phosphoglycerate mutase activity xrefs

[sjm41]

Currently we have:

phosphoglycerate mutase activity
    |_2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity
    |_2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity

id: GO:0004619
name: phosphoglycerate mutase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-phosphoglycerate = 3-phosphoglycerate." [RHEA:15901]
xref: MetaCyc:3PGAREARR-RXN
xref: RHEA:15901
is_a: GO:0016868 ! intramolecular transferase activity, phosphotransferases

id: GO:0046537
name: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity
def: "Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D glycerate; this reaction does not require the cofactor 2,3-bisphosphoglycerate." [EC:5.4.2.12]
xref: EC:5.4.2.12 {source="skos:exactMatch"}
is_a: GO:0004619 ! phosphoglycerate mutase activity

id: GO:0046538
name: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity
def: "Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate; this reaction mechanism uses 2,3-bisphosphoglycerate as a phosphate donor." [EC:5.4.2.11]
xref: EC:5.4.2.11 {source="skos:exactMatch"}
xref: KEGG_REACTION:R01516
is_a: GO:0004619 ! phosphoglycerate mutase activity

---

• MetaCyc:3PGAREARR-RXN (https://biocyc.org/META/NEW-IMAGE?object=3PGAREARR-RXN) corresponds to EC:5.4.2.12, so should be moved from GO:0004619 to GO:0046537

• MetaCyc:RXN-15513 (https://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-15513) corresponds to EC:5.4.2.11, so should be added to GO:0046538

• RHEA:15901 (https://www.rhea-db.org/rhea/15901) covers both EC:5.4.2.11 and EC:5.4.2.12, so it's probably fine to have that on the parent term (GO:0004619), though it would be accurate to also add it to both child terms (GO:0046537, GO:0046538)

[sjm41]

@pgaudet I tried adding RHEA:15901 to both child terms (as well as the parent) but it seems this isn't allowed?

[sjm41]

No need to add RHEA:15901 to both child terms (as well as the parent) - closing.

[sjm41]

Looking at this one again....

We currently have this:

phosphoglycerate mutase activity (GO:0004619) = RHEA:15901
    |_2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538) = EC:5.4.2.11 
    |_2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity (GO:0046537) = EC:5.4.2.12

id: GO:0004619
name: phosphoglycerate mutase activity
def: "Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate." [RHEA:15901]
xref: RHEA:15901
is_a: GO:0016868 ! intramolecular phosphotransferase activity
property_value: term_tracker_item "#24905" xsd:anyURI
property_value: term_tracker_item "#25780" xsd:anyURI

id: GO:0046538
name: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity
def: "Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; this reaction mechanism uses 2,3-bisphosphoglycerate as a phosphate donor." [EC:5.4.2.11]
xref: EC:5.4.2.11 {source="skos:exactMatch"}
xref: KEGG_REACTION:R01516
xref: MetaCyc:RXN-15513
is_a: GO:0004619 ! phosphoglycerate mutase activity
property_value: term_tracker_item "#24905" xsd:anyURI
property_value: term_tracker_item "#25780" xsd:anyURI

id: GO:0046537
name: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity
def: "Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; this reaction does not require the cofactor 2,3-bisphosphoglycerate." [EC:5.4.2.12]
xref: EC:5.4.2.12 {source="skos:exactMatch"}
xref: MetaCyc:3PGAREARR-RXN
is_a: GO:0004619 ! phosphoglycerate mutase activity
property_value: term_tracker_item "#24905" xsd:anyURI
property_value: term_tracker_item "#25780" xsd:anyURI

EC:5.4.2.11 says:
The enzymes from vertebrates, platyhelminths, mollusks, annelids, crustaceans, insects, algae, some fungi, yeast and some bacteria (particularly Gram-negative) require 2,3-bisphospho-D-glycerate as a cofactor.

EC:5.4.2.12 says:
The enzymes from higher plants, algae, some fungi, nematodes, sponges, coelenterates, myriapods, arachnids, echinoderms, archaea and some bacteria (particularly Gram-positive) have maximum activity in the absence of 2,3-bisphospho-D-glycerate.

RHEA:15901 is agnostic to the co-factor and is therefore mapped by RHEA to both ECs.

So, a couple of issues here:

• it should be possible to annotate to either of the child terms (corresponding to the specific ECs) here, so the parent grouping term (GO:0004619) should either be 'do not annotate' or obsoleted. (The term is used in 33 EXP annotations)
• currently, the RHEA xref is only on the parent term, but it would be better to be a broadMatch on the two child terms so that the participant chemicals can be accessed.

What do you think @pgaudet ?

If we propose obsoletion of the parent term, GO:0004619, note that is in the logical def of these 3 GO terms (though I haven't investigated whether it is strictly needed in those LDs):

id: GO:0006096
name: glycolytic process
intersection_of: has_part GO:0004619 ! phosphoglycerate mutase activity

id: GO:0061719
name: glucose catabolic process to pyruvate utilizing ADP
intersection_of: has_part GO:0004619 ! phosphoglycerate mutase activity

id: GO:0061722
name: sulphoglycolysis
intersection_of: has_part GO:0004619 ! phosphoglycerate mutase activity

[pgaudet]

Editors' discussion: proposal to merge the two specific terms into the parent

[sjm41]

ExplorEnz view:

EC | 5.4.2.12
Reaction: | 2-phospho-D-glycerate = 3-phospho-D-glycerate

EC | 5.4.2.11
Reaction: | 2-phospho-D-glycerate = 3-phospho-D-glycerate (overall reaction)
(1a) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Nτ-phospho-L-histidine + 2/3-phospho-D-glycerate
(1b) [enzyme]-Nτ-phospho-L-histidine + 2-phospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate
(1c) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Nτ-phospho-L-histidine + 3-phospho-D-glycerate
(1d) [enzyme]-Nτ-phospho-L-histidine + 2/3-bisphospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate

ie. 5.4.2.11 includes a bunch of 'sub-reactions'

So, merging into the parent makes sense

[pgaudet]

More details on the subreactions here: https://www.enzyme-database.org/query.php?ec=5.4.2.12

[pgaudet]

Annotations are here: geneontology/go-annotation#5503

[sjm41]

Hi @pgaudet @raymond91125 Do we need to wait for annotations to be fixed, or can this merge happen now?

[sjm41]

Thanks @raymond91125 !