SPAC1093.02

Summary: PAINT inference from characterised PNPOs (S. cerevisiae PDX3); sound.

Reason: No S. pombe assay is cached. The activity rests on family membership (UniProt SIMILARITY, PROSITE PYRIDOX_OXIDASE signature) and UniProt's curated by-similarity function statement (ECO:0000250), matching the PAINT node seeded by characterised PNPOs (S. cerevisiae PDX3, E. coli PdxH, human PNPO).

Summary: InterPro/RHEA mapping; consistent.

Reason: The mapping rests on the InterPro PNPO signature (IPR000659), which the record carries; with family membership and UniProt's by-similarity function statement (ECO:0000250) this supports the activity, though no S. pombe assay is cached.

Summary: PAINT inference of a mitochondrial location, inherited within the pyridoxamine 5'-phosphate oxidase family; peripheral to the PLP salvage function.

Reason: The IBA places SPAC1093.02 inside the PNPO clade whose characterised members (S. cerevisiae Pdx3 and Arabidopsis AT5G49970, the PAINT sources) carry the organellar location, and nothing specific to the S. pombe protein argues for loss of it. The UniProt record has no SUBCELLULAR LOCATION comment and no transit peptide, so there is no direct S. pombe evidence either way; the support is family membership. Kept as non-core because the location is not where the core PLP salvage activity has been shown to act.

Summary: InterPro mapping to pyridoxine biosynthesis; PNPO acts in salvage interconversion rather than the fungal de novo route (snz1).

Reason: PNPO-family membership and UniProt's by-similarity function statement (ECO:0000250) place the enzyme at the PNP/PMP -> PLP step, which UniProt's PATHWAY assigns to PLP salvage. The enzyme consumes pyridoxine 5'-phosphate rather than forming pyridoxine, so the legacy InterPro2GO mapping is laterally replaced by PLP biosynthesis (GO:0042823), which the gene already carries by IBA.

Proposed replacements: pyridoxal 5'-phosphate biosynthetic process

Summary: FMN cofactor; subsidiary.

Reason: FMN is the cofactor of the PNPO family; UniProt curates FMN binding by similarity (ECO:0000250) and maps the FMN-binding residues from human PNPO (Q9NVS9) and E. coli PdxH (P0AFI7). True, but a cofactor-binding term subsidiary to the oxidase activity.

Summary: Generic InterPro-derived parent of the specific activity, which is already annotated.

Reason: Correct but general. The InterPro PNPO conserved-site signature (IPR019740) and UniProt's by-similarity catalytic activity (PMP oxidation with release of ammonium, EC 1.4.3.5) specify the CH-NH2 oxidase as pyridoxamine phosphate oxidase (GO:0004733), which the gene already carries. Evidence is family membership; no S. pombe assay is cached.

Proposed replacements: pyridoxamine phosphate oxidase activity

Summary: Broad parent of the PLP biosynthesis term asserted elsewhere in this review.

Reason: True but uninformative. Both PNPO reactions (from PNP and from PMP) yield PLP, so the accepted pyridoxal 5'-phosphate biosynthetic process (GO:0042823; is_a vitamin B6 biosynthetic process, is_a this term) already entails it. Support is UniProt's PATHWAY placement in PLP salvage, assigned from PNPO-family membership.

Summary: Curator inference: PMP oxidation to PLP.

Reason: Curator inference from the PMP oxidase activity. UniProt curates PMP oxidation to PLP by similarity (ECO:0000250), and the protein belongs to the PNPO family; no S. pombe metabolic data are cached.

Summary: PAINT inference: PNPO converts PNP/PMP to PLP.

Reason: PLP formation follows from the PNP/PMP oxidase activity, which rests on PNPO-family membership and UniProt's by-similarity function statement (ECO:0000250); the UniProt pathway places it in PLP salvage.