1KHO

Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 

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This is version 1.3 of the entry. See complete history


Literature

The first strain of Clostridium perfringens isolated from an avian source has an alpha-toxin with divergent structural and kinetic properties.

Justin, N.Walker, N.Bullifent, H.L.Songer, G.Bueschel, D.M.Jost, H.Naylor, C.Miller, J.Moss, D.S.Titball, R.W.Basak, A.K.

(2002) Biochemistry 41: 6253-6262

  • DOI: https://doi.org/10.1021/bi012015v
  • Primary Citation of Related Structures:  
    1KHO

  • PubMed Abstract: 

    Clostridium perfringens alpha-toxin is a 370-residue, zinc-dependent, phospholipase C that is the key virulence determinant in gas gangrene. It is also implicated in the pathogenesis of sudden death syndrome in young animals and necrotic enteritis in chickens. Previously characterized alpha-toxins from different strains of C. perfringens are almost identical in sequence and biochemical properties. We describe the cloning, nucleotide sequencing, expression, characterization, and crystal structure of alpha-toxin from an avian strain, SWan C. perfringens (SWCP), which has a large degree of sequence variation and altered substrate specificity compared to these strains. The structure of alpha-toxin from strain CER89L43 has been previously reported in open (active site accessible to substrate) and closed (active site obscured by loop movements) conformations. The SWCP structure is in an open-form conformation, with three zinc ions in the active site. This is the first example of an open form of alpha-toxin crystallizing without the addition of divalent cations to the crystallization buffer, indicating that the protein can retain three zinc ions bound in the active site. The topology of the calcium binding site formed by residues 269, 271, 336, and 337, which is essential for membrane binding, is significantly altered in comparison with both the open and closed alpha-toxin structures. We are able to relate these structural changes to the different substrate specificity and membrane binding properties of this divergent alpha-toxin. This will provide essential information when developing an effective vaccine that will protect against C. perfringens infection in a wide range of domestic livestock.


  • Organizational Affiliation

    School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alpha-toxin
A, B
370Clostridium perfringensMutation(s): 0 
Gene Names: CPA
Membrane Entity: Yes 
UniProt
Find proteins for Q9RF12 (Clostridium perfringens)
Explore Q9RF12 
Go to UniProtKB:  Q9RF12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RF12
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.23α = 90
b = 117.23β = 90
c = 220.59γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations