7DFT

Crystal structure of Xanthomonas oryzae ClpP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Dysregulation of ClpP by Small-Molecule Activators Used Against Xanthomonas oryzae pv. oryzae Infections.

Yang, T.Zhang, T.Zhou, X.Wang, P.Gan, J.Song, B.Yang, S.Yang, C.G.

(2021) J Agric Food Chem 69: 7545-7553

  • DOI: https://doi.org/10.1021/acs.jafc.1c01470
  • Primary Citation of Related Structures:  
    7DFT, 7DFU

  • PubMed Abstract: 

    Rice bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae ( Xoo ) is considered a destructive plant bacterial disease. The looming crisis of antibiotic resistance necessitates the discovery of antibiotics with new modes of action. Activated caseinolytic protease P (ClpP) can degrade bacterial FtsZ proteins that are essential for cell division; thus, we hypothesized that small-molecule-induced dysregulation of Xoo ClpP may result in degradation of Xoo FtsZ to treat leaf blight diseases. In this work, we have determined the crystal structures of Xoo ClpP, and its mutant bound with ADEP4, which revealed the action modes of Xoo ClpP assemblies and Xoo FtsZ degradation by dysregulated Xoo ClpP in the presence of small-molecule activators, such as ONC212 and ADEP4. Additionally, an antibacterial assessment demonstrated that ONC212 displays excellent activity against Xoo and prevents rice bacterial leaf blight in vivo . Thus, these unique antibacterial effects of small-molecule activators of Xoo ClpP represent a potential strategy for the development of agricultural antibiotics by targeting bacterial ClpP.


  • Organizational Affiliation

    State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E
A, B, C, D, E, F, G
208Xanthomonas oryzaeMutation(s): 0 
Gene Names: clpPADT25_23080ADT27_15185EYR26_04825
EC: 3.4.21.92
UniProt
Find proteins for Q5H434 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85))
Explore Q5H434 
Go to UniProtKB:  Q5H434
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5H434
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.548α = 90
b = 132.548β = 90
c = 187.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22037007

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description