3PEE

Structure of the C. difficile TcdB cysteine protease domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Defining an allosteric circuit in the cysteine protease domain of Clostridium difficile toxins.

Shen, A.Lupardus, P.J.Gersch, M.M.Puri, A.W.Albrow, V.E.Garcia, K.C.Bogyo, M.

(2011) Nat Struct Mol Biol 18: 364-371

  • DOI: https://doi.org/10.1038/nsmb.1990
  • Primary Citation of Related Structures:  
    3PEE

  • PubMed Abstract: 

    An internal cysteine protease domain (CPD) autoproteolytically regulates Clostridium difficile glucosylating toxins by releasing a cytotoxic effector domain into target cells. CPD activity is itself allosterically regulated by the eukaryote-specific molecule inositol hexakisphosphate (InsP(6)). Although allostery controls the function of most proteins, the molecular details underlying this regulatory mechanism are often difficult to characterize. Here we use chemical probes to show that apo-CPD is in dynamic equilibrium between active and inactive states. InsP(6) markedly shifts this equilibrium toward an active conformer that is further restrained upon binding a suicide substrate. Structural analyses combined with systematic mutational and disulfide bond engineering studies show that residues within a β-hairpin region functionally couple the InsP(6)-binding site to the active site. Collectively, our results identify an allosteric circuit that allows bacterial virulence factors to sense and respond to the eukaryotic environment.


  • Organizational Affiliation

    Department of Pathology, Stanford School of Medicine, Stanford, CA, USA. ashen2@stanford.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin BA [auth B],
B [auth A]
254Clostridioides difficile 630Mutation(s): 0 
Gene Names: CD0660tcdB
EC: 2.4.1
UniProt
Find proteins for Q189K3 (Clostridioides difficile (strain 630))
Explore Q189K3 
Go to UniProtKB:  Q189K3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ189K3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.11α = 90
b = 45.71β = 103.48
c = 87.35γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2011-08-31
    Changes: Database references
  • Version 1.3: 2020-10-14
    Changes: Derived calculations, Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Refinement description