› 1sez

X-ray diffraction
2.9Å resolution

Crystal Structure of Protoporphyrinogen IX Oxidase

Released:
DOI: 10.2210/pdb1sez/pdb
PDB entry 1sez coloured by chain, front view.
PDB entry 1sez coloured by chain, side view.
PDB entry 1sez coloured by chain, top view.
Source organism: Nicotiana tabacum
Primary publication:
Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis.
Koch M, Breithaupt C, Kiefersauer R, Freigang J, Huber R, Messerschmidt A
EMBO J 23 1720-8 (2004)
PMID: 15057273

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 domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-518763 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protoporphyrinogen oxidase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 504 amino acids
Theoretical weight: 55.9 KDa
Source organism: Nicotiana tabacum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O24164 (Residues: 1-504; Coverage: 100%)
Gene names: PPOX2, PPXII
Sequence domains: Flavin containing amine oxidoreductase
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 2 x FAD
2 bound ligands:
Ligand OMN 2 x OMN
Ligand TON 2 x TON
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2221
Unit cell:
a: 119.09Å b: 147.25Å c: 127.04Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.267 0.227 0.293
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

35 review citations

Evolution in action: plants resistant to herbicides.
Powles et al. (2010)
34 more

17 mentions without citation

Making and breaking heme.
Celis et al. (2019)
16 more