3O5U

Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex with protocatechuate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

X-ray structures of 4-chlorocatechol 1,2-dioxygenase adducts with substituted catechols: new perspectives in the molecular basis of intradiol ring cleaving dioxygenases specificity.

Ferraroni, M.Kolomytseva, M.Scozzafava, A.Golovleva, L.Briganti, F.

(2013) J. Struct. Biol. 181: 274-282

  • DOI: 10.1016/j.jsb.2012.11.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystallographic structures of 4-chlorocatechol 1,2-dioxygenase (4-CCD) complexes with 3,5-dichlorocatechol, protocatechuate (3,4-dihydroxybenzoate), hydroxyquinol (benzen-1,2,4-triol) and pyrogallol (benzen-1,2,3-triol), which act as substrates ...

    The crystallographic structures of 4-chlorocatechol 1,2-dioxygenase (4-CCD) complexes with 3,5-dichlorocatechol, protocatechuate (3,4-dihydroxybenzoate), hydroxyquinol (benzen-1,2,4-triol) and pyrogallol (benzen-1,2,3-triol), which act as substrates or inhibitors of the enzyme, have been determined and analyzed. 4-CCD from the Gram-positive bacterium Rhodococcus opacus 1CP is a Fe(III) ion containing enzyme specialized in the aerobic biodegradation of chlorocatechols. The structures of the 4-CCD complexes show that the catechols bind the catalytic iron ion in a bidentate mode displacing Tyr169 and the benzoate ion (found in the native enzyme structure) from the metal coordination sphere, as found in other adducts of intradiol dioxygenases with substrates. The analysis of the present structures allowed to identify the residues selectively involved in recognition of the diverse substrates. Furthermore the structural comparison with the corresponding complexes of catechol 1,2-dioxygenase from the same Rhodococcus strain (Rho-1,2-CTD) highlights significant differences in the binding of the tested catechols to the active site of the enzyme, particularly in the orientation of the aromatic ring substituents. As an example the 3-substituted catechols are bound with the substituent oriented towards the external part of the 4-CCD active site cavity, whereas in the Rho-1,2-CTD complexes the 3-substituents were placed in the internal position. The present crystallographic study shed light on the mechanism that allows substrate recognition inside this class of high specific enzymes involved in the biodegradation of recalcitrant pollutants.


    Organizational Affiliation

    Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy. marta.ferraroni@unifi.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chlorocatechol 1,2-dioxygenase
A, B
257Rhodococcus opacusMutation(s): 0 
Gene Names: clcA
EC: 1.13.11.-
Find proteins for O67987 (Rhodococcus opacus)
Go to UniProtKB:  O67987
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DHB
Query on DHB

Download SDF File 
Download CCD File 
A, B
3,4-DIHYDROXYBENZOIC ACID
C7 H6 O4
YQUVCSBJEUQKSH-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MYY
Query on MYY

Download SDF File 
Download CCD File 
A
(2R)-3-(PHOSPHONOOXY)-2-(TETRADECANOYLOXY)PROPYL PALMITATE
C33 H65 O8 P
GLOXZZHEZYKXNV-WJOKGBTCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.166 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 87.310α = 90.00
b = 87.310β = 90.00
c = 185.921γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MAR345dtbdata collection
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release