1QM6

Closed form of Clostridium perfringens alpha-toxin strain NCTC8237


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Characterisation of the Calcium-Binding C-Terminal Domain of Clostridium Perfringens Alpha-Toxin

Naylor, C.E.Jepson, M.Crane, D.T.Titball, R.W.Miller, J.Basak, A.K.Bolgiano, B.

(1999) J.Mol.Biol. 294: 757

  • DOI: 10.1006/jmbi.1999.3279
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Alpha-toxin is the key determinant in gas-gangrene. The toxin, a phospholipase C, cleaves phosphatidylcholine in eukaryotic cell membranes. Calcium ions have been shown to be required for the specific binding of toxin to membranes prior to phospholip ...

    Alpha-toxin is the key determinant in gas-gangrene. The toxin, a phospholipase C, cleaves phosphatidylcholine in eukaryotic cell membranes. Calcium ions have been shown to be required for the specific binding of toxin to membranes prior to phospholipid cleavage. Reported X-ray crystallographic structures of the toxin show that the C-terminal domain has a fold that is analogous to the eukaryotic calcium and membrane-binding C2 domains. We report the binding sites for three calcium ions that have been identified, by crystallographic methods, in the C-terminal domain of the protein close to the postulated membrane-binding surface. The position of these ions at the tip of the domain, and their function (to facilitate membrane binding) is similar to that of calcium ions observed bound to C2 domains. Using the optical spectroscopic techniques of circular dichroism (CD) and fluorescence spectroscopy, pronounced changes to both near and far-UV CD and tryptophan emission fluorescence upon addition of calcium to the C-terminal domain of alpha-toxin have been observed. The changes in near-UV CD, fluorescence enhancement and a 2 nm blue-shift in the fluorescence emission spectrum are consistent with tryptophan residue(s) becoming more immobilised in a hydrophobic environment. Calcium binding appears to be low-affinity: Kd approximately 175-250 microM at pH 8 assuming a 1:1 stoichiometry. as measured by spectroscopic methods.


    Related Citations: 
    • Structure of the Key Toxin in Gas-Gangrene
      Naylor, C.E.,Eaton, J.T.,Howells, A.,Justin, N.,Moss, D.S.,Titball, R.W.,Basak, A.K.
      (1998) Nat.Struct.Mol.Biol. 5: 738
    • Crystallisation and Preliminary X-Ray Diffraction Studies of Alpha-Toxin from Two Different Strains (Nctc-8237 and Cer89L43) of Clostridium Perfringens
      Basak, A.K.,Howells, A.,Eaton, J.T.,Moss, D.S.,Naylor, C.,Miller, J.,Titball, R.W.
      (1998) Acta Crystallogr.,Sect.D 54: 1425


    Organizational Affiliation

    Department of Crystallography, Birkbeck College, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE C
A, B
370Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)Mutation(s): 0 
Gene Names: plc (cpa)
EC: 3.1.4.3
Find proteins for Q0TV31 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Go to UniProtKB:  Q0TV31
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.220 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 149.540α = 90.00
b = 149.540β = 90.00
c = 193.830γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
CNSrefinement
CNSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation, Other