3G0I

Complex of Aspergillus niger epoxide hydrolase with valpromide (2-propylpentanamide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage

Reetz, M.T.Bocola, M.Wang, L.W.Sanchis, J.Cronin, A.Arand, M.Zou, J.Archelas, A.Bottalla, A.L.Naworyta, A.Mowbray, S.L.

(2009) J.Am.Chem.Soc. 131: 7334-7343

  • DOI: 10.1021/ja809673d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Directed evolution of enzymes as enantioselective catalysts in organic chemistry is an alternative to traditional asymmetric catalysis using chiral transition-metal complexes or organocatalysts, the different approaches often being complementary. Mor ...

    Directed evolution of enzymes as enantioselective catalysts in organic chemistry is an alternative to traditional asymmetric catalysis using chiral transition-metal complexes or organocatalysts, the different approaches often being complementary. Moreover, directed evolution studies allow us to learn more about how enzymes perform mechanistically. The present study concerns a previously evolved highly enantioselective mutant of the epoxide hydrolase from Aspergillus niger in the hydrolytic kinetic resolution of racemic glycidyl phenyl ether. Kinetic data, molecular dynamics calculations, molecular modeling, inhibition experiments, and X-ray structural work for the wild-type (WT) enzyme and the best mutant reveal the basis of the large increase in enantioselectivity (E = 4.6 versus E = 115). The overall structures of the WT and the mutant are essentially identical, but dramatic differences are observed in the active site as revealed by the X-ray structures. All of the experimental and computational results support a model in which productive positioning of the preferred (S)-glycidyl phenyl ether, but not the (R)-enantiomer, forms the basis of enhanced enantioselectivity. Predictions regarding substrate scope and enantioselectivity of the best mutant are shown to be possible.


    Related Citations: 
    • Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases
      Zou, J.,Hallberg, B.M.,Bergfors, T.,Oesch, F.,Arand, M.,Mowbray, S.L.,Jones, T.A.
      (2000) Structure 8: 111


    Organizational Affiliation

    Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mulheim/Ruhr, Germany. reetz@mpi-muelheim.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epoxide hydrolase
A, B
394Aspergillus nigerMutation(s): 0 
Gene Names: hyl1
EC: 3.3.2.3
Find proteins for Q9UR30 (Aspergillus niger)
Go to UniProtKB:  Q9UR30
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VPR
Query on VPR

Download SDF File 
Download CCD File 
A, B
2-PROPYLPENTANAMIDE
VALPROMIDE
C8 H17 N O
OMOMUFTZPTXCHP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VPRKi: 250000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.985α = 90.00
b = 89.655β = 105.31
c = 75.812γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-01-28 
  • Released Date: 2009-06-09 
  • Deposition Author(s): Zou, J., Mowbray, S.L.

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description