5N0L

The structure of the cofactor binding GAF domain of the nutrient sensor CodY from Clostridium difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027.

Daou, N.Wang, Y.Levdikov, V.M.Nandakumar, M.Livny, J.Bouillaut, L.Blagova, E.Zhang, K.Belitsky, B.R.Rhee, K.Wilkinson, A.J.Sun, X.Sonenshein, A.L.

(2019) PLoS One 14: e0206896-e0206896

  • DOI: https://doi.org/10.1371/journal.pone.0206896
  • Primary Citation of Related Structures:  
    5N0L

  • PubMed Abstract: 

    Toxin synthesis and endospore formation are two of the most critical factors that determine the outcome of infection by Clostridioides difficile. The two major toxins, TcdA and TcdB, are the principal factors causing damage to the host. Spores are the infectious form of C. difficile, permit survival of the bacterium during antibiotic treatment and are the predominant cell form that leads to recurrent infection. Toxin production and sporulation have their own specific mechanisms of regulation, but they share negative regulation by the global regulatory protein CodY. Determining the extent of such regulation and its detailed mechanism is important for understanding the linkage between two apparently independent biological phenomena and raises the possibility of creating new ways of limiting infection. The work described here shows that a codY null mutant of a hypervirulent (ribotype 027) strain is even more virulent than its parent in a mouse model of infection and that the mutant expresses most sporulation genes prematurely during exponential growth phase. Moreover, examining the expression patterns of mutants producing CodY proteins with different levels of residual activity revealed that expression of the toxin genes is dependent on total CodY inactivation, whereas most sporulation genes are turned on when CodY activity is only partially diminished. These results suggest that, in wild-type cells undergoing nutrient limitation, sporulation genes can be turned on before the toxin genes.


  • Organizational Affiliation

    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-sensing transcriptional pleiotropic repressor CodY
A, B, C, D, E
A, B, C, D, E, F
159Clostridioides difficileMutation(s): 0 
Gene Names: codYBN1095_790003BN1096_560190BN1097_540194
UniProt
Find proteins for Q18BE1 (Clostridioides difficile (strain 630))
Explore Q18BE1 
Go to UniProtKB:  Q18BE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ18BE1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.89α = 90
b = 190.39β = 90
c = 43.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesGM042219

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 2.0: 2018-11-21
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 2.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description