Terminal oxygenase of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Specific Interactions between the ferredoxin and terminal oxygenase components of a class IIB Rieske nonheme iron oxygenase, carbazole 1,9a-dioxygenase.

Inoue, K.Ashikawa, Y.Umeda, T.Abo, M.Katsuki, J.Usami, Y.Noguchi, H.Fujimoto, Z.Terada, T.Yamane, H.Nojiri, H.

(2009) J Mol Biol 392: 436-451

  • DOI: https://doi.org/10.1016/j.jmb.2009.07.029
  • Primary Citation of Related Structures:  
    3GCE, 3GCF

  • PubMed Abstract: 

    Carbazole 1,9a-dioxygenase (CARDO) consists of terminal oxygenase (Oxy), ferredoxin (Fd), and ferredoxin reductase (Red) components and is a member of the Rieske nonheme iron oxygenases. Rieske nonheme iron oxygenases are divided into five subclasses (IA, IB, IIA, IIB, and III) based on the number of constituents and the nature of their redox centers. Each component of a class IIB CARDO from Nocardioides aromaticivorans IC177 was purified, and the interchangeability of the electron transfer reactions with each component from the class III CARDOs was investigated. Despite the fact that the Fds of both classes are Rieske-type, strict specificities between the Oxy and Fd components were observed. On the other hand, the Fd and Red components were interchangeable, even though the Red components differ in cofactor composition; the class IIB Red contains flavin-adenine-dinucleotide (FAD)- and NADH-binding domains, whereas the class III Red has a chloroplast-type [2Fe-2S] cluster in addition to the FAD- and NADH-binding domains. The crystal structures of the class IIB Oxy and Fd components were compared to the previously reported Fd:Oxy complex structure of class III CARDO. This comparison suggested residues in common between class IIB and class III CARDOs that are important for interactions between Fd and Oxy. In the class IIB CARDOs, these included His75 and Glu71 in Fd and Lys20 and Glu357 in Oxy for electrostatic interactions, and Phe74 and Pro90 in Fd and Trp21, Leu359, and Val367 in Oxy for hydrophobic interactions. The residues that formed the interacting surface but were not conserved between classes were thought to be necessary to form the appropriate geometry and to determine electron transfer specificity between Fd and Oxy.

  • Organizational Affiliation

    Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Terminal oxygenase component of carbazole 1,9a-dioxygenase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
394Nocardioides aromaticivoransMutation(s): 0 
Gene Names: carAa
Find proteins for Q2HWI0 (Nocardioides aromaticivorans)
Explore Q2HWI0 
Go to UniProtKB:  Q2HWI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2HWI0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FES

Download Ideal Coordinates CCD File 
AA [auth C]
BB [auth J]
EA [auth D]
FB [auth K]
IA [auth E]
AA [auth C],
BB [auth J],
EA [auth D],
FB [auth K],
IA [auth E],
JB [auth L],
NA [auth F],
NB [auth M],
Q [auth A],
RA [auth G],
SB [auth N],
UA [auth H],
V [auth B],
YA [auth I],
YB [auth O]
Fe2 S2
Query on FE2

Download Ideal Coordinates CCD File 
AB [auth J]
DA [auth D]
EB [auth K]
HA [auth E]
IB [auth L]
AB [auth J],
DA [auth D],
EB [auth K],
HA [auth E],
IB [auth L],
MA [auth F],
MB [auth M],
P [auth A],
QA [auth G],
RB [auth N],
TA [auth H],
U [auth B],
XA [auth I],
XB [auth O],
Z [auth C]
Query on CL

Download Ideal Coordinates CCD File 
AC [auth O]
BA [auth C]
CA [auth C]
CB [auth J]
DB [auth J]
AC [auth O],
BA [auth C],
CA [auth C],
CB [auth J],
DB [auth J],
FA [auth D],
GA [auth D],
GB [auth K],
HB [auth K],
JA [auth E],
KA [auth E],
KB [auth L],
LA [auth E],
LB [auth L],
OA [auth F],
OB [auth M],
PA [auth F],
PB [auth M],
QB [auth M],
R [auth A],
S [auth A],
SA [auth G],
T [auth A],
TB [auth N],
UB [auth N],
VA [auth H],
VB [auth N],
W [auth B],
WA [auth H],
WB [auth N],
X [auth B],
Y [auth B],
ZA [auth I],
ZB [auth O]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 280.002α = 90
b = 161.661β = 118.65
c = 194.665γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance