› 6alo

X-ray diffraction
1.79Å resolution

VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and a peroxysuccinate intermediate

Released:
DOI: 10.2210/pdb6alo/pdb
PDB entry 6alo coloured by chain, front view.
PDB entry 6alo coloured by chain, side view.
PDB entry 6alo coloured by chain, top view.
Source organism: Streptomyces vinaceus
Primary publication:
Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase.
Mitchell AJ, Dunham NP, Martinie RJ, Bergman JA, Pollock CJ, Hu K, Allen BD, Chang WC, Silakov A, Bollinger JM, Krebs C, Boal AK
J Am Chem Soc 139 13830-13836 (2017)
PMID: 28823155

Function and Biology Details

Reaction catalysed: 
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180511 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-ketoglutarate-dependent L-arginine hydroxylase Chain: A
Molecule details ›
Chain: A
Length: 394 amino acids
Theoretical weight: 43.31 KDa
Source organism: Streptomyces vinaceus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6WZB0 (Residues: 1-358; Coverage: 100%)
Gene name: vioC
Sequence domains: Taurine catabolism dioxygenase TauD, TfdA family
Structure domains: Clavaminate synthase-like

Ligands and Environments

3 bound ligands:
Ligand FE2 1 x FE2
Ligand ARG 1 x ARG
Ligand OKG 1 x OKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: C2
Unit cell:
a: 80.76Å b: 66.653Å c: 62.889Å
α: 90° β: 109.21° γ: 90°
R-values:
R R work R free
0.177 0.175 0.203
Expression system: Escherichia coli

Quick links

Citations

9 review citations

2-Oxoglutarate-Dependent Oxygenases.
Islam et al. (2018)
8 more