4GPK

Crystal structure of NprR in complex with its cognate peptide NprX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1093/nar/gkt546

  • 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- ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NprR
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)
Go to UniProtKB:  G5DDY8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NprX peptide
M, N, O, P, Q, R, S, T, U, V, W, X
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.270 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 122.240α = 108.25
b = 133.350β = 104.83
c = 137.500γ = 103.83
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
ADSCdata collection
XSCALEdata scaling
RESOLVEphasing
SHELXphasing
PDB_EXTRACTdata extraction
SHELXDphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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