3SK0

structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant DhaA12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Dynamics and hydration explain failed functional transformation in dehalogenase design.

Sykora, J.Brezovsky, J.Koudelakova, T.Lahoda, M.Fortova, A.Chernovets, T.Chaloupkova, R.Stepankova, V.Prokop, Z.Smatanova, I.K.Hof, M.Damborsky, J.

(2014) Nat Chem Biol 10: 428-430

  • DOI: 10.1038/nchembio.1502
  • Primary Citation of Related Structures:  
    3SK0

  • PubMed Abstract: 
  • We emphasize the importance of dynamics and hydration for enzymatic catalysis and protein design by transplanting the active site from a haloalkane dehalogenase with high enantioselectivity to nonselective dehalogenase. Protein crystallography confirms that the active site geometry of the redesigned dehalogenase matches that of the target, but its enantioselectivity remains low ...

    We emphasize the importance of dynamics and hydration for enzymatic catalysis and protein design by transplanting the active site from a haloalkane dehalogenase with high enantioselectivity to nonselective dehalogenase. Protein crystallography confirms that the active site geometry of the redesigned dehalogenase matches that of the target, but its enantioselectivity remains low. Time-dependent fluorescence shifts and computer simulations revealed that dynamics and hydration at the tunnel mouth differ substantially between the redesigned and target dehalogenase.


    Related Citations: 
    • Crystal structure of haloalkane dehalogenase mutant DhaA12 from Gram-positive bacterium Rhodococcus rhodochrous NCIMB13064
      Lahoda, M., Koudelakova, T., Stsiapanava, A., Mesters, J., Damborsky, J., Kuta-Smatanova, I.
      () To be published --: --

    Organizational Affiliation

    1] Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic. [2] International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Haloalkane dehalogenaseA311Rhodococcus rhodochrousMutation(s): 8 
Gene Names: dhaA
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.583α = 90
b = 68.689β = 90
c = 84.37γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references
  • Version 1.2: 2014-05-21
    Changes: Database references
  • Version 1.3: 2014-06-04
    Changes: Database references
  • Version 1.4: 2017-11-08
    Changes: Database references, Refinement description