› 6ymh

X-ray diffraction
2.42Å resolution

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

Released:
DOI: 10.2210/pdb6ymh/pdb
PDB entry 6ymh coloured by chain, front view.
PDB entry 6ymh coloured by chain, side view.
PDB entry 6ymh 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 Chains: AAA, BBB
Molecule details ›
Chains: AAA, BBB
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 2 x FMN
2 bound ligands:
Ligand SO4 1 x SO4
Ligand PLP 1 x PLP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P61
Unit cell:
a: 54.164Å b: 54.164Å c: 271.968Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.193 0.19 0.259
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Protein engineering and iterative multimodule optimization for vitamin B6 production in Escherichia coli.
Liu et al. (2023)

2 mentions without citation

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