1GYG

R32 CLOSED FORM OF ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS STRAIN CER89L43


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of the C. Perfringens Alpha-Toxin with the Active Site Closed by a Flexible Loop Region

Eaton, J.T.Naylor, C.Howells, A.Moss, D.Titball, R.W.Basak, A.K.

(2002) J Mol Biol 319: 275

  • DOI: https://doi.org/10.1016/S0022-2836(02)00290-5
  • Primary Citation of Related Structures:  
    1GYG

  • PubMed Abstract: 

    Clostridium perfringens biotype A strains are the causative agents of gas-gangrene in man and are also implicated as etiological agents in sudden death syndrome in young domestic livestock. The main virulence factor produced by these strains is a zinc-dependent, phosphatidylcholine-preferring phospholipase C (alpha-toxin). The crystal structure of alpha-toxin, at pH 7.5, with the active site open and therefore accessible to substrate has previously been reported, as has calcium-binding to the C-terminal domain of the enzyme at pH 4.7. Here we focus on conformation changes in the N-terminal domain of alpha-toxin in crystals grown at acidic pH. These changes result in both the obscuring of the toxin active site and the loss of one of three zinc ions from it. Additionally, this "closed" form contains a small alpha helix, not present in the open structure, which hydrogen bonds to both the N and C-terminal domains. In conjunction with the previously reported findings that alpha-toxin can exist in active and inactive forms and that Thr74Ile and Phe69Cys substitutions markedly reduced the haemolytic activity of the enzyme, our work suggests that these loop conformations play a critical role in the activity of the toxin.


  • Organizational Affiliation

    Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOLIPASE C
A, B
370Clostridium perfringensMutation(s): 1 
EC: 3.1.4.3
Membrane Entity: Yes 
UniProt
Find proteins for P0C216 (Clostridium perfringens (strain 13 / Type A))
Explore P0C216 
Go to UniProtKB:  P0C216
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C216
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.4α = 90
b = 151.4β = 90
c = 195.5γ = 120
Software Package:
Software NamePurpose
DMmodel building
SCALEPACKdata scaling
AMoREphasing
X-PLORphasing
MLPHAREphasing
DMphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-13
    Type: Initial release
  • Version 1.1: 2011-06-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description