3FWH

Structure of haloalkane dehalogenase mutant Dha15 (I135F/C176Y) from Rhodococcus rhodochrous


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels.

Stsiapanava, A.Dohnalek, J.Gavira, J.A.Kuty, M.Koudelakova, T.Damborsky, J.Kuta Smatanova, I.

(2010) Acta Crystallogr.,Sect.D 66: 962-969

  • DOI: 10.1107/S0907444910027101
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 is a bacterial enzyme that shows catalytic activity for the hydrolytic degradation of the highly toxic industrial pollutant 1,2,3-trichloropropane (TCP). Mutagenesis focused on ...

    The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 is a bacterial enzyme that shows catalytic activity for the hydrolytic degradation of the highly toxic industrial pollutant 1,2,3-trichloropropane (TCP). Mutagenesis focused on the access tunnels of DhaA produced protein variants with significantly improved activity towards TCP. Three mutants of DhaA named DhaA04 (C176Y), DhaA14 (I135F) and DhaA15 (C176Y + I135F) were constructed in order to study the functional relevance of the tunnels connecting the buried active site of the protein with the surrounding solvent. All three protein variants were crystallized using the sitting-drop vapour-diffusion technique. The crystals of DhaA04 belonged to the orthorhombic space group P2(1)2(1)2(1), while the crystals of DhaA14 and DhaA15 had triclinic symmetry in space group P1. The crystal structures of DhaA04, DhaA14 and DhaA15 with ligands present in the active site were solved and refined using diffraction data to 1.23, 0.95 and 1.22 A, resolution, respectively. Structural comparisons of the wild type and the three mutants suggest that the tunnels play a key role in the processes of ligand exchange between the buried active site and the surrounding solvent.


    Related Citations: 
    • Crystals of DhaA mutants from Rhodococcus rhodochrous NCIMB 13064 diffracted to ultrahigh resolution: crystallization and preliminary diffraction analysis
      Stsiapanava, A.,Koudelakova, T.,Lapkouski, M.,Pavlova, M.,Damborsky, J.,Kuta Smatanova, I.
      (2008) Acta Crystallogr.,Sect.F F64: 137
    • Pathways and Mechanisms for Product Release in Engineered Haloalkane Dehalogenase DhaA Explored using Classical and Random Acceleration Molecular Dynamics Simulations
      Klvana, M.,Pavlova, M.,Koudelakova, T.,Chaloupkova, R.,Dvorak, P.,Stsiapanava, A.,Kuty, M.,Kuta Smatanova, I.,Dohnalek, J.,Kulhanek, P.,Wade, R.C.,Damborsky, J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Haloalkane dehalogenase
A
299Rhodococcus spMutation(s): 2 
Gene Names: dhaA
EC: 3.8.1.5
Find proteins for P0A3G3 (Rhodococcus sp)
Go to UniProtKB:  P0A3G3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.130 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.524α = 115.48
b = 44.370β = 98.41
c = 46.541γ = 109.60
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
HKL-2000data collection
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-28
    Type: Database references