7VRG

Crystal structure of chitinase-h from O. furnacalis in complex with Lynamicin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Lynamicin B is a Potential Pesticide by Acting as a Lepidoptera-Exclusive Chitinase Inhibitor.

Lu, Q.Xu, L.Liu, L.Zhou, Y.Liu, T.Song, Y.Ju, J.Yang, Q.

(2021) J Agric Food Chem 69: 14086-14091

  • DOI: https://doi.org/10.1021/acs.jafc.1c05385
  • Primary Citation of Related Structures:  
    7VRG

  • PubMed Abstract: 

    Insect group h chitinase is a promising target for designing non-target safe pesticides in that it is exclusively distributed in lepidopteran insects, over 80% of which are agricultural pests. In this work, lynamicin B was discovered to be an inhibitor of Of Chi-h, the group h chitinase from the lepidopteran pest Ostrinia furnacalis . Lynamicin B was revealed to competitively inhibit Of Chi-h with a K i value of 8.76 μM and does not significantly inhibit other chitinases. The co-crystal structure of lynamicin B and Of Chi-h revealed that the dichloroindolyl group of lynamicin B occupies an unexplored pocket below subsites +1 and +2 of the substrate-binding cleft, which is vital for its selectivity. Feeding experiments demonstrated that lynamicin B exhibited high insecticidal activities against other lepidopteran pests Mythimna separata and Spodoptera frugiperda besides O. furnacalis . Moreover, lynamicin B did not affect Trichogramma ostriniae , a natural enemy of O. furnacalis . This study provides a natural-derived potent pesticide for the control of lepidopteran pests, leaving its natural enemy unaffected.


  • Organizational Affiliation

    School of Bioengineering, Dalian University of Technology, Dalian 116024, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase
A, B
540Ostrinia furnacalisMutation(s): 0 
Gene Names: OfChi-h
UniProt
Find proteins for Q4AE59 (Ostrinia furnacalis)
Explore Q4AE59 
Go to UniProtKB:  Q4AE59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4AE59
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth L],
D [auth C]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.908α = 113.634
b = 77.859β = 109.902
c = 81.972γ = 95
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description