5ZNX

Crystal structure of CM14-treated HlyU from Vibrio vulnificus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Small-molecule inhibitor of HlyU attenuates virulence of Vibrio species.

Lee, Z.W.Kim, B.S.Jang, K.K.Bang, Y.J.Kim, S.Ha, N.C.Jung, Y.H.Lee, H.J.Han, H.J.Kim, J.S.Kim, J.Sahu, P.K.Jeong, L.S.Kim, M.H.Choi, S.H.

(2019) Sci Rep 9: 4346-4346

  • DOI: https://doi.org/10.1038/s41598-019-39554-y
  • Primary Citation of Related Structures:  
    5ZNX

  • PubMed Abstract: 

    Increasing antibiotic resistance has led to the development of new strategies to combat bacterial infection. Anti-virulence strategies that impair virulence of bacterial pathogens are one of the novel approaches with less selective pressure for developing resistance than traditional strategies that impede viability. In this study, a small molecule CM14 [N-(4-oxo-4H-thieno[3,4-c]chromen-3-yl)-3-phenylprop-2-ynamide] that inhibits the activity of HlyU, a transcriptional regulator essential for the virulence of the fulminating human pathogen Vibrio vulnificus, has been identified. Without affecting bacterial growth or triggering the host cell death, CM14 reduces HlyU-dependent expression of virulence genes in V. vulnificus. In addition to the decreased hemolysis of human erythrocytes, CM14 impedes host cell rounding and lysis caused by V. vulnificus. Notably, CM14 significantly enhances survival of mice infected with V. vulnificus by alleviating hepatic and renal dysfunction and systemic inflammation. Biochemical, mass spectrometric, and mutational analyses revealed that CM14 inhibits HlyU from binding to target DNA by covalently modifying Cys30. Remarkably, CM14 decreases the expression of various virulence genes of other Vibrio species and thus attenuates their virulence phenotypes. Together, this molecule could be an anti-virulence agent against HlyU-harboring Vibrio species with a low selective pressure for the emergence of resistance.


  • Organizational Affiliation

    National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology and Center for Food Safety and Toxicology, Seoul National University, Seoul, 08826, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional activator102Vibrio vulnificus CMCP6Mutation(s): 0 
UniProt
Find proteins for A0A3Q0L222 (Vibrio vulnificus (strain CMCP6))
Explore A0A3Q0L222 
Go to UniProtKB:  A0A3Q0L222
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q0L222
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.142α = 90
b = 35.142β = 90
c = 180.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
MOLREPmodel building
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description