› 6daw

X-ray diffraction
2.1Å resolution

X-ray crystal structure of NapI L-arginine desaturase bound to Fe(II), L-arginine, and acetate

Released:
DOI: 10.2210/pdb6daw/pdb
PDB entry 6daw coloured by chain, front view.
PDB entry 6daw coloured by chain, side view.
PDB entry 6daw coloured by chain, top view.
Source organism: Streptomyces lusitanus
Primary publication:
Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of α-Heteroatom Assistance.
Dunham NP, Chang WC, Mitchell AJ, Martinie RJ, Zhang B, Bergman JA, Rajakovich LJ, Wang B, Silakov A, Krebs C, Boal AK, Bollinger JM
J Am Chem Soc 140 7116-7126 (2018)
PMID: 29708749

Function and Biology Details

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-579437 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
TauD/TfdA-like domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 342 amino acids
Theoretical weight: 38.25 KDa
Source organism: Streptomyces lusitanus
Expression system: Escherichia coli
UniProt:
  • Canonical: S4TL40 (Residues: 1-334; Coverage: 100%)
Sequence domains: Taurine catabolism dioxygenase TauD, TfdA family
Structure domains: Clavaminate synthase-like

Ligands and Environments

3 bound ligands:
Ligand FE2 2 x FE2
Ligand ARG 2 x ARG
Ligand ACT 4 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P62
Unit cell:
a: 121.631Å b: 121.631Å c: 82.054Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.203 0.248
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Reinvigorating the Chiral Pool: Chemoenzymatic Approaches to Complex Peptides and Terpenoids.
Stout et al. (2021)
5 more

3 mentions without citation

Catalytic divergencies in the mechanism of L-arginine hydroxylating nonheme iron enzymes.
Ali et al. (2024)
2 more