Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodococcus Opacus 1CP

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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This is version 1.7 of the entry. See complete history


Crystal structure of 3-chlorocatechol 1,2-dioxygenase key enzyme of a new modified ortho-pathway from the Gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol.

Ferraroni, M.Kolomytseva, M.P.Solyanikova, I.P.Scozzafava, A.Golovleva, L.A.Briganti, F.

(2006) J Mol Biol 360: 788-799

  • DOI: https://doi.org/10.1016/j.jmb.2006.05.046
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the 3-chlorocatechol 1,2-dioxygenase from the Gram-positive bacterium Rhodococcus opacus (erythropolis) 1CP, a Fe(III) ion-containing enzyme specialized in the aerobic biodegradation of 3-chloro- and methyl-substituted catechols, has been solved by molecular replacement techniques using the coordinates of 4-chlorocatechol 1,2-dioxygenase from the same organism (PDB code 1S9A) as a starting model and refined at 1.9 A resolution (R(free) 21.9%; R-factor 17.4%). The analysis of the structure and of the kinetic parameters for a series of different substrates, and the comparison with the corresponding data for the 4-chlorocatechol 1,2-dioxygenase isolated from the same bacterial strain, provides evidence of which active site residues are responsible for the observed differences in substrate specificity. Among the amino acid residues expected to interact with substrates, only three are altered Val53(Ala53), Tyr78(Phe78) and Ala221(Cys224) (3-chlorocatechol 1,2-dioxygenase(4-chlorocatechol 1,2-dioxygenase)), clearly identifying the substitutions influencing substrate selectivity in these enzymes. The crystallographic asymmetric unit contains eight subunits (corresponding to four dimers) that show heterogeneity in the conformation of a co-crystallized molecule bound to the catalytic non-heme iron(III) ion resembling a benzohydroxamate moiety, probably a result of the breakdown of recently discovered siderophores synthesized by Gram-positive bacteria. Several different modes of binding benzohydroxamate into the active site induce distinct conformations of the interacting protein ligands Tyr167 and Arg188, illustrating the plasticity of the active site origin of the more promiscuous substrate preferences of the present enzyme.

  • Organizational Affiliation

    Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H
254Rhodococcus opacusMutation(s): 0 
Find proteins for Q8G9L3 (Rhodococcus opacus)
Explore Q8G9L3 
Go to UniProtKB:  Q8G9L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8G9L3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LPP

Download Ideal Coordinates CCD File 
CA [auth D]
HA [auth E]
K [auth A]
LA [auth F]
P [auth B]
CA [auth D],
HA [auth E],
K [auth A],
LA [auth F],
P [auth B],
PA [auth G],
TA [auth H],
V [auth C]
C35 H69 O8 P
Query on BHO

Download Ideal Coordinates CCD File 
BA [auth D]
GA [auth E]
J [auth A]
KA [auth F]
O [auth B]
BA [auth D],
GA [auth E],
J [auth A],
KA [auth F],
O [auth B],
OA [auth G],
SA [auth H],
U [auth C]
C7 H7 N O2
Query on FE

Download Ideal Coordinates CCD File 
AA [auth D]
FA [auth E]
I [auth A]
JA [auth F]
N [auth B]
AA [auth D],
FA [auth E],
I [auth A],
JA [auth F],
N [auth B],
NA [auth G],
RA [auth H],
T [auth C]
Query on MG

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
IA [auth E]
L [auth A]
M [auth A]
DA [auth D],
EA [auth D],
IA [auth E],
L [auth A],
M [auth A],
MA [auth F],
Q [auth B],
QA [auth G],
R [auth B],
S [auth B],
UA [auth H],
VA [auth H],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.179α = 85.37
b = 86.61β = 66.53
c = 93.447γ = 76.94
Software Package:
Software NamePurpose
DENZOdata 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: 2006-08-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-06-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2018-12-19
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2019-05-29
    Changes: Data collection, Other
  • Version 1.7: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description