› 6ylz

X-ray diffraction
1.56Å resolution

X-ray structure of the K72I,Y129F,R133L, H199A quadruple mutant of PNP-oxidase from E. coli

Released:
DOI: 10.2210/pdb6ylz/pdb
PDB entry 6ylz coloured by chain, front view.
PDB entry 6ylz coloured by chain, side view.
PDB entry 6ylz coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Identification and characterization of the pyridoxal 5'-phosphate allosteric site in Escherichia coli pyridoxine 5'-phosphate oxidase.
Barile A, Battista T, Fiorillo A, di Salvo ML, Malatesta F, Tramonti A, Ilari A, Contestabile R
J Biol Chem 296 100795
PMID: 34019876

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 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 Chain: AAA
Molecule details ›
Chain: AAA
Length: 218 amino acids
Theoretical weight: 25.44 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AFI7 (Residues: 1-218; Coverage: 100%)
Gene names: JW1630, b1638, pdxH
Sequence domains:

Ligands and Environments


Cofactor: Ligand FMN 1 x FMN
2 bound ligands:
Ligand SO4 2 x SO4
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P3121
Unit cell:
a: 63.776Å b: 63.776Å c: 124.727Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.172 0.171 0.202
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Elucidating the Interaction between Pyridoxine 5'-Phosphate Oxidase and Dopa Decarboxylase: Activation of B6-Dependent Enzyme.
Al Mughram et al. (2022)
1 more

1 mention without citation

Identification and characterization of the pyridoxal 5'-phosphate allosteric site in Escherichia coli pyridoxine 5'-phosphate oxidase.
Barile et al. (2021)