› 4ivm

X-ray diffraction
2.77Å resolution

Structure of human protoporphyrinogen IX oxidase(R59G)

Released:
DOI: 10.2210/pdb4ivm/pdb
PDB entry 4ivm coloured by chain, front view.
PDB entry 4ivm coloured by chain, side view.
PDB entry 4ivm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Quantitative structural insight into human variegate porphyria disease.
Wang B, Wen X, Qin X, Wang Z, Tan Y, Shen Y, Xi Z
J Biol Chem 288 11731-40 (2013)
PMID: 23467411

Function and Biology Details

Reaction catalysed: 
Protoporphyrinogen-IX + 3 O(2) = protoporphyrin-IX + 3 H(2)O(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-156166 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protoporphyrinogen oxidase Chain: B
Molecule details ›
Chain: B
Length: 483 amino acids
Theoretical weight: 51.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P50336 (Residues: 1-477; Coverage: 100%)
Gene name: PPOX
Sequence domains: Flavin containing amine oxidoreductase
Structure domains: FAD/NAD(P)-binding domain

Ligands and Environments


Cofactor: Ligand FAD 1 x FAD
2 bound ligands:
Ligand ACJ 1 x ACJ
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: R32
Unit cell:
a: 136.098Å b: 136.098Å c: 158.361Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.173 0.24
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

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

2 mentions without citation

Quantitative structural insight into human variegate porphyria disease.
Wang et al. (2013)
1 more