3RK4

Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 

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This is version 1.3 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: 10.1107/S1399004713026254
  • Primary Citation of Related Structures:  
    4HZG, 3RK4, 4FWB

  • 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-trichloroprop ...

    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: 

    Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Haloalkane dehalogenaseA299Rhodococcus rhodochrousMutation(s): 5 
Gene Names: dhaA, DhaA31
EC: 3.8.1.5
Find proteins for P0A3G2 (Rhodococcus rhodochrous)
Explore P0A3G2 
Go to UniProtKB:  P0A3G2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.551α = 115.34
b = 44.37β = 98.56
c = 46.411γ = 109.59
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 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2014-03-05
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description