5YAO

The complex structure of SZ529 and expoxid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report



Literature

Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations

Sun, Z.Wu, L.Bocola, M.Chan, H.C.S.Lonsdale, R.Kong, X.D.Yuan, S.Zhou, J.Reetz, M.T.

(2018) J Am Chem Soc 140: 310-318

  • DOI: 10.1021/jacs.7b10278
  • Primary Citation of Related Structures:  
    5YAO, 5YNG, 5YQT

  • PubMed Abstract: 
  • Directed evolution of limonene epoxide hydrolase (LEH), which catalyzes the hydrolytic desymmetrization reactions of cyclopentene oxide and cyclohexene oxide, results in (R,R)- and (S,S)-selective mutants. Their crystal structures combined with exten ...

    Directed evolution of limonene epoxide hydrolase (LEH), which catalyzes the hydrolytic desymmetrization reactions of cyclopentene oxide and cyclohexene oxide, results in (R,R)- and (S,S)-selective mutants. Their crystal structures combined with extensive theoretical computations shed light on the mechanistic intricacies of this widely used enzyme. From the computed activation energies of various pathways, we discover the underlying stereochemistry for favorable reactions. Surprisingly, some of the most enantioselective mutants that rapidly convert cyclohexene oxide do not catalyze the analogous transformation of the structurally similar cyclopentene oxide, as shown by additional X-ray structures of the variants harboring this slightly smaller substrate. We explain this puzzling observation on the basis of computational calculations which reveal a disrupted alignment between nucleophilic water and cyclopentene oxide due to the pronounced flexibility of the binding pocket. In contrast, in the stereoselective reactions of cyclohexene oxide, reactive conformations are easily reached. The unique combination of structural and computational data allows insight into mechanistic details of this epoxide hydrolase and provides guidance for future protein engineering in reactions of structurally different substrates.


    Organizational Affiliation

    Fachbereich Chemie der Philipps Universität , Hans-Meerwein-Strasse, 35032 Marburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Limonene-1,2-epoxide hydrolaseAB155Rhodococcus erythropolisMutation(s): 4 
Gene Names: limA
EC: 3.3.2.8
Find proteins for Q9ZAG3 (Rhodococcus erythropolis)
Explore Q9ZAG3 
Go to UniProtKB:  Q9ZAG3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3ZS
Query on 3ZS

Download CCD File 
A
(1R,5S)-6-oxabicyclo[3.1.0]hexane
C5 H8 O
GJEZBVHHZQAEDB-SYDPRGILSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.226α = 90
b = 61.097β = 90
c = 120.793γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Strategic Priority Research Program (B) of the Chinese Academy of SciencesChinaXDB20000000
Science and Technology Commission of Shanghai MunicipalityChina15JC1400403

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release