3HO6

Structure-function analysis of inositol hexakisphosphate-induced autoprocessing in clostridium difficile toxin A

• PDB DOI: https://doi.org/10.2210/pdb3HO6/pdb

• Classification: TOXIN
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-01 Released: 2009-06-23 
• Deposition Author(s): Pruitt, R.N., Lacy, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.198 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Structure-function analysis of inositol hexakisphosphate-induced autoprocessing in Clostridium difficile toxin A.

Pruitt, R.N., Chagot, B., Cover, M., Chazin, W.J., Spiller, B., Lacy, D.B.

(2009) J Biol Chem 284: 21934-21940

• PubMed: 19553670 
• DOI: https://doi.org/10.1074/jbc.M109.018929
• Primary Citation of Related Structures:  
  3HO6


• PubMed Abstract: 
  

  The action of Clostridium difficile toxins A and B depends on inactivation of host small G-proteins by glucosylation. Cellular inositol hexakisphosphate (InsP6) induces an autocatalytic cleavage of the toxins, releasing an N-terminal glucosyltransferase domain into the host cell cytosol. We have defined the cysteine protease domain (CPD) responsible for autoprocessing within toxin A (TcdA) and report the 1.6 A x-ray crystal structure of the domain bound to InsP6. InsP6 is bound in a highly basic pocket that is separated from an unusual active site by a beta-flap structure. Functional studies confirm an intramolecular mechanism of cleavage and highlight specific residues required for InsP6-induced TcdA processing. Analysis of the structural and functional data in the context of sequences from similar and diverse origins highlights a C-terminal extension and a pi-cation interaction within the beta-flap that appear to be unique among the large clostridial cytotoxins.

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Organizational Affiliation: 

Departments of Microbiology and Immunology, Nashville, Tennessee 37232.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.74 kDa 
• Atom Count: 4,734 
• Modelled Residue Count: 495 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin A	A, B	267	Clostridioides difficile	Mutation(s): 0  Gene Names: tcdA, toxA EC: 3.4.22
UniProt
Find proteins for P16154 (Clostridioides difficile) Explore P16154  Go to UniProtKB:  P16154

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	C [auth A], D [auth B]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.198 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.312	α = 90
b = 43.5	β = 112.88
c = 94.692	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Pruitt, R.N., Lacy, D.B.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-10-14
  Changes: Derived calculations, Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references