1EHY

X-ray structure of the epoxide hydrolase from agrobacterium radiobacter ad1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The x-ray structure of epoxide hydrolase from Agrobacterium radiobacter AD1. An enzyme to detoxify harmful epoxides.

Nardini, M.Ridder, I.S.Rozeboom, H.J.Kalk, K.H.Rink, R.Janssen, D.B.Dijkstra, B.W.

(1999) J.Biol.Chem. 274: 14579-14586


  • PubMed Abstract: 
  • Epoxide hydrolases catalyze the cofactor-independent hydrolysis of reactive and toxic epoxides. They play an essential role in the detoxification of various xenobiotics in higher organisms and in the bacterial degradation of several environmental pol ...

    Epoxide hydrolases catalyze the cofactor-independent hydrolysis of reactive and toxic epoxides. They play an essential role in the detoxification of various xenobiotics in higher organisms and in the bacterial degradation of several environmental pollutants. The first x-ray structure of one of these, from Agrobacterium radiobacter AD1, has been determined by isomorphous replacement at 2.1-A resolution. The enzyme shows a two-domain structure with the core having the alpha/beta hydrolase-fold topology. The catalytic residues, Asp107 and His275, are located in a predominantly hydrophobic environment between the two domains. A tunnel connects the back of the active-site cavity with the surface of the enzyme and provides access to the active site for the catalytic water molecule, which in the crystal structure, has been found at hydrogen bond distance to His275. Because of a crystallographic contact, the active site has become accessible for the Gln134 side chain, which occupies a position mimicking a bound substrate. The structure suggests Tyr152/Tyr215 as the residues involved in substrate binding, stabilization of the transition state, and possibly protonation of the epoxide oxygen.


    Related Citations: 
    • Primary Structure and Catalytic Mechanism of the Epoxide Hydrolase from Agrobacterium Radiobacter AD1
      Rink, R.,Fennema, M.,Smids, M.,Dehmel, U.,Janssen, D.B.
      (1997) J.Biol.Chem. 272: 14650
    • Enantioselectivity of a Recombinant Epoxide Hydrolase from Agrobacterium Radiobacter
      Lutje Spelberg, J.H.,Rink, R.,Kellogg, R.M.,Janssen, D.B.
      (1998) Tetrahedron 9: 459
    • Kinetic Mechanism of the Enantioselective Conversion of Styrene Oxide by Epoxide Hydrolase from Agrobacterium Radiodacter AD1
      Jacobs, M.H.J.,Van Den Wijngaard, A.J.,Pentenga, M.,Janssen, D.B.
      (1998) Biochemistry 37: 18119
    • Mutation of Tyrosine Residues Involved in the Alkylation Half Reaction of Epoxide Hydrolase from Agrobacterium Radiodacter AD1 Results in Improved Enantioselectivity
      Rink, R.,Lutje Spelberg, J.H.,Pieters, R.J.,Kingma, J.,Nardini, M.,Kellogg, R.M.,Dijkstra, B.W.,Janssen, D.B.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Laboratory of Biophysical Chemistry and BIOSON Research Institute, Department of Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
A, B, C, D
294Rhizobium radiobacterMutation(s): 0 
Gene Names: echA
EC: 3.3.2.3
Find proteins for O31243 (Rhizobium radiobacter)
Go to UniProtKB:  O31243
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.624α = 90.00
b = 100.201β = 100.68
c = 96.879γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-05-09
    Type: Structure summary