Metabolism of folate and pterines (R-HSA-196757)

[ukemi]

• Make mouse models
  - http://noctua.geneontology.org/editor/graph/gomodel:671ae02600003666?
  - http://noctua.geneontology.org/editor/graph/gomodel:67369e7600003835?
  - http://noctua.geneontology.org/editor/graph/gomodel:67369e7600003532?
  - http://noctua.geneontology.org/editor/graph/gomodel:67369e7600001890?
  - http://noctua.geneontology.org/editor/graph/gomodel:67369e7600001117?
• Should R-HSA-200646 and R-HSA-200729 contain a proton in the reaction and be mapped to GO:0140211? PMID:17962486
• Should R-HSA-197972 be mappped to [GO:0004146] dihydrofolate reductase activity instead of [GO:0033560] folate reductase activity?
• It appears that 10-formyltetrahydrofolyl polyglutamate macromolecule (CHEBI:28010) is not in GO, but is the output of R-HSA-197958.
• Re-examine logical defs of folate metabolism terms in the ontology.
• Is tetrahydrofolyl-poly(glutamic acid) macromolecule CHEBI:28624 correct? Should it be CHEBI:58580 - tetrahydrofolyl-poly(glutamate) macromolecule instead?
• The MF mapped to R-HSA-200711 is [formate-tetrahydrofolate ligase activity] which according to the definition requires THF as a substrate. However, the input of the reaction is the polyglutamate-conjugated moiety. Does working on a part of that molecule satisfy the definition?
• If we decide that the GO MF defs are valid for portions of molecules, should R-HSA-6808496 be mapped to 10-formyltetrahydrofolate dehydrogenase (GO:0016155)?
• The MFs on R-HSA-200718 and R-HSA-200676 can be refined to the NADP+ specific terms. The cytosolic enzymes use NADP+ and the mitochondrial ones use NAD+. Actually the "L" protein can use both, but do we want to be consistent with the molecules in the reaction?
• The preceding event for R-HSA-6801328 can't be right. No shared output-input.
• The MFs on R-HSA-6801462 and R-HSA-6801328 are swapped.
• If you feed mice tritiated serine, it labels formate (PMID: 29483189)should R-HSA-5694137 run in the opposite direction? @deustp01
• 5-methyltetrahydrofolate is not folic acid. Should R-HSA-200652 be mapped to '[GO:0046943] carboxylic acid transmembrane transporter activity' instead of 'folic acid transporter activity'?

[deustp01]

Should R-HSA-200646 and R-HSA-200729 contain a proton in the reaction and be mapped to GO:0140211? PMID:17962486

One proton added as input and as output to each reaction.
GO MF term changed to GO:0140211 (more specific child of previous MF term)
PMID:17962486 added to the list of literature references.
DP Hill added as reviewer for the two modified reactions.
Changes will be publicly visible in the March 2025 Reactome release

[ukemi]

There is evidence that mouse Fpgs can't work on 5-methyltetrahydrofolate, so I am leaving this mouse model branch out. PMID: 6548641