8C7U

Transcriptional pleiotropic repressor CodY from Enterococcus faecalis in complex with Leu and a 30-bp DNA fragment encompassing two overlapping binding sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural insights into CodY activation and DNA recognition.

Hainzl, T.Bonde, M.Almqvist, F.Johansson, J.Sauer-Eriksson, A.E.

(2023) Nucleic Acids Res 51: 7631-7648

  • DOI: https://doi.org/10.1093/nar/gkad512
  • Primary Citation of Related Structures:  
    8C7O, 8C7S, 8C7T, 8C7U

  • PubMed Abstract: 

    Virulence factors enable pathogenic bacteria to infect host cells, establish infection, and contribute to disease progressions. In Gram-positive pathogens such as Staphylococcus aureus (Sa) and Enterococcus faecalis (Ef), the pleiotropic transcription factor CodY plays a key role in integrating metabolism and virulence factor expression. However, to date, the structural mechanisms of CodY activation and DNA recognition are not understood. Here, we report the crystal structures of CodY from Sa and Ef in their ligand-free form and their ligand-bound form complexed with DNA. Binding of the ligands-branched chain amino acids and GTP-induces conformational changes in the form of helical shifts that propagate to the homodimer interface and reorient the linker helices and DNA binding domains. DNA binding is mediated by a non-canonical recognition mechanism dictated by DNA shape readout. Furthermore, two CodY dimers bind to two overlapping binding sites in a highly cooperative manner facilitated by cross-dimer interactions and minor groove deformation. Our structural and biochemical data explain how CodY can bind a wide range of substrates, a hallmark of many pleiotropic transcription factors. These data contribute to a better understanding of the mechanisms underlying virulence activation in important human pathogens.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, 901 87 Umeå, Sweden.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-sensing transcriptional pleiotropic repressor CodY
A, B, C, D
262Enterococcus faecalis V583Mutation(s): 0 
Gene Names: codYCGZ46_07460CUM81_01520DAI13_08275EY666_04655GTI81_07970H9Q64_02750JFI91_04250
UniProt
Find proteins for Q834K5 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q834K5 
Go to UniProtKB:  Q834K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ834K5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (29-MER)30Staphylococcus aureus
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (30-MER)30Staphylococcus aureus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.747α = 90
b = 98.692β = 90
c = 168.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-15
    Changes: Source and taxonomy