Crystal structure of NprR in complex with its cognate peptide NprX

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.276 

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This is version 1.3 of the entry. See complete history


Peptide-binding dependent conformational changes regulate the transcriptional activity of the quorum-sensor NprR.

Zouhir, S.Perchat, S.Nicaise, M.Perez, J.Guimaraes, B.Lereclus, D.Nessler, S.

(2013) Nucleic Acids Res 41: 7920-7933

  • DOI: https://doi.org/10.1093/nar/gkt546
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The transcriptional regulator NprR controls the expression of genes essential for the adaptative response of Bacillus cereus. NprR belongs to the RNPP family of directly regulated quorum sensors from Gram-positive bacteria. It is activated by the re-imported signaling peptide NprX. To elucidate the activation mechanism of this quorum-sensing system, we analyzed the conformation changes induced on binding of NprX. We solved the crystal structure of the NprR/NprX binary complex and characterized the apo form of NprR in solution. We demonstrated that apo NprR is a dimer that switches to a tetramer in the presence of NprX. Mutagenesis, and functional analysis allowed us to identify the protein and peptide residues directly involved in the NprR activation process. Based on the comparison with the Rap proteins, we propose a model for the peptide-induced conformational change allowing the apo dimer to switch to an active tetramer specifically recognizing target DNA sequences.

  • Organizational Affiliation

    CNRS, UPR3082, Laboratoire d'Enzymologie et Biochimie Structurales, Gif sur Yvette 91198, France, INRA, UMR1319 Micalis, La Minière, Guyancourt 78280, France, AgroParisTech, UMR1319 Micalis, Jouy-en-Josas 78350, France, Université Paris-Sud, UMR8619, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Orsay 91405, France and Synchrotron SOLEIL, 91192 Gif sur Yvette, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
372Bacillus thuringiensis serovar thuringiensisMutation(s): 0 
Gene Names: nprR
Find proteins for G5DDY8 (Bacillus thuringiensis serovar thuringiensis)
Explore G5DDY8 
Go to UniProtKB:  G5DDY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG5DDY8
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NprX peptide
M, N, O, P, Q
M, N, O, P, Q, R, S, T, U, V, W, X
8N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.276 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.24α = 108.25
b = 133.35β = 104.83
c = 137.5γ = 103.83
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references