8JBW

Crystal structure of ZtHPPD-(+)-Usnic acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Development of 4-Hydroxyphenylpyruvate Dioxygenase as a Novel Crop Fungicide Target.

Yu, X.H.Dong, J.Fan, C.P.Chen, M.X.Li, M.Zheng, B.F.Hu, Y.F.Lin, H.Y.Yang, G.F.

(2023) J Agric Food Chem 71: 19396-19407

  • DOI: https://doi.org/10.1021/acs.jafc.3c05260
  • Primary Citation of Related Structures:  
    8JBW

  • PubMed Abstract: 

    Plant pathogenic fungi pose a significant threat to crop yields and quality, and the emergence of fungicide resistance has further exacerbated the problem in agriculture. Therefore, there is an urgent need for efficient and environmentally friendly fungicides. In this study, we investigated the antifungal activity of (+)-Usnic acid and its inhibitory effect on crop pathogenic fungal 4-hydroxyphenylpyruvate dioxygenases (HPPDs) and determined the structure of Zymoseptoria tritici HPPD ( Zt HPPD)-(+)-Usnic acid complex. Thus, the antifungal target of (+)-Usnic acid and its inhibitory basis toward HPPD were uncovered. Additionally, we discovered a potential lead fungicide possessing a novel scaffold that displayed remarkable antifungal activities. Furthermore, our molecular docking analysis revealed the unique binding mode of this compound with Zt HPPD, explaining its high inhibitory effect. We concluded that HPPD represents a promising target for the control of phytopathogenic fungi, and the new compound serves as a novel starting point for the development of fungicides and dual-purpose pesticides.


  • Organizational Affiliation

    National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxyphenylpyruvate dioxygenase419Zymoseptoria triticiMutation(s): 0 
Gene Names: HPPD
EC: 1.13.11.27
UniProt
Find proteins for O42764 (Zymoseptoria tritici)
Explore O42764 
Go to UniProtKB:  O42764
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO42764
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AIY
Query on AIY

Download Ideal Coordinates CCD File 
C [auth A](9bR)-2,6-diethanoyl-8,9b-dimethyl-3,7,9-tris(oxidanyl)dibenzofuran-1-one
C18 H16 O7
WEYVVCKOOFYHRW-SFHVURJKSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
B [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.348α = 90
b = 110.348β = 90
c = 80.849γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data 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 China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary