The structure of chitin deacetylase VdPDA1 from Verticillium dahliae

Experimental Data Snapshot

  • Resolution: 2.64 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Inhibition of chitin deacetylases to attenuate plant fungal diseases.

Liu, L.Xia, Y.Li, Y.Zhou, Y.Su, X.Yan, X.Wang, Y.Liu, W.Cheng, H.Wang, Y.Yang, Q.

(2023) Nat Commun 14: 3857-3857

  • DOI: https://doi.org/10.1038/s41467-023-39562-7
  • Primary Citation of Related Structures:  
    8HE1, 8HE2, 8HE4, 8HF9, 8HFA

  • PubMed Abstract: 

    Phytopathogenic fungi secrete chitin deacetylase (CDA) to escape the host's immunological defense during infection. Here, we showed that the deacetylation activity of CDA toward chitin is essential for fungal virulence. Five crystal structures of two representative and phylogenetically distant phytopathogenic fungal CDAs, VdPDA1 from Verticillium dahliae and Pst_13661 from Puccinia striiformis f. sp. tritici, were obtained in ligand-free and inhibitor-bound forms. These structures suggested that both CDAs have an identical substrate-binding pocket and an Asp-His-His triad for coordinating a transition metal ion. Based on the structural identities, four compounds with a benzohydroxamic acid (BHA) moiety were obtained as phytopathogenic fungal CDA inhibitors. BHA exhibited high effectiveness in attenuating fungal diseases in wheat, soybean, and cotton. Our findings revealed that phytopathogenic fungal CDAs share common structural features, and provided BHA as a lead compound for the design of CDA inhibitors aimed at attenuating crop fungal diseases.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NodB homology domain-containing protein
A, B, C, D, E
253Verticillium dahliaeMutation(s): 0 
Gene Names: VD0003_g2480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.64 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.617α = 90
b = 125.899β = 90
c = 127.007γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32001938

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description