5UQL

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

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

  • 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 (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.jsb.2017.04.006
  • Primary Citation of Related Structures:  
    5UQK, 5UQL, 5UQM, 5UQN, 5UQT

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin A558Clostridioides difficileMutation(s): 0 
Gene Names: toxAtcdA
EC: 3.4.22
UniProt
Find proteins for P16154 (Clostridioides difficile)
Explore P16154 
Go to UniProtKB:  P16154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16154
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U2F
Query on U2F

Download Ideal Coordinates CCD File 
C [auth A]URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-NQQHDEILSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.116α = 90
b = 142.116β = 90
c = 63.003γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Veterans AffairsUnited StatesBX002943
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI095755
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM008320

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description