2BOY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2006.05.046

  • 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 catech ...

    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.


    Related Citations: 
    • Preliminary Crystallographic Analysis of 3-Chlorocatechol 1,2 Dioxygenase of a New Modified Ortho-Patway from the Gram Positive Rhodococcus Opacus 1Cp Grown on 2-Chlorophenol
      Ferraroni, M.,Ruiz Tarifa, M.Y.,Scozzafava, A.,Solyanikova, I.P.,Kolomytseva, M.P.,Golovleva, L.A.,Briganti, F.
      (2003) Acta Crystallogr.,Sect.D 59: 188


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-CHLOROCATECHOL 1,2-DIOXYGENASE
A, B, C, D, E, F, G, H
254Rhodococcus opacusMutation(s): 0 
Gene Names: clcA2 (clcA3)
EC: 1.13.11.1
Find proteins for Q8G9L3 (Rhodococcus opacus)
Go to UniProtKB:  Q8G9L3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
LPP
Query on LPP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE; L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT; 3-SN-PHOSPHATIDIC ACID; 1,2-DIPALMITOYLDISODIUM SALT
C35 H69 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-N
 Ligand Interaction
BHO
Query on BHO

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
BENZHYDROXAMIC ACID
C7 H7 N O2
VDEUYMSGMPQMIK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 83.179α = 85.37
b = 86.610β = 66.53
c = 93.447γ = 76.94
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-06-06
    Type: Data collection, Database references, Derived calculations
  • Version 1.4: 2018-12-19
    Type: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-05-08
    Type: Data collection, Experimental preparation
  • Version 1.6: 2019-05-29
    Type: Data collection, Other