4FWB

Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31 in complex with 1, 2, 3 - trichloropropane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31.

Lahoda, M.Mesters, J.R.Stsiapanava, A.Chaloupkova, R.Kuty, M.Damborsky, J.Kuta Smatanova, I.

(2014) Acta Crystallogr D Biol Crystallogr 70: 209-217

  • DOI: https://doi.org/10.1107/S1399004713026254
  • Primary Citation of Related Structures:  
    3RK4, 4FWB, 4HZG

  • PubMed Abstract: 

    Haloalkane dehalogenases catalyze the hydrolytic cleavage of carbon-halogen bonds, which is a key step in the aerobic mineralization of many environmental pollutants. One important pollutant is the toxic and anthropogenic compound 1,2,3-trichloropropane (TCP). Rational design was combined with saturation mutagenesis to obtain the haloalkane dehalogenase variant DhaA31, which displays an increased catalytic activity towards TCP. Here, the 1.31 Å resolution crystal structure of substrate-free DhaA31, the 1.26 Å resolution structure of DhaA31 in complex with TCP and the 1.95 Å resolution structure of wild-type DhaA are reported. Crystals of the enzyme-substrate complex were successfully obtained by adding volatile TCP to the reservoir after crystallization at pH 6.5 and room temperature. Comparison of the substrate-free structure with that of the DhaA31 enzyme-substrate complex reveals that the nucleophilic Asp106 changes its conformation from an inactive to an active state during the catalytic cycle. The positions of three chloride ions found inside the active site of the enzyme indicate a possible pathway for halide release from the active site through the main tunnel. Comparison of the DhaA31 variant with wild-type DhaA revealed that the introduced substitutions reduce the volume and the solvent-accessibility of the active-site pocket.


  • Organizational Affiliation

    Institute of Complex Systems, FFPW and CENAKVA, University of South Bohemia in Ceske Budejovice, Zamek 136, 373 33 Nove Hrady, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Haloalkane dehalogenase292Rhodococcus rhodochrousMutation(s): 5 
Gene Names: dhaADhaA31
EC: 3.8.1.5
UniProt
Find proteins for P0A3G2 (Rhodococcus rhodochrous)
Explore P0A3G2 
Go to UniProtKB:  P0A3G2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3G2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.498α = 115.32
b = 44.395β = 97.7
c = 46.538γ = 109.58
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2014-03-05
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Structure summary
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description