› 6mp8

X-ray diffraction
1.89Å resolution

X-ray crystal structure of VioC bound to Fe(II), D-arginine, and 2-oxoglutarate

Released:
DOI: 10.2210/pdb6mp8/pdb
PDB entry 6mp8 coloured by chain, front view.
PDB entry 6mp8 coloured by chain, side view.
PDB entry 6mp8 coloured by chain, top view.
Source organism: Streptomyces vinaceus
Primary publication:
α-Amine Desaturation of d-Arginine by the Iron(II)- and 2-(Oxo)glutarate-Dependent l-Arginine 3-Hydroxylase, VioC.
Dunham NP, Mitchell AJ, Del Río Pantoja JM, Krebs C, Bollinger JM, Boal AK
Biochemistry 57 6479-6488 (2018)
PMID: 30403469

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180510 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-ketoglutarate-dependent L-arginine hydroxylase Chain: A
Molecule details ›
Chain: A
Length: 338 amino acids
Theoretical weight: 37.49 KDa
Source organism: Streptomyces vinaceus
UniProt:
  • Canonical: Q6WZB0 (Residues: 21-358; Coverage: 94%)
Gene name: vioC
Sequence domains: Taurine catabolism dioxygenase TauD, TfdA family
Structure domains: Clavaminate synthase-like

Ligands and Environments

3 bound ligands:
Ligand AKG 1 x AKG
Ligand FE2 1 x FE2
Ligand DAR 1 x DAR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: C2
Unit cell:
a: 79.957Å b: 67.039Å c: 62.13Å
α: 90° β: 108.15° γ: 90°
R-values:
R R work R free
0.222 0.22 0.256

Quick links

Citations

8 citation in other articles

A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases.
Rajakovich et al. (2019)
7 more