6JAV | pdb_00006jav

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

• PDB DOI: https://doi.org/10.2210/pdb6JAV/pdb

• Classification: HYDROLASE
• Organism(s): Ostrinia furnacalis
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2019-01-25 Released: 2019-05-15 
• Deposition Author(s): Chen, W., Zhou, Y., Yang, Q.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

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

Chen, W., Zhou, Y., Yang, Q.

(2019) J Biological Chem 294: 9358-9364

• PubMed: 31053640 
• DOI: https://doi.org/10.1074/jbc.RA119.007812
• Primary Citation 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. 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.

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Organizational Affiliation: 
• From the State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing 100193, China and.
School of Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.
From the State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing 100193, China and [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.1 kDa 
• Atom Count: 3,442 
• Modeled Residue Count: 377 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Group II chitinase	A	389	Ostrinia furnacalis	Mutation(s): 0  EC: 3.2.1.14
UniProt
Find proteins for A0A221ZS22 (Ostrinia furnacalis) Explore A0A221ZS22  Go to UniProtKB:  A0A221ZS22
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BC0 (Subject of Investigation/LOI)	B [auth A]	2-{[(4-chlorophenyl)methyl]sulfanyl}-7-methyl-N-(prop-2-en-1-yl)-7,8-dihydropyrido[4',3':4,5]thieno[2,3-d]pyrimidin-4-amine C20 H19 Cl N4 S2 BXZWDXRSYVMRMU-UHFFFAOYSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.643	α = 90
b = 98.643	β = 90
c = 94.884	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Chen, W., Zhou, Y., Yang, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31425021

Revision History  

• 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
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-13
  Changes: Structure summary