8WBO | pdb_00008wbo

Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] mutant D18N complexed with sulfate ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Deciphering the stereo-specific catalytic mechanisms of cis-epoxysuccinate hydrolases producing L(+)-tartaric acid.

Dong, S.Xuan, J.Feng, Y.Cui, Q.

(2024) J Biological Chem 300: 105635-105635

  • DOI: https://doi.org/10.1016/j.jbc.2024.105635
  • Primary Citation Related Structures: 
    8WBK, 8WBL, 8WBM, 8WBN, 8WBO, 8WBP, 8WBQ, 8WBR, 8WBS, 8WBT

  • PubMed Abstract: 

    Microbial epoxide hydrolases, cis-epoxysuccinate hydrolases (CESHs), have been utilized for commercial production of enantiomerically pure L(+)- and D(-)-tartaric acids for decades. However, the stereo-catalytic mechanism of CESH producing L(+)-tartaric acid (CESH[L]) remains unclear. Herein, the crystal structures of two CESH[L]s in ligand-free, product-complexed, and catalytic intermediate forms were determined. These structures revealed the unique specific binding mode for the mirror-symmetric substrate, an active catalytic triad consisting of Asp-His-Glu, and an arginine providing a proton to the oxirane oxygen to facilitate the epoxide ring-opening reaction, which has been pursued for decades. These results provide the structural basis for the rational engineering of these industrial biocatalysts.


  • Organizational Affiliation
    • CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 29.54 kDa 
  • Atom Count: 2,134 
  • Modeled Residue Count: 237 
  • Deposited Residue Count: 264 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epoxide hydrolase264Rhodococcus opacusMutation(s): 1 
Gene Names: eph
UniProt
Find proteins for Q1KLR5 (Rhodococcus opacus)
Explore Q1KLR5 
Go to UniProtKB:  Q1KLR5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1KLR5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.804α = 90
b = 59.521β = 108.41
c = 68.677γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171203

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Structure summary