2DHD

CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKANE DEHALOGENASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Observed: 0.189 

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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
Expand
  • 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0AK
Query on 0AK		AL-PEPTIDE LINKINGC6 H10 Cl N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.8α = 90
b = 72.8β = 90
c = 41.4γ = 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: 1994-07-31
    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