8XIZ | pdb_00008xiz

Crystal structure of an epoxide hydrolase mutant A250IC/L344V from Aspergillus usamii E001 at 2.17 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Literature

Rational mutagenesis of an epoxide hydrolase and its structural mechanism for the enantioselectivity improvement toward chiral ortho-fluorostyrene oxide.

Lu, Z.Y.Liao, X.Jing, W.W.Liu, K.K.Ren, Q.G.He, Y.C.Hu, D.

(2024) Int J Biol Macromol 282: 136864-136864

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.136864
  • Primary Citation of Related Structures:  
    8XIZ

  • PubMed Abstract: 

    Chiral (S)-o-fluorostyrene oxide (oFSO) and vicinal diol (R)-o-fluorophenylethane-1,2-diol (oFPED) are important intermediates for synthesizing treatments for neuropathic diseases. This study aimed to engineer Aspergillus usamii epoxide hydrolase (AuEH2) through a rational mutagenesis strategy to customize high enantioselectivity mutant for rac-oFSO. Out of 181 single-site mutants screened, six showed elevated enantiomeric ratio (E value) ranging from 32 to 108 according to E value and activity mutability landscapes. By combinatorial mutagenesis of A250I with other five single-site mutants, we constructed five double-site mutants, with the best-performing mutant, D5 (A250I/L344V), achieving an E value of 180. This mutant enabled the efficient kinetic resolution of 400 mM rac-oFSO in pure water system using E. coli/Aueh2 A250I/L344V , yielding (S)-oFSO (>99 % ee s , 50 % yield s ) and (R)-oFPED (>99 % ee p , 50 % yield p ) with space-time yields (STYs) of 331.5 and 376.1 g/L/d, respectively. Combining crystal structure resolution with theoretical computations clarified the enantioselectivity mechanism of D5, demonstrating that A250I reduced the funnel-shaped substrate binding pocket (SBP) while L344V extended its bottom, enhancing specific recognition of (R)-oFSO and inhibiting (S)-oFSO hydrolysis. These findings provide valuable insights for designing highly enantioselective enzyme mutants, advancing the field of asymmetric synthesis of chiral compounds using green biocatalytic processes.


  • Organizational Affiliation
    • School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, PR China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microsomal epoxide hyddrolase
A, B
431Aspergillus usamiiMutation(s): 2 
Gene Names: EH2
EC: 3.3.2.9
UniProt
Find proteins for T2B4K5 (Aspergillus usamii)
Explore T2B4K5 
Go to UniProtKB:  T2B4K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2B4K5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.049α = 90
b = 51.287β = 90.52
c = 133.812γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
AMPLEphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22308034

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references, Structure summary