6JAW

Crystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 1 in complex with a napthalimide derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Literature

Structural dissection reveals a general mechanistic principle for group II chitinase (ChtII) inhibition.

Chen, W.Zhou, Y.Yang, Q.

(2019) J Biol Chem 294: 9358-9364

  • DOI: 10.1074/jbc.RA119.007812
  • Primary Citation of Related Structures:  
    6JAV, 6JAW, 6JAX, 6JAY

  • PubMed Abstract: 
  • Small-molecule inhibitors of insect chitinases have potential applications for controlling insect pests. Insect group II chitinase (ChtII) is the most important chitinase in insects and functions throughout all developmental stages. However, the possibility of inhibiting ChtII by small molecules has not been explored yet ...

    Small-molecule inhibitors of insect chitinases have potential applications for controlling insect pests. Insect group II chitinase (ChtII) is the most important chitinase in insects and functions throughout all developmental stages. However, the possibility of inhibiting ChtII by small molecules has not been explored yet. Here, we report the structural characteristics of four molecules that exhibited similar levels of inhibitory activity against Of ChtII, a group II chitinase from the agricultural pest Asian corn borer Ostrinia furnacalis These inhibitors were chitooctaose ((GlcN) 8 ), dipyrido-pyrimidine derivative (DP), piperidine-thienopyridine derivative (PT), and naphthalimide derivative (NI). The crystal structures of the Of ChtII catalytic domain complexed with each of the four inhibitors at 1.4-2.0 Å resolutions suggested they all exhibit similar binding modes within the substrate-binding cleft; specifically, two hydrophobic groups of the inhibitor interact with +1/+2 tryptophan and a -1 hydrophobic pocket. The structure of the (GlcN) 8 complex surprisingly revealed that the oligosaccharide chain of the inhibitor is orientated in the opposite direction to that previously observed in complexes with other chitinases. Injection of the inhibitors into 4th instar O. furnacalis larvae led to defects in development and pupation. The results of this study provide insights into a general mechanistic principle that confers inhibitory activity against ChtII, which could facilitate rational design of agrochemicals that target ecdysis of insect pests.


    Organizational Affiliation

    School of Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Group II chitinaseA389Ostrinia furnacalisMutation(s): 0 
EC: 3.2.1.14
UniProt
Find proteins for A0A221ZS22 (Ostrinia furnacalis)
Explore A0A221ZS22 
Go to UniProtKB:  A0A221ZS22
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BBO (Subject of Investigation/LOI)
Query on BBO

Download Ideal Coordinates CCD File 
B [auth A]2-[3-(morpholin-4-yl)propyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione
C19 H20 N2 O3
GQPIEFFYGONFTJ-UHFFFAOYSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BBO Binding MOAD:  6JAW Ki: 2180 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.314α = 90
b = 98.314β = 90
c = 94.053γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31425021

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary