1ZMT

Structure of haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in complex with (R)-para-nitro styrene oxide, with a water molecule in the halide-binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Enantioselectivity of an Epoxide Ring Opening Reaction Catalyzed by Halo Alcohol Dehalogenase HheC.

de Jong, R.M.Tiesinga, J.J.W.Villa, A.Tang, L.Janssen, D.B.Dijkstra, B.W.

(2005) J.Am.Chem.Soc. 127: 13338-13343

  • DOI: 10.1021/ja0531733
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Halo alcohol dehalogenase HheC catalyzes the highly enantioselective dehalogenation of vicinal halo alcohols to epoxides, as well as the reverse reaction, the enantioselective and beta-regioselective nucleophilic ring opening of epoxides by pseudo-ha ...

    Halo alcohol dehalogenase HheC catalyzes the highly enantioselective dehalogenation of vicinal halo alcohols to epoxides, as well as the reverse reaction, the enantioselective and beta-regioselective nucleophilic ring opening of epoxides by pseudo-halides such as azide and cyanide. To investigate this latter reaction, we determined X-ray structures of complexes of HheC with the favored and unfavored enantiomers of para-nitrostyrene oxide. The aromatic parts of the two enantiomers bind in a very similar way, but the epoxide ring of the unfavored (S)-enantiomer binds in a nonproductive inverted manner, with the epoxide oxygen and Cbeta atom positions interchanged with respect to those of the favored (R)-enantiomer. The calculated difference in relative Gibbs binding energy is in agreement with the observed loss of a single hydrogen bond in the S bound state with respect to the R bound state. Our results indicate that it is the nonproductive binding of the unfavored (S)-enantiomer, rather than the difference in affinity for the two enantiomers, that allows HheC to catalyze the azide-mediated ring opening of para-nitrostyrene oxide with high enantioselectivity. This work represents a rare opportunity to explain the enantioselectivity of an enzymatic reaction by comparison of crystallographic data on the binding of both the favored and unfavored enantiomers.


    Organizational Affiliation

    Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Haloalcohol dehalogenase HheC
A, B, C, D
254Rhizobium radiobacterMutation(s): 0 
Gene Names: hheC
Find proteins for Q93D82 (Rhizobium radiobacter)
Go to UniProtKB:  Q93D82
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RNO
Query on RNO

Download SDF File 
Download CCD File 
A, B, C, D
(R)-PARA-NITROSTYRENE OXIDE
(2R)-2-(4-NITROPHENYL)OXIRANE
C8 H7 N O3
YKIUTLHCSNCTDZ-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.444α = 90.00
b = 72.041β = 92.88
c = 97.420γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CCP4data scaling
CNXrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance