A Pericyclic Reaction enzyme

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Crystal structure of the multifunctional SAM-dependent enzyme LepI provides insights into its catalytic mechanism.

Chang, M.Zhou, Y.Wang, H.Liu, Z.Zhang, Y.Feng, Y.

(2019) Biochem Biophys Res Commun 515: 255-260

  • DOI: https://doi.org/10.1016/j.bbrc.2019.05.031
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Pericyclic reactions are among the most powerful synthetic transformations widely applied in the synthesis of multiple regioselective and stereoselective carbon-carbon bonds. LepI is a recently identified S-adenosyl-l-methionine (SAM)-dependent enzyme, which could catalyze dehydration, Diels-Alder reaction, and the retro-Claisen rearrangement reactions. However, the mechanism underlying these reactions by LepI remains elusive. Here we report the structure of LepI in complex with SAM as its co-factor, which adopts a typical class I methyltransferase fold. Docking studies are performed to investigate the binding modes of various substrates/products and provide insights into the catalytic mechanism of the multiple reactions catalyzed by LepI. Our study suggests that the dehydration reaction may start from the deprotonation of the hydroxyl group on the pyridone ring of the substrate by LepI H133 , during which R295 and D296 play important roles in substrate binding and stabilizing the reaction intermediate. The stereoselective dehydration is accomplished through the trans-conformer of the leaving alcohol group which is trapped by nearby residues. The pericyclic reactions following dehydration are facilitated by the hydrophobic and hydrophilic interactions in the binding pocket. H133 and R295, two residues not conserved in other methyltransferases, might account for the unique activity of LepI among the SAM-dependent methyltransferase family. Together, this study provides important structural insights into the unique reactions catalyzed by LepI and will shed light on the knowledge of mechanisms of pericyclic reactions.

  • Organizational Affiliation

    Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-methyltransferase lepI
A, B
390Aspergillus flavus NRRL3357Mutation(s): 0 
Gene Names: lepIAFLA_066940
EC: 2.1.1
Find proteins for B8NJH3 (Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167))
Explore B8NJH3 
Go to UniProtKB:  B8NJH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8NJH3
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.842α = 90
b = 62.201β = 113.5
c = 113.556γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)China31670766

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release