1G79

X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1g79a_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	Pyridoxine 5'-phoshate oxidase (PNP oxidase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FMN-binding split barrel	8042082	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	e1g79A1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	PYRIDOXINE 5'-PHOSPHATE OXIDASE	oxidoreductase activity catalytic activity FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphate ion binding identical protein binding oxidoreductase activity catalytic activity FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphate ion binding identical protein binding protein binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding riboflavin binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor pyridoxamine phosphate oxidase activity	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process phosphorus metabolic process water-soluble vitamin metabolic process pyridoxal phosphate metabolic process pyridoxine biosynthetic process pyridoxine metabolic process 'de novo' pyridoxal 5'-phosphate biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	pyridoxal 5'-phosphate synthase M-CSA #677	Escherichia coli pyridoxine 5'-phosphate oxidase is the enzyme catalysing the final step in the synthesis of pyridoxal 5'-phosphate, a vital cofactor in many metabolic processes including amino acid metabolism. This means that the synthetic pathway is of great importance to the survival of the bacteria. The enzyme is also present in higher organisms, and the Escherichia coli form is expected to show significant sequence and structural homology to the mammalian form. Of particular interest is the second binding site of PLP which protects the product of the reaction from release into the cell so it can be transferred directly onto the enzymes that require it.	Defined by 1 residue: ARG:A-197 \| Explore in 3D: M-CSA Motif Definition At least 2 residues must be present to support Structure Motif searching. EC: 1.4.3.5 (PDB Primary Data)

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.