3T0Y

Structure of the PhyR anti-anti-sigma domain bound to the anti-sigma factor, NepR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.102 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of a protein partner switch that regulates the general stress response of alpha-proteobacteria

Herrou, J.Rotskoff, G.Luo, Y.Roux, B.Crosson, S.

(2012) Proc.Natl.Acad.Sci.USA 109: E1415-E1423

  • DOI: 10.1073/pnas.1116887109

  • PubMed Abstract: 
  • α-Proteobacteria uniquely integrate features of two-component signal transduction (TCS) and alternative sigma factor (σ) regulation to control transcription in response to general stress. The core of this regulatory system is the PhyR protein, which ...

    α-Proteobacteria uniquely integrate features of two-component signal transduction (TCS) and alternative sigma factor (σ) regulation to control transcription in response to general stress. The core of this regulatory system is the PhyR protein, which contains a σ-like (SL) domain and a TCS receiver domain. Aspartyl phosphorylation of the PhyR receiver in response to stress signals promotes binding of the anti-σ factor, NepR, to PhyR-SL. This mechanism, whereby NepR switches binding between its cognate σ factor and phospho-PhyR (PhyR∼P), controls transcription of the general stress regulon. We have defined the structural basis of the PhyR∼P/NepR interaction in Caulobacter crescentus and characterized the effect of aspartyl phosphorylation on PhyR structure by molecular dynamics simulations. Our data support a model in which phosphorylation of the PhyR receiver domain promotes its dissociation from the PhyR-SL domain, which exposes the NepR binding site. A highly dynamic loop-helix region (α3-α4) of the PhyR-SL domain plays an important role in PhyR∼P binding to NepR in vitro, and in stress-dependent activation of transcription in vivo. This study provides a foundation for understanding the protein-protein interactions and protein structural dynamics that underpin general stress adaptation in a large and metabolically diverse clade of the bacterial kingdom.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Response regulator
A, C
142Caulobacter vibrioides (strain NA1000 / CB15N)Mutation(s): 0 
Gene Names: phyR
Find proteins for A0A0H3CBZ6 (Caulobacter vibrioides (strain NA1000 / CB15N))
Go to UniProtKB:  A0A0H3CBZ6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NepR
B, D
68Caulobacter vibrioides (strain NA1000 / CB15N)Mutation(s): 0 
Gene Names: nepR
Find proteins for A0A0H3CFC9 (Caulobacter vibrioides (strain NA1000 / CB15N))
Go to UniProtKB:  A0A0H3CFC9
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 75.370α = 90.00
b = 105.320β = 90.00
c = 97.940γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHENIXrefinement
HKL-2000data reduction
SOLVEphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-06-27
    Type: Database references