Crystal structure determination of catechol 1,2-dioxygenase from rhodococcus opacus 1CP in complex with 3-chlorocatechol

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 

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Catechol 1,2-dioxygenase from the Gram-positive Rhodococcus opacus 1CP: Quantitative structure/activity relationship and the crystal structures of native enzyme and catechols adducts.

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

(2010) J Struct Biol 170: 548-564

  • DOI: https://doi.org/10.1016/j.jsb.2009.12.023
  • Primary Citation of Related Structures:  
    3HGI, 3HHX, 3HHY, 3HJ8, 3HJQ, 3HJS, 3HKP, 3I4V, 3I4Y, 3I51

  • PubMed Abstract: 

    The first crystallographic structures of a catechol 1,2-dioxygenase from a Gram-positive bacterium Rhodococcus opacus 1CP (Rho 1,2-CTD), a Fe(III) ion containing enzyme specialized in the aerobic biodegradation of catechols, and its adducts with catechol, 3-methylcatechol, 4-methylcatechol, pyrogallol (benzene-1,2,3-triol), 3-chlorocatechol, 4-chlorocatechol, 3,5-dichlorocatechol, 4,5-dichlorocatechol and protocatechuate (3,4-dihydroxybenzoate) have been determined and analyzed. This study represents the first extensive characterization of catechols adducts of 1,2-CTDs. The structural analyses reveal the diverse modes of binding to the active metal iron ion of the tested catechols thus allowing to identify the residues selectively involved in recognition of the diverse substrates by this class of enzymes. The comparison is further extended to the structural and functional characteristics of the other 1,2-CTDs isolated from Gram-positive and Gram-negative bacteria. Moreover the high structural homology of the present enzyme with the 3-chlorocatechol 1,2-dioxygenase from the same bacterium are discussed in terms of their different substrate specificity. The catalytic rates for Rho 1,2-CTD conversion of the tested compounds are also compared with the calculated energies of the highest occupied molecular orbital (E(HOMO)) of the substrates. A quantitative relationship (R=0.966) between the ln k(cat) and the calculated electronic parameter E(HOMO) was obtained for catechol, 3-methylcatechol, 4-methylcatechol, pyrogallol, 3-chlorocatechol, 4-chlorocatechol. This indicates that for these substrates the rate-limiting step of the reaction cycle is dependent on their nucleophilic reactivity. The discrepancies observed in the quantitative relationship for 3,5-dichlorocatechol, 4,5-dichlorocatechol and protocatechuate are ascribed to the sterical hindrances leading to the distorted binding of such catechols observed in the corresponding structures.

  • 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
Catechol 1,2-dioxygenase280Rhodococcus opacusMutation(s): 0 
Find proteins for P95607 (Rhodococcus opacus)
Explore P95607 
Go to UniProtKB:  P95607
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95607
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6PL

Download Ideal Coordinates CCD File 
C42 H85 N O8 P
Query on 3CE

Download Ideal Coordinates CCD File 
C [auth A]3-chlorobenzene-1,2-diol
C6 H5 Cl O2
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Binding Affinity Annotations 
IDSourceBinding Affinity
3CE Binding MOAD:  3I4V Ki: 700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.655α = 90
b = 37.886β = 95.31
c = 75.26γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata 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: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations