4NBB

Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Non-heme Iron Oxygenase, Carbazole 1,9a-Dioxygenase

Inoue, K.Usami, Y.Ashikawa, Y.Noguchi, H.Umeda, T.Yamagami-Ashikawa, A.Horisaki, T.Uchimura, H.Terada, T.Nakamura, S.Shimizu, K.Habe, H.Yamane, H.Fujimoto, Z.Nojiri, H.

(2014) Appl.Environ.Microbiol. --: --

  • DOI: 10.1128/AEM.04000-13
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Carbazole 1,9a-dioxygenase (CARDO), a Rieske nonheme iron oxygenase (RO), is a three-component system composed of a terminal oxygenase (Oxy), ferredoxin, and a ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously ...

    Carbazole 1,9a-dioxygenase (CARDO), a Rieske nonheme iron oxygenase (RO), is a three-component system composed of a terminal oxygenase (Oxy), ferredoxin, and a ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy-encoding gene from Janthinobacterium sp. strain J3 generated the I262V, F275W, Q282N, and Q282Y Oxy derivatives, which showed oxygenation capabilities different from those of 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. The I262V, F275W, and Q282Y derivatives 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, 25, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and the imino nitrogen of carbazole. In the crystal structure of the F275W derivative complexed with fluorene, C-9 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.


    Organizational Affiliation

    Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Terminal oxygenase component of carbazole
A, B, C
392Janthinobacterium sp. (strain J3)Mutation(s): 1 
Gene Names: carAa
Find proteins for Q84II6 (Janthinobacterium sp. (strain J3))
Go to UniProtKB:  Q84II6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ferredoxin CarAc
D, E, F
115Pseudomonas resinovoransMutation(s): 0 
Gene Names: carAc
Find proteins for Q8GI16 (Pseudomonas resinovorans)
Go to UniProtKB:  Q8GI16
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B, C
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
9CA
Query on 9CA

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Download CCD File 
B, C
9H-CARBAZOLE
C12 H9 N
UJOBWOGCFQCDNV-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
A, B, C, D, E, F
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

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Download CCD File 
A, B, C
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 98.424α = 90.00
b = 90.083β = 104.26
c = 105.324γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
HKL-2000data scaling
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release