Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 65.02 kDa 
• Atom Count: 4549 
• Residue Count: 537 
• Unique protein chains: 1

3SRZ

Clostridium difficile toxin A (TcdA) glucolsyltransferase domain bound to UDP-glucose

• DOI: 10.2210/pdb3SRZ/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridioides difficile 630
• Expression System: Bacillus megaterium
• Mutation(s): No 


• Deposited: 2011-07-07 Released: 2012-02-01 
• Deposition Author(s): Pruitt, R.N., Chumbler, N.M., Farrow, M.A., Seeback, S.A., Friedman, D.B., Spiller, B.W., Lacy, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.248 
• R-Value Work: 0.177 
• R-Value Observed: 0.183 

Literature

Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity.

Pruitt, R.N., Chumbler, N.M., Rutherford, S.A., Farrow, M.A., Friedman, D.B., Spiller, B., Lacy, D.B.

(2012) J Biol Chem 287: 8013-8020

• PubMed: 22267739 
• DOI: 10.1074/jbc.M111.298414
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.

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Organizational Affiliation: 

Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Toxin A	A	555	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD0663, CD630_06630, tcdA EC: 2.4.1
Find proteins for Q189K5 (Clostridioides difficile (strain 630)) Go to UniProtKB:  Q189K5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG	A	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.248 
• R-Value Work: 0.177 
• R-Value Observed: 0.183 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.779	α = 90
b = 141.779	β = 90
c = 63.351	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-07 
• Released Date: 2012-02-01 
Deposition Author(s): Pruitt, R.N., Chumbler, N.M., Farrow, M.A., Seeback, S.A., Friedman, D.B., Spiller, B.W., Lacy, D.B.

Revision History 

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2012-02-08
  Changes: Database references
• Version 1.2: 2012-03-28
  Changes: Database references