3N0R

Structure of the PhyR stress response regulator at 1.25 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.251 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A structural model of anti-anti-sigma inhibition by a two-component receiver domain: the PhyR stress response regulator

Herrou, J.Foreman, R.Fiebig, A.Crosson, S.

(2010) Mol.Microbiol. 78: 290-304

  • DOI: 10.1111/j.1365-2958.2010.07323.x

  • PubMed Abstract: 
  • PhyR is a hybrid stress regulator conserved in α-proteobacteria that contains an N-terminal σ-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-σ factor. ...

    PhyR is a hybrid stress regulator conserved in α-proteobacteria that contains an N-terminal σ-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-σ factor. PhyR thus functions as an anti-anti-σ factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as σ(T) and its anti-σ factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 Å resolution, which provides insight into the mechanism of anti-anti-σ regulation. Direct intramolecular contact between the PhyR receiver and SL domains spans regions σ₂ and σ₄, likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of α4-β5-α5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions σ₂ and σ₄ in the SL domain to open about a flexible connector loop and bind anti-σ factor.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. The Committee on Microbiology, The University of Chicago, Chicago, IL, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Response regulator
A
286Caulobacter vibrioides (strain ATCC 19089 / CB15)Mutation(s): 1 
Find proteins for Q9A2S9 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Go to UniProtKB:  Q9A2S9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.251 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.182α = 90.00
b = 61.198β = 108.73
c = 53.025γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
MAR345dtbdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance