› 2ivd

X-ray diffraction
2.3Å resolution

Structure of protoporphyrinogen oxidase from Myxococcus xanthus with acifluorfen

Released:
DOI: 10.2210/pdb2ivd/pdb
PDB entry 2ivd coloured by chain, front view.
PDB entry 2ivd coloured by chain, side view.
PDB entry 2ivd coloured by chain, top view.
Source organism: Myxococcus xanthus
Primary publication:
Crystal structure of protoporphyrinogen oxidase from Myxococcus xanthus and its complex with the inhibitor acifluorfen.
Corradi HR, Corrigall AV, Boix E, Mohan CG, Sturrock ED, Meissner PN, Acharya KR
J Biol Chem 281 38625-33 (2006)
PMID: 17046834

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

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157500 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protoporphyrinogen oxidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 478 amino acids
Theoretical weight: 50.4 KDa
Source organism: Myxococcus xanthus
Expression system: Escherichia coli
UniProt:
  • Canonical: P56601 (Residues: 2-471; Coverage: 100%)
Gene names: hemY, pgoX
Sequence domains: Flavin containing amine oxidoreductase
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 2 x FAD
3 bound ligands:
Ligand ACJ 2 x ACJ
Ligand GOL 5 x GOL
Ligand TWN 1 x TWN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX14.1
Spacegroup: P4212
Unit cell:
a: 148.918Å b: 148.918Å c: 131.924Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.234 0.283
Expression system: Escherichia coli

Quick links

Citations

10 review citations

The biochemistry of heme biosynthesis.
Heinemann et al. (2008)
9 more

6 mentions without citation

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product.
Dailey et al. (2017)
5 more