5UQK

Clostridium difficile toxin A (TcdA) glucosyltransferase domain in complex with U2F

  • Classification: TRANSFERASE
  • Organism(s): Clostridioides difficile
  • Expression System: Bacillus megaterium

  • Deposited: 2017-02-08 Released: 2017-05-10 
  • Deposition Author(s): Alvin, J.W., Lacy, D.B.
  • Funding Organization(s): Department of Veterans Affairs; National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.851 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Clostridium difficile toxin glucosyltransferase domains in complex with a non-hydrolyzable UDP-glucose analogue.

Alvin, J.W.Lacy, D.B.

(2017) J. Struct. Biol. 198: 203-209

  • DOI: 10.1016/j.jsb.2017.04.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clostridium difficile is the leading cause of hospital-acquired diarrhea and pseudomembranous colitis worldwide. The organism produces two homologous toxins, TcdA and TcdB, which enter and disrupt host cell function by glucosylating and thereby inact ...

    Clostridium difficile is the leading cause of hospital-acquired diarrhea and pseudomembranous colitis worldwide. The organism produces two homologous toxins, TcdA and TcdB, which enter and disrupt host cell function by glucosylating and thereby inactivating key signalling molecules within the host. As a toxin-mediated disease, there has been a significant interest in identifying small molecule inhibitors of the toxins' glucosyltransferase activities. This study was initiated as part of an effort to identify the mode of inhibition for a small molecule inhibitor of glucosyltransferase activity called apigenin. In the course of trying to get co-crystals with this inhibitor, we determined five different structures of the TcdA and TcdB glucosyltransferase domains and made use of a non-hydrolyzable UDP-glucose substrate. While we were able to visualize apigenin bound in one of our structures, the site was a crystal packing interface and not likely to explain the mode of inhibition. Nevertheless, the structure allowed us to capture an apo-state (one without the sugar nucleotide substrate) of the TcdB glycosyltransferase domain that had not been previously observed. Comparison of this structure with structures obtained in the presence of a non-hydrolyzable UDP-glucose analogue have allowed us to document multiple conformations of a C-terminal loop important for catalysis. We present our analysis of these five new structures with the hope that it will advance inhibitor design efforts for this important class of biological toxins.


    Organizational Affiliation

    Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37232, USA. Electronic address: borden.lacy@vanderbilt.edu.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37232, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toxin A
A
558Clostridioides difficileMutation(s): 0 
Gene Names: toxA (tcdA)
EC: 3.4.22.-
Find proteins for P16154 (Clostridioides difficile)
Go to UniProtKB:  P16154
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
U2F
Query on U2F

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-NQQHDEILSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.851 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 142.810α = 90.00
b = 142.810β = 90.00
c = 66.074γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Veterans AffairsUnited StatesBx002943
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI095755
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM008320

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-06-14
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence