7VX2

Crystal Structure of the Y53F/N55A/I80F/L114V/I116V mutant of LEH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Rational enzyme design for enabling biocatalytic Baldwin cyclization and asymmetric synthesis of chiral heterocycles.

Li, J.K.Qu, G.Li, X.Tian, Y.Cui, C.Zhang, F.G.Zhang, W.Ma, J.A.Reetz, M.T.Sun, Z.

(2022) Nat Commun 13: 7813-7813

  • DOI: https://doi.org/10.1038/s41467-022-35468-y
  • Primary Citation of Related Structures:  
    7VWD, 7VWM, 7VX2, 7XEE, 7XEF

  • PubMed Abstract: 

    Chiral heterocyclic compounds are needed for important medicinal applications. We report an in silico strategy for the biocatalytic synthesis of chiral N- and O-heterocycles via Baldwin cyclization modes of hydroxy- and amino-substituted epoxides and oxetanes using the limonene epoxide hydrolase from Rhodococcus erythropolis. This enzyme normally catalyzes hydrolysis with formation of vicinal diols. Firstly, the required shutdown of the undesired natural water-mediated ring-opening is achieved by rational mutagenesis of the active site. In silico enzyme design is then continued with generation of the improved mutants. These variants prove to be versatile catalysts for preparing chiral N- and O-heterocycles with up to 99% conversion, and enantiomeric ratios up to 99:1. Crystal structural data and computational modeling reveal that Baldwin-type cyclizations, catalyzed by the reprogrammed enzyme, are enabled by reshaping the active-site environment that directs the distal RHN and HO-substituents to be intramolecular nucleophiles.


  • Organizational Affiliation

    Department of Chemistry, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Limonene-1,2-epoxide hydrolase
A, B, C, D
155Rhodococcus erythropolisMutation(s): 5 
Gene Names: limA
EC: 3.3.2.8
UniProt
Find proteins for Q9ZAG3 (Rhodococcus erythropolis)
Explore Q9ZAG3 
Go to UniProtKB:  Q9ZAG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZAG3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.154α = 90
b = 84.039β = 90
c = 93.371γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description