2DHE | pdb_00002dhe

CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKANE DEHALOGENASE

• PDB DOI: https://doi.org/10.2210/pdb2DHE/pdb

• Classification: DEHALOGENASE
• Organism(s): Xanthobacter autotrophicus
• Mutation(s): No 


• Deposited: 1993-06-24 Released: 1994-08-31 
• Deposition Author(s): Verschueren, K.H.G., Dijkstra, B.W.

---

Experimental Data Snapshot

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

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

• PubMed: 8515812 
• DOI: https://doi.org/10.1038/363693a0
• Primary Citation Related Structures: 
  2DHC, 2DHD, 2DHE


• 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. 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.

---

Organizational Affiliation: 
• BIOSON Research Institute and Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.21 kDa 
• Atom Count: 2,665 
• Modeled Residue Count: 310 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HALOALKANE DEHALOGENASE	A	310	Xanthobacter autotrophicus	Mutation(s): 0  EC: 3.8.1.5
UniProt
Find proteins for P22643 (Xanthobacter autotrophicus) Explore P22643  Go to UniProtKB:  P22643

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

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

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95	α = 90
b = 72.6	β = 90
c = 41.5	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-08-31 
Deposition Author(s): Verschueren, K.H.G., Dijkstra, B.W.

Revision History  

• 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
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations