6KXH

Alp1U_Y247F mutant in complex with Fluostatin C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mutation of an atypical oxirane oxyanion hole improves regioselectivity of the alpha / beta-fold epoxide hydrolase Alp1U.

Zhang, L.De, B.C.Zhang, W.Mandi, A.Fang, Z.Yang, C.Zhu, Y.Kurtan, T.Zhang, C.

(2020) J Biol Chem 295: 16987-16997

  • DOI: 10.1074/jbc.RA120.015563
  • Primary Citation of Related Structures:  
    6KXH, 6KXR, 7CLZ

  • PubMed Abstract: 
  • Epoxide hydrolases (EHs) have been characterized and engineered as biocatalysts that convert epoxides to valuable chiral vicinal diol precursors of drugs and bioactive compounds. Nonetheless, the regioselectivity control of the epoxide ring opening by EHs remains challenging ...

    Epoxide hydrolases (EHs) have been characterized and engineered as biocatalysts that convert epoxides to valuable chiral vicinal diol precursors of drugs and bioactive compounds. Nonetheless, the regioselectivity control of the epoxide ring opening by EHs remains challenging. Alp1U is an α/β-fold EH that exhibits poor regioselectivity in the epoxide hydrolysis of fluostatin C (compound 1) and produces a pair of stereoisomers. Herein, we established the absolute configuration of the two stereoisomeric products and determined the crystal structure of Alp1U. A Trp-186/Trp-187/Tyr-247 oxirane oxygen hole was identified in Alp1U that replaced the canonical Tyr/Tyr pair in α/β-EHs. Mutation of residues in the atypical oxirane oxygen hole of Alp1U improved the regioselectivity for epoxide hydrolysis on 1. The single site Y247F mutation led to highly regioselective (98%) attack at C-3 of 1, whereas the double mutation W187F/Y247F resulted in regioselective (94%) nucleophilic attack at C-2. Furthermore, single-crystal X-ray structures of the two regioselective Alp1U variants in complex with 1 were determined. These findings allowed insights into the reaction details of Alp1U and provided a new approach for engineering regioselective epoxide hydrolases.


    Organizational Affiliation

    Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, and South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; University of the Chinese Academy of Sciences, Beijing, China. Electronic address: wzhang@scsio.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative hydrolaseA, B, C, D339Streptomyces ambofaciens ATCC 23877Mutation(s): 1 
Gene Names: SAMT0137SAMT0138SAM23877_0167SAM23877_7506
EC: 3.3.2.3
UniProt
Find proteins for A0A0K2AJY3 (Streptomyces ambofaciens (strain ATCC 23877 / 3486 / DSM 40053 / JCM 4204 / NBRC 12836 / NRRL B-2516))
Explore A0A0K2AJY3 
Go to UniProtKB:  A0A0K2AJY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K2AJY3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.477α = 90
b = 101.562β = 90
c = 117.481γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina41606193
National Natural Science Foundation of ChinaChina31820103003

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references, Structure summary
  • Version 1.2: 2020-12-30
    Changes: Database references