gibberellin 2-beta-dioxygenase activity merges

Looks like the 6 terms below should be merged into GO:0045543: id: GO:0045543 name: gibberellin 2-beta-dioxygenase activity namespace: molecular_function def: "Catalysis of the reaction: a gibberellin + 2-oxoglutarate + O2 = a 2-beta-hydroxygibberellin + succinate + CO2." [GOC:kad, RHEA:15005] synonym: "gibberellin 2-beta-hydroxylase activity" RELATED [EC:1.14.11.13] synonym: "gibberellin 2-oxidase activity" EXACT [] synonym: "gibberellin 2beta-dioxygenase activity" RELATED [EC:1.14.11.13] synonym: "gibberellin 2beta-hydroxylase activity" RELATED [EC:1.14.11.13] xref: EC:1.14.11.13 xref: RHEA:15005 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22382" xsd:anyURI

[x] GO:0102111 - 23 annotations - 1 EXP UniProt id: GO:0102111 name: gibberellin A20,2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: gibberellin A20 + 2-oxoglutarate + O2 = gibberellin A29 + succinate + carbon dioxide." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN-113 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc says this is version of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity)
[x] GO:0102924 - 23 annotations - 1 EXP UniProt id: GO:0102924 name: gibberellin A44,2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: 2 H+ + gibberellin A44 + 2-oxoglutarate + O2 = gibberellin A98 + succinate + carbon dioxide." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN-886 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc says this is version of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity)
[x] GO:0102652 - 23 annotations - 1 EXP UniProt id: GO:0102652 name: gibberellin A9,2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: gibberellin A9 + 2-oxoglutarate + O2 = gibberellin A51 + succinate + carbon dioxide." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN-171 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => ~MetaCyc says this is version of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity)~ gibberellin 3-beta-dioxygenase activity ; GO:0016707
[x] GO:0103055 - 2 annotations - only IEAs id: GO:0103055 name: gibberelli A15, 2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: gibberellin A15 + 2-oxoglutarate + O2 = gibberellin A24 + succinate + carbon dioxide + H2O." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN1F-163 xref: RHEA:60780 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc just maps this to EC:1.14.11.- but it looks like another instance of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity)
[x] GO:0103054 - 2 annotations - only IEAs id: GO:0103054 name: gibberellin A12, 2-oxoglutarate:oxygen oxidoreductase activity (gibberellin A15-forming) def: "Catalysis of the reaction: gibberellin A12 + O2 + 2-oxoglutarate = gibberellin A15 + carbon dioxide + succinate." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN1F-162 xref: RHEA:60776 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc just maps this to EC:1.14.11.- ~but it looks like another instance of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity)~ replace by gibberellin 20-oxidase activity ; GO:0045544.
[x] GO:0103056 - 2 annotations - only IEAs id: GO:0103056 name: gibberellin A53, 2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: gibberellin A53 + O2 + 2-oxoglutarate = gibberellin A44 diacid + carbon dioxide + succinate." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN1F-167 xref: RHEA:60800 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc just maps this to EC:1.14.11.- ~but it looks like another instance of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity)~ gibberellin 20-oxidase activity ; GO:0045544.

There are more terms:

[x] GO:0102714 gibberellin A12,oxoglutarate:oxygen oxidoreductase activity: represents the same reaction as gibberellin 3-beta-dioxygenase activity ; GO:0016707, according to xref MetaCyc:RXN-6544
[x] GO:0102712 gibberellin A13,oxoglutarate:oxygen oxidoreductase activity: represents the same reaction as gibberellin 3-beta-dioxygenase activity ; GO:0016707, according to xref MetaCyc:RXN-6542
[x] GO:0102715 gibberellin A17,oxoglutarate:oxygen oxidoreductase activity: represents the same reaction as gibberellin 3-beta-dioxygenase activity ; GO:0016707, according to xref MetaCyc:RXN-6546
[x] GO:0102711 gibberellin A25,oxoglutarate:oxygen oxidoreductase activity: represents the same reaction as gibberellin 3-beta-dioxygenase activity ; GO:0016707, according to xref MetaCyc:RXN-6541
[x] GO:0102716 gibberellin A28,oxoglutarate:oxygen oxidoreductase activity: represents the same reaction as gibberellin 3-beta-dioxygenase activity ; GO:0016707, according to xref MetaCyc:RXN-6547
[x] GO:0102652 gibberellin A9,2-oxoglutarate:oxygen oxidoreductase activity: represents the same reaction as gibberellin 3-beta-dioxygenase activity ; GO:0016707, according to xref MetaCyc:RXN-171
[x] GO:0102972 gibberellin A12,2-oxoglutarate:oxygen oxidoreductase activity (gibberellin A110-forming): represents the same activity as gibberellin 2-beta-dioxygenase activity ; GO:0045543, according to MetaCyc:RXN-947 xref
[x] GO:0102663 gibberellin A34,2-oxoglutarate:oxygen oxidoreductase activity: represents the same activity as gibberellin 2-beta-dioxygenase activity ; GO:0045543, according to MetaCyc:RXN-292 xref
[x] GO:0102653 gibberellin A51,2-oxoglutarate:oxygen oxidoreductase activity: represents the same activity as gibberellin 2-beta-dioxygenase activity ; GO:0045543, according to MetaCyc:RXN-172 xref
[x] GO:0103010 gibberellin A53,2-oxoglutarate:oxygen oxidoreductase activity (GA97-forming) represents the same activity as gibberellin 2-beta-dioxygenase activity ; GO:0045543, according to MetaCyc:RXN-991 xref
[x] GO:0103057 gibberellin A19, 2-oxoglutarate:oxygen oxidoreductase activity: represents the same activity as gibberellin 20-oxidase activity ; GO:0045544, according to MetaCyc:RXN1F-169
[x] GO:0102755 gibberellin-15(closed lactone form),2-oxoglutarate:oxygen oxidoreductase (3beta-hydroxylating) activity: MetaCyc:RXN-7680
[x] GO:0102713 gibberellin A25 hydroxylase activity: : represents the same reaction as gibberellin 3-beta-dioxygenase activity ; GO:0016707 according to MetaCyc:RXN-6543
[x] GO:0102738 (gibberellin-14), 2-oxoglutarate:oxygen oxidoreductase activity: represents the same activity as gibberellin 20-oxidase activity ; GO:0045544, according to MetaCyc:RXN-7589
[x] GO:0102739 (gibberellin-36), 2-oxoglutarate:oxygen oxidoreductase activity: represents the same activity as gibberellin 20-oxidase activity ; GO:0045544, according to MetaCyc:RXN-7591

According to wikipedia, there are 136 GAs: https://en.wikipedia.org/wiki/Gibberellin

I suppose we may want to keep some major ones (if there are), but other terms that were not in the original list don't have annotations (see https://github.com/geneontology/go-annotation/issues/5445), so for now I will obsolete them.

GO:0045544 gibberellin 20-oxidase activity

Fixed definition from: "Catalysis of the oxidation of C-20 gibberellins to form the corresponding C-19 lactones." [PMID:7604047]

to : "Catalysis of the reaction: 2 2-oxoglutarate + gibberellin A12 (GA12) + H+ + 3 O2 = 3 CO2 + gibberellin A9 (GA9) + 2 H2O + 2 succinate. This reaction results in the oxidation of C-20 gibberellins to form the corresponding C-19 lactones, via a three-step oxidation at C-20 of the GA skeleton. Also converts GA53 to GA20. GA25 is also formed as a minor product." [PMID:32652020, PMID:7604047]

Added RHEA xrefs +xref: RHEA:60768 {source="skos:narrowMatch"} +xref: RHEA:60772 {source="skos:narrowMatch"} +xref: RHEA:60780 {source="skos:narrowMatch"} +xref: RHEA:60796 {comment="skos:narrowMatch"}

[x] C-19 gibberellin 2-beta-dioxygenase activity: 2 EXP TAIR, obsolete & replace by parent gibberellin 2-beta-dioxygenase activity
[x] C-20 gibberellin 2-beta-dioxygenase activity: 5 EXP TAIR, obsolete & replace by parent gibberellin 2-beta-dioxygenase activity
[x] GO:0102494 GA20 2,3-desaturase activity: no annotations. Based on MetaCyc xref (MetaCyc:RXN-14317), corresponds to gibberellin 3-beta-dioxygenase activity ; GO:0016707.
[x] GA5 2,3 epoxidase activity: no annotations. Based on MetaCyc xref (MetaCyc:RXN-14327), corresponds to gibberellin 3-beta-dioxygenase activity ; GO:0016707.
[x] GA5 3beta-hydroxylase activity: no annotations. Based on MetaCyc xref (MetaCyc:RXN-14318), corresponds to gibberellin 3-beta-dioxygenase activity ; GO:0016707.

Obsolete GO:0047927 -name: gibberellin-44 dioxygenase activity -namespace: molecular_function -def: "Catalysis of the reaction: gibberellin 44 + 2-oxoglutarate + O2 = gibberellin 19 + succinate + CO2." [EC:1.14.11.12, MetaCyc:GIBBERELLIN-44-DIOXYGENASE-RXN] -synonym: "(gibberellin-44), 2-oxoglutarate:oxygen oxidoreductase activity" RELATED [EC:1.14.11.12] -synonym: "(gibberellin-44),2-oxoglutarate:oxygen oxidoreductase activity" RELATED [EC:1.14.11.12] -synonym: "gibberellin A44 oxidase activity" RELATED [EC:1.14.11.12] -synonym: "oxygenase, gibberellin A44 oxidase activity" RELATED [EC:1.14.11.12] -xref: EC:1.14.11.12 -xref: MetaCyc:RXN1F-168 -xref: RHEA:16033

because it is an intermediate in gibberellin 20-oxidase activity GO:0045544, see PMID:32652020. No annotations, so associations in EC or in RHEA.

Another family:

[x] GO:0102123 gibberellin A4 16alpha,17 epoxidase activity - 0 annotations def: "Catalysis of the reaction: gibberellin A4 + O2 + H+ + NAD(P)H = 16alpha,17-epoxy gibberellin A4 + H2O + NAD(P)." [EC:1.14.-.-, GOC:pz] xref: MetaCyc:RXN-11385
[x] GO:0102124 gibberellin A12 16alpha,17 epoxidase activity - 0 annotations namespace: molecular_function def: "Catalysis of the reaction: gibberellin A12 + O2 + H+ + NAD(P)H = 16alpha, 17-epoxy gibberellin A12 + H2O + NAD(P)." [EC:1.14.-.-, GOC:pz] xref: MetaCyc:RXN-11387
[x] GO:0102125 - 0 annotations name: gibberellin A9 16alpha,17 epoxidase activity namespace: molecular_function def: "Catalysis of the reaction: gibberellin A9 + O2 + H+ + NAD(P)H = 16alpha, 17-epoxy gibberellin A9 + H2O + NAD(P)." [EC:1.14.-.-, GOC:pz] xref: MetaCyc:RXN-11388

MetaCyc states:

Although the exact biochemical reactions carried out by this enzyme have not been identified to date, based on comparisons with other cytochrome P450 enzymes, it is likely that NAD(P)H and O2 are involved in this reaction.

Based on the lack of understanding of the reaction and the ack of annotations, I will obsolete these as well.

geneontology / go-ontology

gibberellin 2-beta-dioxygenase activity merges #28852