Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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This is version 1.2 of the entry. See complete history


Conformational Changes and Reaction of Clostridial Glycosylating Toxins.

Ziegler, M.O.P.Jank, T.Aktories, K.Schulz, G.E.

(2008) J Mol Biol 377: 1346

  • DOI: https://doi.org/10.1016/j.jmb.2007.12.065
  • Primary Citation of Related Structures:  
    2VK9, 2VKD, 2VKH

  • PubMed Abstract: 

    The crystal structures of the catalytic fragments of 'lethal toxin' from Clostridium sordellii and of 'alpha-toxin' from Clostridium novyi have been established. Almost half of the residues follow the chain fold of the glycosyl-transferase type A family of enzymes; the other half forms large alpha-helical protrusions that are likely to confer specificity for the respective targeted subgroup of Rho proteins in the cell. In the crystal, the active center of alpha-toxin contained no substrates and was disassembled, whereas that of lethal toxin, which was ligated with the donor substrate UDP-glucose and cofactor Mn2+, was catalytically competent. Surprisingly, the structure of lethal toxin with Ca2+ (instead of Mn2+) at the cofactor position showed a bound donor substrate with a disassembled active center, indicating that the strictly octahedral coordination sphere of Mn2+ is indispensable to the integrity of the enzyme. The homologous structures of alpha-toxin without substrate, distorted lethal toxin with Ca2+ plus donor, active lethal toxin with Mn2+ plus donor and the homologous Clostridium difficile toxin B with a hydrolyzed donor have been lined up to show the geometry of several reaction steps. Interestingly, the structural refinement of one of the three crystallographically independent molecules of Ca2+-ligated lethal toxin resulted in the glucosyl half-chair conformation expected for glycosyl-transferases that retain the anomeric configuration at the C1'' atom. A superposition of six acceptor substrates bound to homologous enzymes yielded the position of the nucleophilic acceptor atom with a deviation of <1 A. The resulting donor-acceptor geometry suggests that the reaction runs as a circular electron transfer in a six-membered ring, which involves the deprotonation of the nucleophile by the beta-phosphoryl group of the donor substrate UDP-glucose.

  • Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, D-79104 Freiburg im Breisgau, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-TOXIN551Clostridium novyiMutation(s): 0 
Find proteins for Q46149 (Clostridium novyi)
Explore Q46149 
Go to UniProtKB:  Q46149
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46149
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.612α = 90
b = 154.612β = 90
c = 77.605γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance