› 3vmi

X-ray diffraction
2Å resolution

Carbazole- and oxygen-bound complex between oxygenase and ferredoxin in carbazole 1,9a-dioxygenase

Released:
DOI: 10.2210/pdb3vmi/pdb
PDB entry 3vmi coloured by chain, front view.
PDB entry 3vmi coloured by chain, side view.
PDB entry 3vmi coloured by chain, top view.
Source organisms:
Primary publication:
Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase.
Ashikawa Y, Fujimoto Z, Usami Y, Inoue K, Noguchi H, Yamane H, Nojiri H
BMC Struct Biol 12 15 (2012)
PMID: 22727022

Function and Biology Details

Reaction catalysed: 
9H-carbazole + NAD(P)H + O(2) = 2'-aminobiphenyl-2,3-diol + NAD(P)(+)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183053 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Rieske domain-containing protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 392 amino acids
Theoretical weight: 44.91 KDa
Source organism: Janthinobacterium sp. J3
Expression system: Escherichia coli
UniProt:
  • Canonical: Q84II6 (Residues: 1-384; Coverage: 100%)
Gene name: carAa
Sequence domains:
Structure domains:
Ferredoxin CarAc Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 115 amino acids
Theoretical weight: 12.45 KDa
Source organism: Pseudomonas resinovorans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8GI16 (Residues: 1-107; Coverage: 100%)
Gene name: carAc
Sequence domains: Rieske [2Fe-2S] domain
Structure domains: Rieske [2Fe-2S] iron-sulphur domain

Ligands and Environments

4 bound ligands:
Ligand FE2 3 x FE2
Ligand FES 6 x FES
Ligand OXY 3 x OXY
Ligand 9CA 2 x 9CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 98.012Å b: 89.611Å c: 104.82Å
α: 90° β: 104.18° γ: 90°
R-values:
R R work R free
0.205 0.205 0.24
Expression system: Escherichia coli

Quick links

Citations

3 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)
2 more

5 mentions without citation

Carbon-fluorine bond cleavage mediated by metalloenzymes.
Wang et al. (2020)
4 more