3ZJX

Clostridium perfringens epsilon toxin mutant H149A bound to octyl glucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Clostridium Perfringens Epsilon Toxin H149A Mutant as a Platform for Receptor Binding Studies.

Bokori-Brown, M.Kokkinidou, M.C.Savva, C.G.Da Costa, S.P.Naylor, C.E.Cole, A.R.Moss, D.S.Basak, A.K.Titball, R.W.

(2013) Protein Sci 22: 650

  • DOI: https://doi.org/10.1002/pro.2250
  • Primary Citation of Related Structures:  
    3ZJX

  • PubMed Abstract: 

    Clostridium perfringens epsilon toxin (Etx) is a pore-forming toxin responsible for a severe and rapidly fatal enterotoxemia of ruminants. The toxin is classified as a category B bioterrorism agent by the U.S. Government Centres for Disease Control and Prevention (CDC), making work with recombinant toxin difficult. To reduce the hazard posed by work with recombinant Etx, we have used a variant of Etx that contains a H149A mutation (Etx-H149A), previously reported to have reduced, but not abolished, toxicity. The three-dimensional structure of H149A prototoxin shows that the H149A mutation in domain III does not affect organisation of the putative receptor binding loops in domain I of the toxin. Surface exposed tyrosine residues in domain I of Etx-H149A (Y16, Y20, Y29, Y30, Y36 and Y196) were mutated to alanine and mutants Y30A and Y196A showed significantly reduced binding to MDCK.2 cells relative to Etx-H149A that correlated with their reduced cytotoxic activity. Thus, our study confirms the role of surface exposed tyrosine residues in domain I of Etx in binding to MDCK cells and the suitability of Etx-H149A for further receptor binding studies. In contrast, binding of all of the tyrosine mutants to ACHN cells was similar to that of Etx-H149A, suggesting that Etx can recognise different cell surface receptors. In support of this, the crystal structure of Etx-H149A identified a glycan (β-octyl-glucoside) binding site in domain III of Etx-H149A, which may be a second receptor binding site. These findings have important implications for developing strategies designed to neutralise toxin activity.


  • Organizational Affiliation

    Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom. m.bokori-brown@exeter.ac.uk


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EPSILON-TOXIN
A, B, C, D
289Clostridium perfringens DMutation(s): 1 
UniProt
Find proteins for E7D8R1 (Clostridium perfringens D)
Explore E7D8R1 
Go to UniProtKB:  E7D8R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE7D8R1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.709α = 90
b = 123.709β = 90
c = 127.314γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-05-08
    Changes: Database references
  • Version 1.2: 2015-04-01
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary