3VMI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insight into the substrate- and dioxygenbinding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9adioxygenase

Ashikawa, Y.Fujimoto, Z.Usami, Y.Inoue, K.Noguchi, H.Yamane, H.Nojiri, H.

(2012) BMC Struct Biol 12: 15-15

  • DOI: https://doi.org/10.1186/1472-6807-12-15
  • Primary Citation of Related Structures:  
    3VMG, 3VMH, 3VMI

  • PubMed Abstract: 

    Dihydroxylation of tandemly linked aromatic carbons in a cis-configuration, catalyzed by multicomponent oxygenase systems known as Rieske nonheme iron oxygenase systems (ROs), often constitute the initial step of aerobic degradation pathways for various aromatic compounds. Because such RO reactions inherently govern whether downstream degradation processes occur, novel oxygenation mechanisms involving oxygenase components of ROs (RO-Os) is of great interest. Despite substantial progress in structural and physicochemical analyses, no consensus exists on the chemical steps in the catalytic cycles of ROs. Thus, determining whether conformational changes at the active site of RO-O occur by substrate and/or oxygen binding is important. Carbazole 1,9a-dioxygenase (CARDO), a RO member consists of catalytic terminal oxygenase (CARDO-O), ferredoxin (CARDO-F), and ferredoxin reductase. We have succeeded in determining the crystal structures of oxidized CARDO-O, oxidized CARDO-F, and both oxidized and reduced forms of the CARDO-O: CARDO-F binary complex.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Terminal oxygenase component of carbazole
A, B, C
392Janthinobacterium sp. J3Mutation(s): 0 
Gene Names: carAa
EC: 1.14.12.22
UniProt
Find proteins for Q84II6 (Janthinobacterium sp. (strain J3))
Explore Q84II6 
Go to UniProtKB:  Q84II6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84II6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin component of carbazole
D, E, F
115Pseudomonas resinovoransMutation(s): 0 
Gene Names: carAc
EC: 1.14.12.22
UniProt
Find proteins for Q8GI16 (Pseudomonas resinovorans)
Explore Q8GI16 
Go to UniProtKB:  Q8GI16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GI16
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
O [auth C]
R [auth D]
S [auth E]
H [auth A],
K [auth B],
O [auth C],
R [auth D],
S [auth E],
T [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
9CA
Query on 9CA

Download Ideal Coordinates CCD File 
M [auth B],
Q [auth C]
9H-CARBAZOLE
C12 H9 N
UJOBWOGCFQCDNV-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
OXY
Query on OXY

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
P [auth C]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.012α = 90
b = 89.611β = 104.18
c = 104.82γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description