nucleoside monophosphate kinase activity terms

[sjm41]

Here's the current tree for these terms:

kinase activity
    |__nucleobase-containing compound kinase activity (GO:0019205) [no xref]
        |__nucleoside monophosphate kinase activity (GO:0050145) [EC:2.7.4.4, RHEA:24036]
            |__(d)CMP kinase activity (GO:0004127) [EC:2.7.4.25, EC:2.7.4.14 {source="skos:broadMatch"}]
                |__CMP kinase activity (GO:0036430) [RHEA:11600]
                |__dCMP kinase activity (GO:0036431) [RHEA:25094]
            |__adenylate kinase activity (GO:0004017) [EC:2.7.4.3, RHEA:12973]
            |__guanylate kinase activity (GO:0004385) [EC:2.7.4.8, RHEA:20780]
            |__thymidylate kinase activity (GO:0004798) [EC:2.7.4.9, RHEA:13517]
            |__UMP/dUMP kinase activity (GO:0009041) [no xref]
                |__dUMP kinase activity (GO:0120136) [RHEA:30655]
                |__UMP kinase activity (GO:0033862) [EC:2.7.4.22, RHEA:24400] [EC:2.7.4.14 {source="skos:broadMatch"}]
        |__(deoxy)nucleoside-phosphate kinase activity (GO:0047507) [EC:2.7.4.13, RHEA:11216]
    |__T2-induced deoxynucleotide kinase activity (GO:0050316) [EC:2.7.4.12, RHEA:12697]
    |__(deoxy)adenylate kinase activity (GO:0047506) [EC:2.7.4.11, RHEA:23100]

Several issues/tasks here:

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Def of nucleoside monophosphate kinase activity (GO:0050145) (""Catalysis of the reaction: ATP + nucleoside monophosphate = ADP + nucleoside diphosphate." [GOC:ai, ISBN:0198506732]") needs updating

• Update def to use RHEA:24036 def "a ribonucleoside 5'-phosphate + ATP = a ribonucleoside 5'-diphosphate + ADP"

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(d)CMP kinase activity (GO:0004127) def is "Catalysis of the reaction: ATP + (d)CMP = ADP + (d)CDP". This matches the EC:2.7.4.25 reaction, but it isn't compatible with def of parent "nucleoside monophosphate kinase activity (GO:0050145)", which doesn't include deoxynucleosides.

• Obsolete (d)CMP kinase activity (GO:0004127) - 12 EXP annotations => re-annotate to one/both current children
• make EC:2.7.4.25 and EC:2.7.4.14 a broadMatch xref on 'CMP kinase activity (GO:0036430)' and 'dCMP kinase activity (GO:0036431)'
• make 'CMP kinase activity (GO:0036430)' a direct child of 'nucleoside monophosphate kinase activity (GO:0050145)'
• make 'dCMP kinase activity (GO:0036431)' a direct child of '(deoxy)nucleoside-phosphate kinase activity (GO:0047507)'

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Current def and name of thymidylate kinase activity (GO:0004798) ("Catalysis of the reaction: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate." [EC:2.7.4.9]) is wrong

• Update def to use current EC/RHEA def: "dTMP + ATP = dTDP + ADP"
• Update name to 'dTMP kinase activity'
• change parent to '(deoxy)nucleoside-phosphate kinase activity (GO:0047507)'

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UMP/dUMP kinase activity (GO:0009041) def is "Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP." [GOC:go_curators]"., but this isn't compatible with def of parent "nucleoside monophosphate kinase activity (GO:0050145)", which doesn't include deoxynucleosides.

• Obsolete UMP/dUMP kinase activity (GO:0009041) - 13 EXP annotations => re-annotate to one/both current children
• make 'UMP kinase activity (GO:0033862)' a direct child of 'nucleoside monophosphate kinase activity (GO:0050145)'
• make 'dUMP kinase activity (GO:0120136)' a direct child of '(deoxy)nucleoside-phosphate kinase activity (GO:0047507)'

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• 'T2-induced deoxynucleotide kinase activity (GO:0050316)' has def "Catalysis of the reactions: ATP + dGMP = ADP + dGDP, and ATP + dTMP = ADP + dTDP." [EC:2.7.4.12]", but is xreffed to RHEA:12697, which is only "dGMP + ATP = dGDP + ADP". (GO:0050316 has been used in 1 annotation, and IEA based on RHEA:12697)
• Change def to match RHEA:12697
• make EC:2.7.4.12 a broadMatch xref
• also add EC:2.7.4.12 as broadMatch xref to GO:0004798
• Change name to 'dGMP kinase activity'
• Change parent to (deoxy)nucleoside-phosphate kinase activity (GO:0047507)

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'(deoxy)adenylate kinase activity (GO:0047506)' has def of "ATP + dAMP = ADP + dADP.", which matches EC and RHEA xrefs

• change parent to '(deoxy)nucleoside-phosphate kinase activity (GO:0047507)'

---

• (deoxy)nucleoside-phosphate kinase activity (GO:0047507)' (def: ATP + deoxynucleoside phosphate = ADP + deoxynucleoside diphosphate) needs def updating to match RHEA and currently has no children
• Update def to 'a 2'-deoxyribonucleoside 5'-phosphate + ATP = a 2'-deoxyribonucleoside 5'-diphosphate + ADP'
• Changes above will add required child terms.
• Remove parentheses from '(deoxy)' in term name becauase this suggests the deoxy is optional, which is not the intention
• add 'ATP as phosphate donor' to end of term name, because there are three sister terms named "(deoxy)nucleoside phosphate kinase activity, dTTP as phosphate donor (GO:0106368)', 'deoxy)nucleoside phosphate kinase activity, dGTP as phosphate donor (GO:0106367)', and '(deoxy)nucleoside phosphate kinase activity, GTP as phosphate donor (GO:0106369)'.

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After these changes, the tree will look something like this:

kinase activity
    |__nucleobase-containing compound kinase activity (GO:0019205) [no xref]
        |__nucleoside monophosphate kinase activity (GO:0050145) [EC:2.7.4.4, RHEA:24036]
            |__CMP kinase activity (GO:0036430) [RHEA:11600] [EC:2.7.4.25, EC:2.7.4.14 {source="skos:broadMatch"}]
            |__adenylate kinase activity (GO:0004017) [EC:2.7.4.3, RHEA:12973]
            |__guanylate kinase activity (GO:0004385) [EC:2.7.4.8, RHEA:20780]
            |__UMP kinase activity (GO:0033862) [EC:2.7.4.22, RHEA:24400] EC:2.7.4.14, source="skos:broadMatch"}]
        |__deoxynucleoside-phosphate kinase activity, ATP as phosphate donor (GO:0047507) [EC:2.7.4.13, RHEA:11216]
            |__(deoxy)adenylate kinase activity (GO:0047506) [EC:2.7.4.11, RHEA:23100]
            |__dCMP kinase activity (GO:0036431) [RHEA:25094] [EC:2.7.4.25, EC:2.7.4.14 {source="skos:broadMatch"}]
            |__dUMP kinase activity (GO:0120136) [RHEA:30655]
            |__dTMP kinase activity (GO:0004798) [EC:2.7.4.9, RHEA:13517] [EC:2.7.4.12  {source="skos:broadMatch"}]
            |__dGMP kinase activity (GO:0050316) [RHEA:12697] [EC:2.7.4.12  {source="skos:broadMatch"}]

This reorganization will also then mirror how RHEA organizes the corresponding entries:

RHEA:24036 a ribonucleoside 5'-phosphate + ATP = a ribonucleoside 5'-diphosphate + ADP
    |_ RHEA:24400 UMP + ATP = UDP + ADP
    |_ RHEA:20780 GMP + ATP = GDP + ADP
    |_ RHEA:12973 AMP + ATP = 2 ADP
    |_ RHEA:11600 CMP + ATP = CDP + ADP

RHEA:11216 a 2'-deoxyribonucleoside 5'-phosphate + ATP = a 2'-deoxyribonucleoside 5'-diphosphate + ADP
    |_ RHEA:30655 dUMP + ATP = dUDP + ADP
    |_ RHEA:25094 dCMP + ATP = dCDP + ADP
    |_ RHEA:23100 dAMP + ATP = dADP + ADP
    |_ RHEA:13517 dTMP + ATP = dTDP + ADP
    |_ RHEA:12697 dGMP + ATP = dGDP + ADP

[sjm41]

I've made all the changes above except for the two proposed obsoletions (and dealing with the associations annotations):

• Obsolete (d)CMP kinase activity (GO:0004127) - 12 EXP annotations => re-annotate to one/both current children
• Obsolete UMP/dUMP kinase activity (GO:0009041) - 13 EXP annotations => re-annotate to one/both current children
  @pgaudet Would be good to check these two proposals with you when you're back.

For now, these terms (which are effectively orthogonal grouping terms) are retained, though I've changed their parent term to 'nucleobase-containing compound kinase activity' to make their parentage correct.