4LDZ

Crystal structure of the full-length response regulator DesR in the active state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Allosteric activation of bacterial response regulators: the role of the cognate histidine kinase beyond phosphorylation.

Trajtenberg, F.Albanesi, D.Ruetalo, N.Botti, H.Mechaly, A.E.Nieves, M.Aguilar, P.S.Cybulski, L.Larrieux, N.de Mendoza, D.Buschiazzo, A.

(2014) MBio 5: e02105-e02105

  • DOI: 10.1128/mBio.02105-14
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Response regulators are proteins that undergo transient phosphorylation, connecting specific signals to adaptive responses. Remarkably, the molecular mechanism of response regulator activation remains elusive, largely because of the scarcity of struc ...

    Response regulators are proteins that undergo transient phosphorylation, connecting specific signals to adaptive responses. Remarkably, the molecular mechanism of response regulator activation remains elusive, largely because of the scarcity of structural data on multidomain response regulators and histidine kinase/response regulator complexes. We now address this question by using a combination of crystallographic data and functional analyses in vitro and in vivo, studying DesR and its cognate sensor kinase DesK, a two-component system that controls membrane fluidity in Bacillus subtilis. We establish that phosphorylation of the receiver domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. One of these surfaces is critical for both homodimerization- and kinase-triggered allosteric activations. Moreover, DesK induces a phosphorylation-independent activation of DesR in vivo, uncovering a novel and stringent level of specificity among kinases and regulators. Our results support a model that helps to explain how response regulators restrict phosphorylation by small-molecule phosphoryl donors, as well as cross talk with noncognate sensors.


    Organizational Affiliation

    Institut Pasteur de Montevideo, Laboratorio de Biología Celular de Membranas, Montevideo, Uruguay.,Instituto de Biología Molecular y Celular de Rosario (IBR)-CONICET, Facultad de Cs Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio CONICET Rosario, Rosario, Argentina.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France.,Institut Pasteur de Montevideo, Unit of Protein Crystallography, Montevideo, Uruguay.,alebus@pasteur.edu.uy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulatory protein DesR
A, B
203Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: desR (yocG)
Find proteins for O34723 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34723
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

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Download CCD File 
A, B
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.612α = 90.00
b = 77.646β = 90.00
c = 139.751γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTERrefinement
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references