3G9X

Structure of haloalkane dehalogenase DhaA14 mutant I135F from Rhodococcus rhodochrous


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.115 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 D Biol Crystallogr 66: 962-969

  • DOI: 10.1107/S0907444910027101
  • Primary Citation of Related Structures:  
    3FBW, 3FWH, 3G9X

  • 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 access tunnels of DhaA produced protein variants with significantly improved activity towards TCP ...

    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 Struct Biol Cryst Commun 64: 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Haloalkane dehalogenase A299Rhodococcus sp.Mutation(s): 1 
Gene Names: dhaA
EC: 3.8.1.5
Find proteins for P0A3G3 (Rhodococcus sp)
Explore P0A3G3 
Go to UniProtKB:  P0A3G3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download Ideal Coordinates CCD File 
A
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
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: 0.95 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.115 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.73α = 115.5
b = 44.44β = 97.87
c = 46.63γ = 109.52
Software Package:
Software NamePurpose
SHELXL-97refinement
MOLREPphasing
REFMACrefinement
Cootmodel building
MolProbitymodel building
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description