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 

wwPDB Validation 3D Report Full Report


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.,Sect.D 70: 209-217

  • DOI: 10.1107/S1399004713026254
  • Primary Citation of Related Structures:  

  • 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

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Haloalkane dehalogenase
A
299Rhodococcus rhodochrousMutation(s): 5 
Gene Names: dhaA
EC: 3.8.1.5
Find proteins for P0A3G2 (Rhodococcus rhodochrous)
Go to UniProtKB:  P0A3G2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download 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 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.551α = 115.34
b = 44.370β = 98.56
c = 46.411γ = 109.59
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
MAR345data collection
SHELXL-97refinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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