: "Catalysis of the reaction: geranylgeraniol + nucleoside triphosphate = all-trans-geranyl-geranyl monophosphate + nucleoside diphosphate." [GOC:kd, MetaCyc:RXN-11629] synonym: "geranylgeraniol phosphotransferase activity" EXACT [] is_a: GO:0052673 ! prenol kinase activity

id: GO:0102243 name: ATP:geranylgeraniol phosphotransferase activity def: "Catalysis of the reaction: (E,E)-geranylgeraniol + ATP = H+ + all-trans-geranyl-geranyl monophosphate + ADP." [GOC:pz, RHEA:61660] xref: EC:2.7.1.216 xref: MetaCyc:RXN-12325 xref: RHEA:61660 is_a: GO:0052671 ! geranylgeraniol kinase activity

id: GO:0052672 name: CTP:geranylgeraniol kinase activity def: "Catalysis of the reaction: geranylgeraniol + CTP = all-trans-geranyl-geranyl monophosphate + CDP." [MetaCyc:RXN-11629] synonym: "CTP:geranylgeraniol phosphotransferase activity" EXACT [] xref: EC:2.7.1.216 xref: MetaCyc:RXN-11629 is_a: GO:0052671 ! geranylgeraniol kinase activity

id: GO:0052668 name: CTP:farnesol kinase activity alt_id: GO:0052669 def: "Catalysis of the reaction: 2-trans,-6-trans-farnesol + CTP = 2-trans,-6-trans-farnesyl monophosphate + CDP + H+." [PMID:21395888, RHEA:51680] synonym: "CTP:2-trans,-6-trans-farnesol kinase activity" EXACT [] synonym: "CTP:2-trans,-6-trans-farnesol phosphotransferase activity" EXACT [] synonym: "farnesol kinase activity" RELATED [] synonym: "farnesol phosphotransferase activity" EXACT [] synonym: "trans,trans-farnesol kinase activity" NARROW [] xref: EC:2.7.1.216 xref: MetaCyc:RXN-11625 xref: RHEA:51680 is_a: GO:0052673 ! prenol kinase activity

id: GO:0102237 name: ATP:farnesol kinase activity def: "Catalysis of the reaction: 2-trans,-6-trans-farnesol + ATP = 2-trans,-6-trans-farnesyl monophosphate + ADP + H+." [GOC:pz, RHEA:61656] synonym: "ATP-dependent farnesol kinase activity" RELATED [] xref: MetaCyc:RXN-12304 xref: RHEA:61656 is_a: GO:0052673 ! prenol kinase activity

id: GO:0052670 name: geraniol kinase activity namespace: molecular_function def: "Catalysis of the reaction: geraniol + nucleoside triphosphate = geranyl monophosphate + nucleoside diphosphate." [GOC:kd] synonym: "geraniol phosphotransferase activity" EXACT [] is_a: GO:0052673 ! prenol kinase activity

id: GO:0102238 name: geraniol kinase activity (ATP-dependent) activity namespace: molecular_function def: "Catalysis of the reaction: geraniol + ATP = geranyl monophosphate + ADP + H+." [EC:2.7.1.-, GOC:pz] xref: MetaCyc:RXN-12307 is_a: GO:0052670 ! geraniol kinase activity