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› 4m25

X-ray diffraction
1.84Å resolution

Crystal structure of non-heme iron oxygenase OrfP in complex with Fe and alpha-ketoglutaric acid

Released:
DOI: 10.2210/pdb4m25/pdb
Model geometry
Fit model/data
PDB entry 4m25 coloured by chain, front view.
PDB entry 4m25 coloured by chain, side view.
PDB entry 4m25 coloured by chain, top view.
Source organism: Streptomyces lavendulae subsp. lavendulae
Primary publication:
Biosynthesis of streptolidine involved two unexpected intermediates produced by a dihydroxylase and a cyclase through unusual mechanisms.
Chang CY, Lyu SY, Liu YC, Hsu NS, Wu CC, Tang CF, Lin KH, Ho JY, Wu CJ, Tsai MD, Li TL
Angew Chem Int Ed Engl 53 1943-8 (2014)
PMID: 24505011

Function and Biology Details

Reaction catalysed: 
L-arginine + 2-oxoglutarate + O2 = (2S,3S)-hydroxyarginine + succinate +CO2.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124683 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
TauD/TfdA-like domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 364 amino acids
Theoretical weight: 41.19 KDa
Source organism: Streptomyces lavendulae subsp. lavendulae
Expression system: Escherichia coli
UniProt:
  • Canonical: G9MBV2 (Residues: 1-344; Coverage: 100%)
Gene names: SLAV_37395, vioC
Sequence domains: Taurine catabolism dioxygenase TauD, TfdA family
Structure domains: Clavaminate synthase-like

Ligands and Environments

2 bound ligands:
Ligand FE 8 x FE
Ligand AKG 4 x AKG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSRRC BEAMLINE BL13C1
Spacegroup: P21
Unit cell:
a: 68.205Å b: 117.262Å c: 96.556Å
α: 90° β: 91.86° γ: 90°
R-values:
R R work R free
0.196 0.194 0.232
Expression system: Escherichia coli

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Citations

6 review citations

Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants.
Kal et al. (2017)
5 more