4NBB: Carbazole- And Oxygen-bound Oxygenase With Ile262 Replaced By Val And Ferredoxin Complex Of Carbazole 1,9a-dioxygenase

Carbazole 1,9a-dioxygenase (CARDO), a Rieske non-heme iron oxygenase (RO), is a three-component system composed of terminal oxygenase (Oxy), ferredoxin, and ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy gene from Janthinobacterium sp. strain J3 generated the Oxy derivatives I262V, F275W, Q282N and Q282Y, which showed different oxygenation capabilities than the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. I262V, F275W, and Q282Y catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15 degrees , 25 degrees , and 25 degrees , respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and imino nitrogen of carbazole. In the crystal structure of F275W complexed with fluorene, C9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate binding position that in turn favors specific oxygenation reactions toward various substrates.
PDB ID: 4NBBDownload
MMDB ID: 118628
PDB Deposition Date: 2013/10/23
Updated in MMDB: 2014/03
Experimental Method:
x-ray diffraction
Resolution: 2.05  Å
Source Organism:
Janthinobacterium sp. J3
Similar Structures:
Biological Unit for 4NBB: hexameric; determined by author
Molecular Components in 4NBB
Label Count Molecule
Proteins (6 molecules)
Terminal Oxygenase Component of Carbazole
Molecule annotation
Ferredoxin Carac(Gene symbol: carAc)
Molecule annotation
Chemicals (14 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB