2DHE

CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKANE DEHALOGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase.

Verschueren, K.H.Seljee, F.Rozeboom, H.J.Kalk, K.H.Dijkstra, B.W.

(1993) Nature 363: 693-698

  • DOI: 10.1038/363693a0
  • Primary Citation of Related Structures:  
    2DHE, 2DHD, 2DHC

  • PubMed Abstract: 
  • Crystal structures of haloalkane dehalogenase were determined in the presence of the substrate 1,2-dichloroethane. At pH 5 and 4 degrees C, substrate is bound in the active site without being converted; warming to room temperature causes the substrate's carbon-chlorine bond to be broken, producing a chloride ion with concomitant alkylation of the active-site residue Asp124 ...

    Crystal structures of haloalkane dehalogenase were determined in the presence of the substrate 1,2-dichloroethane. At pH 5 and 4 degrees C, substrate is bound in the active site without being converted; warming to room temperature causes the substrate's carbon-chlorine bond to be broken, producing a chloride ion with concomitant alkylation of the active-site residue Asp124. At pH 6 and room temperature the alkylated enzyme is hydrolysed by a water molecule activated by the His289-Asp260 pair in the active site. These results show that catalysis by the dehalogenase proceeds by a two-step mechanism involving an ester intermediate covalently bound at Asp124.


    Related Citations: 
    • Crystal Structure of Haloalkane Dehalogenase: An Enzyme to Detoxify Halogenated Alkanes
      Franken, S.M., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W.
      (1991) EMBO J 10: 1297
    • Crystallization of Haloalkane Dehalogenase from Xanthobacter Autotrophicus Gj10
      Rozeboom, H.J., Kingma, J., Janssen, D.B., Dijkstra, B.W.
      (1988) J Mol Biol 200: 611

    Organizational Affiliation

    BIOSON Research Institute and Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HALOALKANE DEHALOGENASE A310Xanthobacter autotrophicusMutation(s): 0 
Gene Names: dhlA
EC: 3.8.1.5
Find proteins for P22643 (Xanthobacter autotrophicus)
Explore P22643 
Go to UniProtKB:  P22643
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 2.13 Å
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95α = 90
b = 72.6β = 90
c = 41.5γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other