PDBsum entry: 1ehy

Hydrolase

PDB id: 1ehy

Contents

Protein chains

282 a.a. *

Metals

__K ×4

Waters ×610

* Residue conservation analysis

PDB id:

1ehy

Name:

Hydrolase

Title:

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

Structure:

Protein (soluble epoxide hydrolase). Chain: a, b, c, d. Engineered: yes

Source:

Agrobacterium tumefaciens. Organism_taxid: 358. Strain: ad1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.190 R-free: 0.227

Authors:

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

Key ref:

M.Nardini et al. (1999). The x-ray structure of epoxide hydrolase from Agrobacterium radiobacter AD1. An enzyme to detoxify harmful epoxides. J Biol Chem, 274, 14579-14586. PubMed id: 10329649 DOI: 10.1074/jbc.274.21.14579

Date:

17-Oct-98 Release date: 16-Oct-99

Protein chains

O31243  (O31243_RHIRD) -  Epoxide hydrolase

Seq: 294 a.a.

Struc: 282 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.3.2.3 - Transferred entry: 3.3.2.9 and 3.3.2.10.
• Reaction: An epoxide + H₂O = a glycol

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.274.21.14579

J Biol Chem 274:14579-14586 (1999)

PubMed id: 10329649

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

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

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 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.

Selected figure(s)

Figure 6.
Fig. 6. Stereo view of the water-mediated interaction between Asp^131 and His^275 and of the oxyanion hole in epoxide hydrolase. Hydrogen bonds are shown as dashed lines. Side chains, water molecules, and the HGWP motif are in ball and stick representation. The catalytic water molecule is labeled WAT. The figure was produced using MOLSCRIPT (39).

Figure 8.
Fig. 8. Schematic representation of the catalytic mechanism of epoxide hydrolase. The Michaelis complex with epichlorohydrin is shown before the formation of covalent intermediate, which is indicated by arrows. Hydrogen bonds are shown as dashed lines.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 14579-14586) copyright 1999.

Figures were selected by the author.