6IX4 | pdb_00006ix4

Structure of an epoxide hydrolase from Aspergillus usamii E001 (AuEH2) at 1.51 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.165 (Depositor), 0.165 (DCC) 
  • R-Value Work: 
    0.144 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 
    0.145 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Nearly perfect kinetic resolution of racemic o-nitrostyrene oxide by AuEH2, a microsomal epoxide hydrolase from Aspergillus usamii, with high enantio- and regio-selectivity.

Hu, D.Hu, B.C.Wen, Z.Zhang, D.Liu, Y.Y.Zang, J.Wu, M.C.

(2021) Int J Biol Macromol 169: 1-7

  • DOI: https://doi.org/10.1016/j.ijbiomac.2020.12.074
  • Primary Citation Related Structures: 
    6IX4

  • PubMed Abstract: 

    Only a few known epoxide hydrolases (EHs) displayed activity towards o-nitrostyrene oxide (4a), presumably owing to the large steric hindrance caused by o-nitro substituent. Therefore, excavating EHs with high activity and enantio- and/or regio-selectivity towards racemic (rac-) 4a is essential but challenging. Here, AuEH2 from Aspergillus usamii was expressed in E. coli BL21(DE3). E. coli/Aueh2, an E. coli transformant expressing AuEH2, possessed EH activities of 16.2-184 U/g wet cell towards rac-styrene oxide (1a) and its derivatives (2a-13a), and the largest enantiomeric ratio of 96 towards rac-4a. The regioselectivity coefficients, β R and β S , of AuEH2 were determined to be 99.2% and 98.9%, suggesting that it regiopreferentially attacks the C β in the oxirane rings of (R)- and (S)-4a. Then, the nearly perfect kinetic resolution of 20 mM rac-4a in pure water was carried out using 20 mg/mL wet cells of E. coli/Aueh2 at 25 °C for 50 min, retaining (S)-4a with over 99% ee s and 48.9% yield s , while producing (R)-o-nitrophenyl-1,2-ethanediol (4b) with 95.3% ee p and 49.8% yield p . To elucidate the molecular mechanism of AuEH2 with high enantiopreference for (R)-4a, its crystal structure was solved by X-ray diffraction and the molecular docking of AuEH2 with (R)- or (S)-4a was simulated.


  • Organizational Affiliation
    • Wuxi School of Medicine, Jiangnan University, Wuxi 214122, PR China.

Macromolecule Content 

  • Total Structure Weight: 90.08 kDa 
  • Atom Count: 7,327 
  • Modeled Residue Count: 781 
  • Deposited Residue Count: 794 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Microsomal epoxide hydrolase
A, B
397Aspergillus usamiiMutation(s): 0 
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

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.165 (Depositor), 0.165 (DCC) 
  • R-Value Work:  0.144 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 0.145 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.365α = 90
b = 51.922β = 90.97
c = 133.488γ = 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 ChinaChina21676117

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description