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 report the cloning and sequencing, purification, characterisation and crystal structure of the Caa enzyme ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-TOXINA, B, C, D370Clostridium sardinienseMutation(s): 0 
EC: 3.1.4.3
Membrane Entity: Yes 
UniProt
Find proteins for Q8GCY3 (Clostridium sardiniense)
Explore Q8GCY3 
Go to UniProtKB:  Q8GCY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GCY3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
S [auth C],
V [auth D],
W [auth D],
X [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B],
O [auth C],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
O [auth C],
P [auth C],
T [auth D],
U [auth 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




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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