1OLP

Alpha Toxin from Clostridium Absonum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Clostridium Absonum Alpha-Toxin: New Insights Into Clostridial Phospholipase C Substrate Binding and Specificity

Clark, G., Briggs, D.C., Karasawa, T., Wang, X., Cole, A., Maegawa, T., Jayasekera, P., Naylor, C., Miller, J., Moss, D., Nakamura, S., Basak, A.K., Titball, R.

(2003) J Mol Biol 333: 759

  • DOI: 10.1016/j.jmb.2003.07.016
  • Primary Citation of Related Structures:  
    1OLP

  • PubMed Abstract: 

    • Clostridium absonum phospholipase C (Caa) is a 42.7 kDa protein, which shows 60% amino acid sequence identity with the Clostridium perfringens phospholipase C, or alpha-toxin (Cpa), and has been isolated from patients suffering from gas gangrene. We ...

    Clostridium absonum phospholipase C (Caa) is a 42.7 kDa protein, which shows 60% amino acid sequence identity with the Clostridium perfringens phospholipase C, or alpha-toxin (Cpa), and has been isolated from patients suffering from gas gangrene. We report the cloning and sequencing, purification, characterisation and crystal structure of the Caa enzyme. Caa had twice the phospholipid-hydrolysing (lecithinase) activity, 1.5 times the haemolytic activity and over seven times the activity towards phosphatidylcholine-based liposomes when compared with Cpa. However, the Caa enzyme had a lower activity than Cpa to the free (i.e. not in lipid bilayer) substrate para-nitrophenylphosphorylcholine, towards sphingomyelin-based liposomes and showed half the cytotoxicity. The lethal dose (LD(50)) of Caa in mice was approximately twice that of Cpa. The crystal structure of Caa shows that the 72-93 residue loop is in a conformation different from those of previously determined open-form alpha-toxin structures. This conformational change suggests a role for W84 in membrane binding and a possible route of entry into the active site along a hydrophobic channel created by the re-arrangement of this loop. Overall, the properties of Caa are compatible with a role as a virulence-determinant in gas gangrene caused by C.absonum.

    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 Biol 5: 738
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-TOXINA, B, C, D370Clostridium sardinienseMutation(s): 0 
EC: 3.1.4.3
Find proteins for Q8GCY3 (Clostridium sardiniense)
Explore Q8GCY3 
Go to UniProtKB:  Q8GCY3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.956α = 90
b = 193.592β = 90
c = 92.686γ = 90
Software Package:
Software NamePurpose
AMoREmodel building
REFMACrefinement
SCALAdata scaling
MOLREPphasing
CNSphasing
COMOphasing
AMoREphasing
EPMRphasing
XFITphasing
Ophasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-23
    Type: Initial release
  • Version 1.1: 2012-09-05
    Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance