4IO0

Crystal structure of F128A mutant of an epoxide hydrolase from Bacillus megaterium complexed with its product (R)-3-[1]naphthyloxy-propane-1,2-diol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates.

Kong, X.D.Yuan, S.Li, L.Chen, S.Xu, J.H.Zhou, J.H.

(2014) Proc.Natl.Acad.Sci.USA 111: 15717-15722

  • DOI: 10.1073/pnas.1404915111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Optically pure epoxides are essential chiral precursors for the production of (S)-propranolol, (S)-alprenolol, and other β-adrenergic receptor blocking drugs. Although the enzymatic production of these bulky epoxides has proven difficult, here we rep ...

    Optically pure epoxides are essential chiral precursors for the production of (S)-propranolol, (S)-alprenolol, and other β-adrenergic receptor blocking drugs. Although the enzymatic production of these bulky epoxides has proven difficult, here we report a method to effectively improve the activity of BmEH, an epoxide hydrolase from Bacillus megaterium ECU1001 toward α-naphthyl glycidyl ether, the precursor of (S)-propranolol, by eliminating the steric hindrance near the potential product-release site. Using X-ray crystallography, mass spectrum, and molecular dynamics calculations, we have identified an active tunnel for substrate access and product release of this enzyme. The crystal structures revealed that there is an independent product-release site in BmEH that was not included in other reported epoxide hydrolase structures. By alanine scanning, two mutants, F128A and M145A, targeted to expand the potential product-release site displayed 42 and 25 times higher activities toward α-naphthyl glycidyl ether than the wild-type enzyme, respectively. These results show great promise for structure-based rational design in improving the catalytic efficiency of industrial enzymes for bulky substrates.


    Organizational Affiliation

    State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; jiahai@mail.sioc.ac.cn jianhexu@ecust.edu.cn.,State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China; and jiahai@mail.sioc.ac.cn jianhexu@ecust.edu.cn.,State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China; and.,National Institute of Biological Sciences, Beijing 102206, China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China; and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble epoxide hydrolase
A, B
304Bacillus megateriumMutation(s): 1 
EC: 3.2.2.10
Find proteins for G9BEX6 (Bacillus megaterium)
Go to UniProtKB:  G9BEX6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
RN1
Query on RN1

Download SDF File 
Download CCD File 
A, B
(2R)-3-(naphthalen-1-yloxy)propane-1,2-diol
C13 H14 O3
BYNNMWGWFIGTIC-LLVKDONJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.156 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 109.640α = 90.00
b = 109.640β = 90.00
c = 117.496γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-11-19
    Type: Database references