Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 125.73 kDa 
• Atom Count: 8237 
• Residue Count: 1028 
• Unique protein chains: 1

1EK2

CRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE COMPLEXED WITH CDU INHIBITOR

• DOI: 10.2210/pdb1EK2/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2000-03-06 Released: 2000-05-31 
• Deposition Author(s): Argiriadi, M.A., Morisseau, C., Goodrow, M.H., Dowdy, D.L., Hammock, B.D., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.290 
• R-Value Work: 0.211 

Literature

Binding of alkylurea inhibitors to epoxide hydrolase implicates active site tyrosines in substrate activation.

Argiriadi, M.A., Morisseau, C., Goodrow, M.H., Dowdy, D.L., Hammock, B.D., Christianson, D.W.

(2000) J Biol Chem 275: 15265-15270

• PubMed: 10747889 
• DOI: 10.1074/jbc.M000278200
• Primary Citation of Related Structures:  
  1EK2, 1EK1


• PubMed Abstract: 
  

The structures of two alkylurea inhibitors complexed with murine soluble epoxide hydrolase have been determined by x-ray crystallographic methods. The alkyl substituents of each inhibitor make extensive hydrophobic contacts in the soluble epoxide hydrolase active site, and each urea carbonyl oxygen accepts hydrogen bonds from the phenolic hydroxyl groups of Tyr(381) and Tyr(465). These hydrogen bond interactions suggest that Tyr(381) and/or Tyr(465) are general acid catalysts that facilitate epoxide ring opening in the first step of the hydrolysis reaction; Tyr(465) is highly conserved among all epoxide hydrolases, and Tyr(381) is conserved among the soluble epoxide hydrolases. In one enzyme-inhibitor complex, the urea carbonyl oxygen additionally interacts with Gln(382). If a comparable interaction occurs in catalysis, then Gln(382) may provide electrostatic stabilization of partial negative charge on the epoxide oxygen. The carboxylate side chain of Asp(333) accepts a hydrogen bond from one of the urea NH groups in each enzyme-inhibitor complex. Because Asp(333) is the catalytic nucleophile, its interaction with the partial positive charge on the urea NH group mimics its approach toward the partial positive charge on the electrophilic carbon of an epoxide substrate. Accordingly, alkylurea inhibitors mimic features encountered in the reaction coordinate of epoxide ring opening, and a structure-based mechanism is proposed for leukotoxin epoxide hydrolysis.

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Related Citations: 

• Detoxification of environmental mutagens and carcinogens: Structure, mechanism, and evolution of liver epoxide hydrolase
  Argiriadi, M.A., Morisseau, C., Hammock, B.D., Christianson, D.W.
  (1999) Proc Natl Acad Sci U S A 96: 10637

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Organizational Affiliation: 

Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPOXIDE HYDROLASE	A, B	554	Mus musculus	Mutation(s): 0  Gene Names: Ephx2, Eph2 EC: 3.3.2.3 (PDB Primary Data), 3.3.2.10 (UniProt), 3.1.3.76 (UniProt)
Find proteins for P34914 (Mus musculus) Explore P34914  Go to UniProtKB:  P34914

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDU	A, B	N-CYCLOHEXYL-N'-DECYLUREA C17 H34 N2 O LPXYBLIRYGCMPQ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
CDU	Ki :  6.300000190734863   nM  PDBBind
CDU	IC50:  50   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.290 
• R-Value Work: 0.211 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.9	α = 90
b = 143	β = 90
c = 60	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-03-06 
• Released Date: 2000-05-31 
Deposition Author(s): Argiriadi, M.A., Morisseau, C., Goodrow, M.H., Dowdy, D.L., Hammock, B.D., Christianson, D.W.

Revision History 

• Version 1.0: 2000-05-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance