› 1wv4

X-ray diffraction
2.6Å resolution

X-ray Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in tetragonal crystal form

Released:
DOI: 10.2210/pdb1wv4/pdb
PDB entry 1wv4 coloured by chain, front view.
PDB entry 1wv4 coloured by chain, side view.
PDB entry 1wv4 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme.
Safo MK, Musayev FN, Schirch V
Acta Crystallogr D Biol Crystallogr 61 599-604 (2005)
PMID: 15858270

Function and Biology Details

Reaction catalysed: 
Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142729 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxine/pyridoxamine 5'-phosphate oxidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 218 amino acids
Theoretical weight: 25.59 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AFI7 (Residues: 1-218; Coverage: 100%)
Gene names: JW1630, b1638, pdxH
Sequence domains:
Structure domains: Electron Transport, Fmn-binding Protein; Chain A

Ligands and Environments


Cofactor: Ligand FMN 2 x FMN
1 bound ligand:
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P41
Unit cell:
a: 54.42Å b: 54.42Å c: 164.42Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.258 0.242 0.29
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Vitamin B₆ and Its Role in Cell Metabolism and Physiology.
Parra et al. (2018)
1 more

1 mention without citation

Experimental Evidence for a Revision in the Annotation of Putative Pyridoxamine 5'-Phosphate Oxidases P(N/M)P from Fungi.
Domitrovic et al. (2015)