Annotations: 1CI0

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ci0a_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	Pyridoxine 5'-phoshate oxidase (PNP oxidase)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1ci0b_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	Pyridoxine 5'-phoshate oxidase (PNP oxidase)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PNP-oxidase like	8029702	4002129	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-binding split barrel	8042081	3000856	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	FMN-binding split barrel	8042081	3000856	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Putative_PNPOx	e1ci0A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Putative_PNPOx	ECOD (1.6)
B	Putative_PNPOx	e1ci0B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Putative_PNPOx	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
B	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF10590	Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region (PNP_phzG_C)	Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region	This domain represents one of the two dimerisation regions of the protein, located at the edge of the dimer interface, at the C-terminus, being the last three beta strands, S6, S7, and S8 along with the last three residues to the end. In Swiss:P21159 ...	This domain represents one of the two dimerisation regions of the protein, located at the edge of the dimer interface, at the C-terminus, being the last three beta strands, S6, S7, and S8 along with the last three residues to the end. In Swiss:P21159, S6 runs from residues 178-192, S7 from 200-206 and S8 from 211-215. the extended loop, of residues 167-177 may well be involved in the pocket formed between the two dimers that positions the FMN molecule [1].To date, the only time functional oxidase or phenazine biosynthesis activities have been experimentally demonstrated is when the sequences contain both Pfam:PF01243 and Pfam:PF10590. It is unknown the role performed by each domain in bringing about molecular functions of either oxidase or phenazine activity [2].	Domain
A, B	PF01243	Pyridoxamine 5'-phosphate oxidase (PNPOx_N)	Pyridoxamine 5'-phosphate oxidase	This entry includes pyridoxamine 5'-phosphate oxidases, FMN flavoproteins that catalyse the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This reaction serves as the terminal step in the de novo biosynthesis of ...	This entry includes pyridoxamine 5'-phosphate oxidases, FMN flavoproteins that catalyse the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This reaction serves as the terminal step in the de novo biosynthesis of PLP in Escherichia coli and as a part of the salvage pathway of this coenzyme in both E. coli and mammalian cells [1-5]. The binding sites for FMN and for substrate have been highly conserved throughout evolution. In some species, the coenzyme F420 may perform the FMN role [7]. This entry represents the N-terminal segment of these proteins, which is involved in FMN binding when they form the dimer [5]. In human PNPO, it has been shown that this region contains some of the residues that constitute the PLP allosteric site which regulates its activity [4]. The C-terminal region of these proteins (Pfam:PF10590) is involved in dimerisation and also contributes some residues to the PLP allosteric site. Some of the members included in this entry are involved in phenazine biosynthesis [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PROTEIN (PNP OXIDASE)	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor pyridoxamine phosphate oxidase activity FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor pyridoxamine phosphate oxidase activity catalytic activity	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process small molecule metabolic process metabolic process cellular process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process small molecule metabolic process metabolic process cellular process water-soluble vitamin metabolic process aldehyde biosynthetic process metabolic compound salvage pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process aldehyde metabolic process pyridoxal 5'-phosphate salvage organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate metabolic process	membrane-bounded organelle intracellular anatomical structure mitochondrial intermembrane space mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle envelope lumen intracellular organelle organelle envelope cellular anatomical structure organelle lumen organelle mitochondrial envelope membrane-bounded organelle intracellular anatomical structure mitochondrial intermembrane space mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle envelope lumen intracellular organelle organelle envelope cellular anatomical structure organelle lumen organelle mitochondrial envelope cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019740	Pyridoxamine 5'-phosphate oxidase, conserved site	Conserved Site
A, B	IPR012349	FMN-binding split barrel	Homologous Superfamily
A, B	IPR011576	Pyridoxamine 5'-phosphate oxidase, N-terminal	Domain
A, B	IPR019576	Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal	Domain
A, B	IPR000659	Pyridoxamine 5'-phosphate oxidase	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.