5ZZD

Crystal structure of a protein from Aspergillus flavus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Literature

Crystal structure of LepI, a multifunctional SAM-dependent enzyme which catalyzes pericyclic reactions in leporin biosynthesis.

Chang, Z.Ansbacher, T.Zhang, L.Yang, Y.Ko, T.P.Zhang, G.Liu, W.Huang, J.W.Dai, L.Guo, R.T.Major, D.T.Chen, C.C.

(2019) Org Biomol Chem 17: 2070-2076

  • DOI: https://doi.org/10.1039/c8ob02758g
  • Primary Citation of Related Structures:  
    5ZZD

  • PubMed Abstract: 

    LepI is a novel multifunctional enzyme that catalyzes stereoselective dehydration, Diels-Alder reaction, and retro-Claisen rearrangement. Here we report the crystal structure of LepI in complex with its co-factor S-adenosyl methionine (SAM). LepI forms a tetramer via the N-terminal helical domain and binds to a SAM molecule in the C-terminal catalytic domain. The binding modes of various LepI substrates are investigated by docking simulations, which suggest that the substrates are bound via both hydrophobic and hydrophilic forces, as well as cation-π interactions with the positively charged SAM. The reaction starts with a dehydration step in which H133 possibly deprotonates the pyridone hydroxyl group of the substrate, while D296 might protonate an alkyl-chain hydroxyl group. Subsequent pericyclization may be facilitated by the correct fold of the substrate's alkyl chain and a thermodynamic driving force towards σ-bonds at the expense of π-bonds. These results provide structural insights into LepI catalysis and are important in understanding the mechanism of enzymatic pericyclization.


  • Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-methyltransferase lepI
A, B
387Aspergillus flavus NRRL3357Mutation(s): 0 
Gene Names: lepIAFLA_066940
EC: 2.1.1
UniProt
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
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.438α = 90
b = 62.202β = 113.31
c = 113.166γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
SHELXphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references