› 3hy8

X-ray diffraction
2.5Å resolution

Crystal Structure of Human Pyridoxine 5'-Phosphate Oxidase R229W Mutant

Released:
DOI: 10.2210/pdb3hy8/pdb
PDB entry 3hy8 coloured by chain, front view.
PDB entry 3hy8 coloured by chain, side view.
PDB entry 3hy8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder.
Musayev FN, Di Salvo ML, Saavedra MA, Contestabile R, Ghatge MS, Haynes A, Schirch V, Safo MK
J Biol Chem 284 30949-56 (2009)
PMID: 19759001

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-192639 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxine-5'-phosphate oxidase Chain: A
Molecule details ›
Chain: A
Length: 261 amino acids
Theoretical weight: 30.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NVS9 (Residues: 1-261; Coverage: 100%)
Gene name: PNPO
Sequence domains:
Structure domains: Electron Transport, Fmn-binding Protein; Chain A

Ligands and Environments


Cofactor: Ligand FMN 1 x FMN
2 bound ligands:
Ligand PLP 1 x PLP
Ligand PO4 3 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P3121
Unit cell:
a: 82.27Å b: 82.27Å c: 58.788Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.229 0.226 0.287
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Molecular mechanisms of disease-causing missense mutations.
Stefl et al. (2013)
4 more

4 mentions without citation

Site-selective lysine conjugation methods and applications towards antibody-drug conjugates.
Haque et al. (2021)
3 more