Updates for inositol phosphate kinase activity (GO:0051766) children (definition, X-refs, parent-children relationship)

rozaru commented 5 days ago

Suggestion for the update of inositol phosphate kinase activity tree:

Background: inositol phosphate kinase activity covers:

the phosphorylation of any of the 6 positions of the inositol phosphate ring (inositol phosphate = IP)
the addition of a phosphate to an already phosphorylated position (inositol pyrophosphate = PP-IP)

Issues:

in several cases the GO term name is broad while the definition is specific for a substrate
several ECs cover multiple reactions
to give a consistent name for the GO terms handling inositol pyrophosphates either as product or substrate is not straightforward
A few reaction (especially for PP-IP) are not in Rhea

Update covers:

consistency between chemical names in the definition
adding/removing Xrefs
correcting parent/children relationship

The changes below will keep the current depth (substrate level) for the GO terms.

Another solution would be to simplify the GO term definitions where only the position phosphorylated by the kinase is kept. For example: GO:0052725 inositol-1,3,4-trisphosphate 6-kinase activity GO:0000823 inositol-1,4,5-trisphosphate 6-kinase activity would become 1 GO term: GO:xxxxxxx inositol trisphosphate 6-kinase activity Def:Catalysis of the reaction: 1D-myo-inositol trisphosphate + ATP = 1D-myo-inositol tetrakisphosphate (containing 6-phosphate) + ADP + H+.

The suggested changes to make are in bold (the current depth :

GO:0051766 inositol trisphosphate kinase activity |GO:0052726 inositol-1,3,4-trisphosphate 5-kinase activity (to update) [10 EXP annotations] |GO:0052725 inositol-1,3,4-trisphosphate 6-kinase activity (to update) [1 EXP annotations] |GO:0008440 inositol-1,4,5-trisphosphate 3-kinase activity (to update) [17 EXP annotations] |GO:0000823 inositol-1,4,5-trisphosphate 6-kinase activity (to update) [9 EXP annotations] |__GO:0052835 inositol-3,4,6-trisphosphate 1-kinase activity [4 EXP annotations]

id: GO:0052726 name: inositol-1,3,4-trisphosphate 5-kinase activity xref: EC:2.7.1.159 BROAD xref: KEGG_REACTION:R03428 EXACT xref: MetaCyc:2.7.1.139-RXN EXACT xref: RHEA:13253 EXACT

id: GO:0052725 name: inositol-1,3,4-trisphosphate 6-kinase activity xref: EC:2.7.1.159 BROAD xref: KEGG_REACTION:R03429 EXACT xref: MetaCyc:2.7.1.133-RXN EXACT xref: RHEA:20940 EXACT

id: GO:0008440 name: inositol-1,4,5-trisphosphate 3-kinase activity xref: EC:2.7.1.127 EXACT xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R03433 EXACT xref: MetaCyc:2.7.1.127-RXN EXACT xref: RHEA:11020 EXACT

Notes: EC 2.7.1.151 has a broad specificity

id: GO:0000823 name: inositol-1,4,5-trisphosphate 6-kinase activity xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R05800 EXACT xref: MetaCyc:2.7.1.151-RXN {source="skos:exactMatch"} EXACT xref: RHEA:17717 {source="skos:exactMatch"} EXACT

Notes: EC 2.7.1.151 is a 2 step reaction (RHEA:32359 MetaCyc:RXN-13197) Rhea says: RHEA:32359 is a multi-step reaction: RHEA:17717 + RHEA:11856. This the 2 step reaction is covered by GO:0000823 and GO:0000824 (see below)

GO:0051765 inositol tetrakisphosphate kinase activity |GO:0047325 inositol tetrakisphosphate 1-kinase activity (to update) [10 EXP annotations] |GO:0000824 inositol tetrakisphosphate 3-kinase activity (to update) [6 EXP annotations] |GO:0047326 inositol tetrakisphosphate 5-kinase activity (to update) [2 EXP annotations] |GO:0000825 inositol tetrakisphosphate 6-kinase activity (to update) [7 EXP annotations] |__GO:0032942 inositol tetrakisphosphate 2-kinase activity (to update) [1 EXP annotations] GO:0102731 D-myo-inositol (1,3,4,6)-tetrakisphosphate 2-kinase activity (to update to become child of GO:0032942) [0 annotations]

Except for GO:0032942, the name of the above children GO terms is broad while the definition is for a specific substrate. The name has been updated to match the definition. This what has been done for the children of GO:0051766 inositol trisphosphate kinase activity.

id: GO:0047325 name: inositol-3,4,5,6-tetrakisphosphate 1-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 3,4,5,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+.” [EC:2.7.1.134, MetaCyc:2.7.1.134-RXN] xref: EC:2.7.1.134 EXACT xref: KEGG_REACTION:R03479 EXACT xref: MetaCyc:2.7.1.134-RXN EXACT xref: RHEA:12452 EXACT

Notes: the comment of 2.7.1.134 says that phosphorylates Ins(1,3,4)P3 on O-5 and O-6 which corresponds to EC 2.1.7.159 (GO:0052725 and GO:0052726)

id: GO:0000824 name: inositol-1,4,5,6-tetrakisphosphate 3-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,4,5,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+.” [GOC:elh] synonym: "1D-myo-inositol-tetrakisphosphate 3-kinase activity" BROAD [] synonym: "EC:2.7.1.151" TO REMOVE FROM SYNONYM xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R05801 EXACT xref: MetaCyc:RXN-7162 EXACT xref: RHEA:11856 EXACT

id: GO:0047326 name: inositol-1,3,4,6-tetrakisphosphate 5-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+.” [EC:2.7.1.140, MetaCyc:2.7.1.140-RXN] synonym: "1D-myo-inositol-tetrakisphosphate 5-kinase activity" BROAD [] synonym: "inositol-tetrakisphosphate 5-kinase activity" BROAD [] xref: EC:2.7.1.140 BROAD xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R03478 EXACT xref: MetaCyc:2.7.1.140-RXN EXACT xref: RHEA:12717 EXACT

id: GO:0000825 name: inositol-1,3,4,5-tetrakisphosphate 6-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+.” [GOC:elh] synonym: "1D-myo-inositol-tetrakisphosphate 6-kinase activity" BROAD [] xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R10953 EXACT xref: MetaCyc:RXN-7184 EXACT

Notes: No reaction in Rhea

id: GO:0032942 name: inositol tetrakisphosphate 2-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol tetrakisphosphate + ATP = 1D-myo-inositol pentakisphosphate (containing 2-phosphate) + ADP + H+.” [GOC:hf]

id: GO:0102731 name: inositol-1,3,4,6-tetrakisphosphate 2-kinase activity def: "Catalysis of the reaction: D-myo-inositol 1,3,4,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,2,3,4,6-pentakisphosphate + ADP + H+.” synonym: "D-myo-inositol (1,3,4,6)-tetrakisphosphate 2-kinase activity" EXACT [] xref: MetaCyc:RXN-7185 EXACT is_a: GO:0032942 ! inositol tetrakisphosphate 2-kinase activity

Notes: GO:0102731 is actually a child of GO:0032942, there is no Rhea for this reaction, annotation done in P2G for plant protein

GO:0102732 myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity (to update) [0 EXP annotations] GO:0035299 inositol pentakisphosphate 2-kinase activity (to update) [9 EXP annotations]

These 2 terms could have a grouping term such as what has been done for inositol tretrakisphospahte kinase activity and inositol triphosphate kinase activity. Potential new term: name: inositol pentakisphosphate kinase activity namespace: molecular_function def: "Catalysis of the reaction: inositol pentakisphosphate + ATP = inositol hexakisphosphate + ADP + H+." is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor is_a: GO:0180030 ! inositol phosphate kinase activity

id: GO:0102732 name: inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,2,3,4,6-pentakisphosphate + ATP = 1D-myo-inositol hexakisphosphate + ADP + H+." [MetaCyc:RXN-7186] synonym: “1D-myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity” EXACT [] synonym: "1D-myo-inositol-pentakisphosphate 5-kinase activity" BROAD [] synonym: "inositol-pentakisphosphate 5-kinase activity" BROAD [] xref: EC:2.7.1.140 BROAD xref: MetaCyc:RXN-7186 EXACT

Notes: EC 2.7.1.140 Main reaction: 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ATP <=> 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H(+) is covered by GO:0047326 The enzyme from plants and yeast can also use Ins(1,2,3,4,6)P5 as a substrate. This reaction doesn’t exist in Rhea and in KEGG. Used PMID: 12226109 for reaction and updated annotation to have IDA for this GO term.

id: GO:0035299 name: inositol 1,3,4,5,6-pentakisphosphate 2-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ATP = 1D-myo-inositol hexakisphosphate + ADP + H+." [RHEA:20313] xref: EC:2.7.1.158 EXACT xref: KEGG_REACTION:R05202 EXACT xref: MetaCyc:RXN-7163 EXACT xref: RHEA:20313 EXACT

Notes: EC 2.7.1.158 The enzyme can also use Ins(1,4,5,6)P4 and Ins(1,4,5)P3 as substrate. There is no specific GO term for these substrates (any annotation would be to the more general terms GO:0032942 and GO:0051766, respectively).

GO:0000828 inositol hexakisphosphate kinase activity (to update) |GO:0052723 inositol hexakisphosphate 1-kinase activity (to update) [2 EXP annotations] |GO:0052724 inositol hexakisphosphate 3-kinase activity (to update) [1 EXP annotation] |GO:0000830 inositol hexakisphosphate 4-kinase activity [1 EXP annotation] |GO:0000832 inositol hexakisphosphate 5-kinase activity (to update) [2 EXP annotations] |__GO:0000831 inositol hexakisphosphate 6-kinase activity [2 EXP annotations]

Reactions for the production of inositol pyrophosphates (PP-IP)

id: GO:0000828 name: inositol hexakisphosphate kinase activity def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + diphospho-1D-myo-inositol-pentakisphosphate. The isomeric configuration of diphospho-1D-myo-inositol-pentakisphosphate (PP-IP5) is unknown."

id: GO:0052723 name: inositol hexakisphosphate 1-kinase activity def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate." [GOC:jp, PMID:18981179, RHEA:37459] xref: EC:2.7.4.24 BROAD xref: KEGG_REACTION:R05799 EXACT xref: MetaCyc:RXN-10972 EXACT xref: RHEA:37459 EXACT

Notes: 2.7.4.24 also has reaction Rhea:10276 and corresponds to GO:0033857

id: GO:0052724 name: inositol hexakisphosphate 3-kinase activity def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 3-diphospho-1D-myo-inositol (1,2,4,5,6)pentakisphosphate." [GOC:jp, PMID:18981179] xref: EC:2.7.4.21 REMOVE EC (not correct) xref: MetaCyc:RXN-10971

Notes: no EC number and no Rhea reaction

id: GO:0000832 name: inositol hexakisphosphate 5-kinase activity def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate." [MetaCyc:2.7.1.152-RXN, RHEA:12793] xref: EC:2.7.4.21 BROAD xref: KEGG_REACTION:R09087 EXACT xref: MetaCyc:2.7.1.152-RXN EXACT xref: RHEA:12793 EXACT

Notes: 2.7.4.21 covers another reaction Rhea:37467 which has no GO term yet but maybe GO:0033200 if made broader definition.

GO:0000829 inositol heptakisphosphate kinase activity (to update) [6 EXP annotations] |GO:0000833 inositol heptakisphosphate 4-kinase activity (to update) [0 annotations] |GO:0033200 inositol heptakisphosphate 5-kinase activity (to update) [0 annotations] |__GO:0000834 inositol heptakisphosphate 6-kinase activity (to update) [0 annotations] GO:0033857 diphosphoinositol-pentakisphosphate kinase activity (to update, GO:0033857 is a child of GO:0000829) [10 EXP annotations]

Reactions for the production of inositol pyrophosphates (PP2-IP) In the literature often known as diphosphoinositol pentakisphosphate kinase activity which is the name for another similar kinase family see GO:0052839 name: diphosphoinositol tetrakisphosphate kinase activity.

id: GO:0000829 name: inositol heptakisphosphate kinase activity def: "Catalysis of the reaction: ATP + diphospho-1D-myo-inositol-pentakisphosphate = ADP + bis(diphospho)-1D-myo-inositol-tetrakisphosphate. The isomeric configurations of the diphospho-1D-myo-inositol-pentakisphosphate (PP-IP5) and bis(diphospho)-1D-myo-inositol-tetrakisphosphate (bis-PP-IP4) are unknown." [GOC:elh, PMID:16429326] synonym: "diphosphoinositol pentakisphosphate kinase activity" EXACT [] synonym: “PP-IP5 kinase activity” EXACT []

id: GO:0000833 name: inositol heptakisphosphate 4-kinase activity def: "Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = ADp + 4,5-bis(diphospho)-1D-myo-inositol (1,2,3,6)tetrakisphosphate." [GOC:elh, PMID:16429326] synonym: "diphosphoinositol-pentakisphosphate 4-kinase activity" EXACT [] synonym: "IP7 4-kinase activity" EXACT []

Note: the reaction is more specific than the term name (substrate specify) not sure what to do with the name, no reaction in Rhea

id: GO:0033200 name: inositol heptakisphosphate 5-kinase activity def: "Catalysis of the reaction: ATP + 4-diphospho-1D-myo-inositol (1,2,3,5,6)pentakisphosphate = ADP + 4,5-bis(diphospho)-1D-myo-inositol (1,2,3,6)tetrakisphosphate , and ATP + 6-diphospho-1D-myo-inositol (1,2,3,4,5)pentakisphosphate = ADP + 5,6-bis(diphospho)-1D-myo-inositol (1,2,3,4)tetrakisphosphate." [PMID:17412958] synonym: "diphosphoinositol-pentakisphosphate 5-kinase activity" EXACT [] synonym: "IP7 5-kinase activity" EXACT [] is_a: GO:0000829 ! inositol heptakisphosphate kinase activity

Note: 2 reactions covered, no reaction in Rhea Missing coverage of 1PP-IP5 to 1,5PP-IP4 which is also covered by 2.7.4.21 covers another reaction Rhea:37467 no GO term yet but maybe GO:0033200 if made a broader definition could be used

id: GO:0000834 name: inositol heptakisphosphate 6-kinase activity def: "Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = ADP +5,6-bis(diphospho)-1D-myo-inositol (1,2,3,4)tetrakisphosphate." [GOC:elh, PMID:16429326]

Note: the reaction is more specific than the term name (substrate specify), no reaction in Rhea

id: GO:0033857 name: inositol heptakisphosphate 1-kinase activity alt_id: GO:0102092 def: "Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = ADP + 1,5-bis(diphospho)-1D-myo-inositol 2,3,4,6-tetrakisphosphate." [EC:2.7.4.24] synonym: "5-diphosphoinositol pentakisphosphate 1-kinase activity" EXACT [] synonym: "PP-InsP5 kinase activity" RELATED [EC:2.7.4.24] synonym: "PP-IP5 kinase activity" RELATED [EC:2.7.4.24] synonym: "PPIP5K" RELATED [] xref: EC:2.7.4.24 BROAD xref: MetaCyc:2.7.4.24-RXN EXACT is_a: GO:0000829 ! inositol heptakisphosphate kinase activity

Notes: GO:0033857 is a child of GO:0000829 2.7.4.24 also has reaction RHEA:37459 and corresponds to GO:0052723

GO:0052836 inositol 5-diphosphate pentakisphosphate 5-kinase activity [0 EXP annotations] GO:0000827 inositol-1,3,4,5,6-pentakisphosphate kinase activity [5 EXP annotations] GO:0052839 inositol diphosphate tetrakisphosphate kinase activity [0 EXP annotations]

These terms are for the production of inositol pyrophosphates

id: GO:0000827 name: inositol-1,3,4,5,6-pentakisphosphate kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate = ADP + diphospho-1D-myo-inositol tetrakisphosphate. The isomeric configuration of diphospho-1D-myo-inositol tetrakisphosphate is unknown." [GOC:elh, PMID:11311242] xref: EC:2.7.4.21 TO DELETE is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor is_a: GO:0180030 ! inositol phosphate kinase activity

Notes: Name not great but difficult to change as inositol pentakisphosphate kinase activity is fore phosphorylating the ring

id: GO:0052836 name: inositol 5-diphosphate pentakisphosphate 5-kinase activity def: "Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol pentakisphosphate = ADP + 5-triphospho-1D-myo-inositolpentakisphosphate." [PMID:11502751, PMID:18355727] is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor is_a: GO:0180030 ! inositol phosphate kinase activity

Notes: Name not great but difficult to change as inositol pentakisphosphate kinase activity is fore phosphorylating the ring

id: GO:0052839 name: diphosphoinositol tetrakisphosphate kinase activity def: "Catalysis of the reaction: ATP + diphospho-1D-myo-inositol tetrakisphosphate = ADP + bis(diphospho)-1D-myo-inositol trisphosphate." [PMID:10827188, PMID:11502751, PMID:18355727] synonym: "PP-IP4 kinase activity" EXACT [] is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor is_a: GO:0180030 ! inositol phosphate kinase activity

Note: See GO:0000829 inositol heptakisphosphate kinase activity which In the literature often known as diphosphoinositol pentakisphosphate kinase

sjm41 commented 3 days ago

[x] Done the changes below.

GO:0051766 inositol trisphosphate kinase activity |GO:0052726 inositol-1,3,4-trisphosphate 5-kinase activity (to update) [10 EXP annotations] |GO:0052725 inositol-1,3,4-trisphosphate 6-kinase activity (to update) [1 EXP annotations] |GO:0008440 inositol-1,4,5-trisphosphate 3-kinase activity (to update) [17 EXP annotations] |GO:0000823 inositol-1,4,5-trisphosphate 6-kinase activity (to update) [9 EXP annotations] |__GO:0052835 inositol-3,4,6-trisphosphate 1-kinase activity [4 EXP annotations]

id: GO:0052726 name: inositol-1,3,4-trisphosphate 5-kinase activity xref: EC:2.7.1.159 BROAD xref: KEGG_REACTION:R03428 EXACT xref: MetaCyc:2.7.1.139-RXN EXACT xref: RHEA:13253 EXACT

id: GO:0052725 name: inositol-1,3,4-trisphosphate 6-kinase activity xref: EC:2.7.1.159 BROAD xref: KEGG_REACTION:R03429 EXACT xref: MetaCyc:2.7.1.133-RXN EXACT xref: RHEA:20940 EXACT

id: GO:0008440 name: inositol-1,4,5-trisphosphate 3-kinase activity xref: EC:2.7.1.127 EXACT xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R03433 EXACT xref: MetaCyc:2.7.1.127-RXN EXACT xref: RHEA:11020 EXACT

Notes: EC 2.7.1.151 has a broad specificity

id: GO:0000823 name: inositol-1,4,5-trisphosphate 6-kinase activity xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R05800 EXACT xref: MetaCyc:2.7.1.151-RXN {source="skos:exactMatch"} EXACT xref: RHEA:17717 {source="skos:exactMatch"} EXACT

sjm41 commented 3 days ago

[x] Done the changes below.

GO:0051765 inositol tetrakisphosphate kinase activity |GO:0047325 inositol tetrakisphosphate 1-kinase activity (to update) [10 EXP annotations] |GO:0000824 inositol tetrakisphosphate 3-kinase activity (to update) [6 EXP annotations] |GO:0047326 inositol tetrakisphosphate 5-kinase activity (to update) [2 EXP annotations] |GO:0000825 inositol tetrakisphosphate 6-kinase activity (to update) [7 EXP annotations] |__GO:0032942 inositol tetrakisphosphate 2-kinase activity (to update) [1 EXP annotations] GO:0102731 D-myo-inositol (1,3,4,6)-tetrakisphosphate 2-kinase activity (to update to become child of GO:0032942) [0 annotations]

Except for GO:0032942, the name of the above children GO terms is broad while the definition is for a specific substrate. The name has been updated to match the definition. This what has been done for the children of GO:0051766 inositol trisphosphate kinase activity.

id: GO:0047325 name: inositol-3,4,5,6-tetrakisphosphate 1-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 3,4,5,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+.” [EC:2.7.1.134, MetaCyc:2.7.1.134-RXN] xref: EC:2.7.1.134 EXACT xref: KEGG_REACTION:R03479 EXACT xref: MetaCyc:2.7.1.134-RXN EXACT xref: RHEA:12452 EXACT

Notes: the comment of 2.7.1.134 says that phosphorylates Ins(1,3,4)P3 on O-5 and O-6 which corresponds to EC 2.1.7.159 (GO:0052725 and GO:0052726)

id: GO:0000824 name: inositol-1,4,5,6-tetrakisphosphate 3-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,4,5,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+.” [GOC:elh] synonym: "1D-myo-inositol-tetrakisphosphate 3-kinase activity" BROAD [] synonym: "EC:2.7.1.151" TO REMOVE FROM SYNONYM xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R05801 EXACT xref: MetaCyc:RXN-7162 EXACT xref: RHEA:11856 EXACT

id: GO:0047326 name: inositol-1,3,4,6-tetrakisphosphate 5-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+.” [EC:2.7.1.140, MetaCyc:2.7.1.140-RXN] synonym: "1D-myo-inositol-tetrakisphosphate 5-kinase activity" BROAD [] synonym: "inositol-tetrakisphosphate 5-kinase activity" BROAD [] xref: EC:2.7.1.140 BROAD xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R03478 EXACT xref: MetaCyc:2.7.1.140-RXN EXACT xref: RHEA:12717 EXACT

id: GO:0000825 name: inositol-1,3,4,5-tetrakisphosphate 6-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H+.” [GOC:elh] synonym: "1D-myo-inositol-tetrakisphosphate 6-kinase activity" BROAD [] xref: EC:2.7.1.151 BROAD xref: KEGG_REACTION:R10953 EXACT xref: MetaCyc:RXN-7184 EXACT

Notes: No reaction in Rhea

id: GO:0032942 name: inositol tetrakisphosphate 2-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol tetrakisphosphate + ATP = 1D-myo-inositol pentakisphosphate (containing 2-phosphate) + ADP + H+.” [GOC:hf]

id: GO:0102731 name: inositol-1,3,4,6-tetrakisphosphate 2-kinase activity def: "Catalysis of the reaction: D-myo-inositol 1,3,4,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,2,3,4,6-pentakisphosphate + ADP + H+.” synonym: "D-myo-inositol (1,3,4,6)-tetrakisphosphate 2-kinase activity" EXACT [] xref: MetaCyc:RXN-7185 EXACT is_a: GO:0032942 ! inositol tetrakisphosphate 2-kinase activity

Notes: GO:0102731 is actually a child of GO:0032942, there is no Rhea for this reaction, annotation done in P2G for plant protein

[x] Done the above changes, except I modified GO:0032942 to be 'inositol-1,4,5,6-tetrakisphosphate 2-kinase activity' associated with MetaCyc:RXN-7182, and then made GO:0102731 a child of 'inositol tetrakisphosphate kinase activity'. This represents the annotations, and better matches the organisation of GO:0051766 inositol trisphosphate kinase activity.

sjm41 commented 8 hours ago

[x] Done the changes below.

New grouping term is:

[Term] id: GO:0120517 name: inositol pentakisphosphate kinase activity namespace: molecular_function def: "Catalysis of the reaction: inositol pentakisphosphate + ATP = inositol hexakisphosphate + ADP + H+." [GOC:curators] is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor is_a: GO:0180030 ! inositol phosphate kinase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28385" xsd:anyURI created_by: sjm creation_date: 2024-07-08T08:02:59Z

GO:0102732 myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity (to update) [0 EXP annotations] GO:0035299 inositol pentakisphosphate 2-kinase activity (to update) [9 EXP annotations]

These 2 terms could have a grouping term such as what has been done for inositol tretrakisphospahte kinase activity and inositol triphosphate kinase activity. Potential new term: name: inositol pentakisphosphate kinase activity namespace: molecular_function def: "Catalysis of the reaction: inositol pentakisphosphate + ATP = inositol hexakisphosphate + ADP + H+." is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor is_a: GO:0180030 ! inositol phosphate kinase activity

id: GO:0102732 name: inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,2,3,4,6-pentakisphosphate + ATP = 1D-myo-inositol hexakisphosphate + ADP + H+." [MetaCyc:RXN-7186] synonym: “1D-myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity” EXACT [] synonym: "1D-myo-inositol-pentakisphosphate 5-kinase activity" BROAD [] synonym: "inositol-pentakisphosphate 5-kinase activity" BROAD [] xref: EC:2.7.1.140 BROAD xref: MetaCyc:RXN-7186 EXACT

Notes: EC 2.7.1.140 Main reaction: 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ATP <=> 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H(+) is covered by GO:0047326 The enzyme from plants and yeast can also use Ins(1,2,3,4,6)P5 as a substrate. This reaction doesn’t exist in Rhea and in KEGG. Used PMID: 12226109 for reaction and updated annotation to have IDA for this GO term.

id: GO:0035299 name: inositol 1,3,4,5,6-pentakisphosphate 2-kinase activity def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ATP = 1D-myo-inositol hexakisphosphate + ADP + H+." [RHEA:20313] xref: EC:2.7.1.158 EXACT xref: KEGG_REACTION:R05202 EXACT xref: MetaCyc:RXN-7163 EXACT xref: RHEA:20313 EXACT

Notes: EC 2.7.1.158 The enzyme can also use Ins(1,4,5,6)P4 and Ins(1,4,5)P3 as substrate. There is no specific GO term for these substrates (any annotation would be to the more general terms GO:0032942 and GO:0051766, respectively).

sjm41 commented 7 hours ago

[x] Done the changes below:

GO:0000828 inositol hexakisphosphate kinase activity (to update) |GO:0052723 inositol hexakisphosphate 1-kinase activity (to update) [2 EXP annotations] |GO:0052724 inositol hexakisphosphate 3-kinase activity (to update) [1 EXP annotation] |GO:0000830 inositol hexakisphosphate 4-kinase activity [1 EXP annotation] |GO:0000832 inositol hexakisphosphate 5-kinase activity (to update) [2 EXP annotations] |__GO:0000831 inositol hexakisphosphate 6-kinase activity [2 EXP annotations]

Reactions for the production of inositol pyrophosphates (PP-IP)

id: GO:0000828 name: inositol hexakisphosphate kinase activity def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + diphospho-1D-myo-inositol-pentakisphosphate. The isomeric configuration of diphospho-1D-myo-inositol-pentakisphosphate (PP-IP5) is unknown."

id: GO:0052723 name: inositol hexakisphosphate 1-kinase activity def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate." [GOC:jp, PMID:18981179, RHEA:37459] xref: EC:2.7.4.24 BROAD xref: KEGG_REACTION:R05799 EXACT xref: MetaCyc:RXN-10972 EXACT xref: RHEA:37459 EXACT

Notes: 2.7.4.24 also has reaction Rhea:10276 and corresponds to GO:0033857

id: GO:0052724 name: inositol hexakisphosphate 3-kinase activity def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 3-diphospho-1D-myo-inositol (1,2,4,5,6)pentakisphosphate." [GOC:jp, PMID:18981179] xref: EC:2.7.4.21 REMOVE EC (not correct) xref: MetaCyc:RXN-10971

Notes: no EC number and no Rhea reaction

id: GO:0000832 name: inositol hexakisphosphate 5-kinase activity def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate." [MetaCyc:2.7.1.152-RXN, RHEA:12793] xref: EC:2.7.4.21 BROAD xref: KEGG_REACTION:R09087 EXACT xref: MetaCyc:2.7.1.152-RXN EXACT xref: RHEA:12793 EXACT

Notes: 2.7.4.21 covers another reaction Rhea:37467 which has no GO term yet but maybe GO:0033200 if made broader definition.

sjm41 commented 7 hours ago

[x] Done the changes below (including the suggestion to change 'inositol heptakisphosphate kinase activity' to 'diphosphoinositol pentakisphosphate kinase activity')