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

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

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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: https://doi.org/10.1128/mBio.02105-14
  • Primary Citation of Related Structures:  
    4LDZ, 4LE0, 4LE1, 4LE2

  • 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 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. The ability to sense and respond to environmental variations is an essential property for cell survival. Two-component systems mediate key signaling pathways that allow bacteria to integrate extra- or intracellular signals. Here we focus on the DesK/DesR system, which acts as a molecular thermometer in B. subtilis, regulating the cell membrane's fluidity. Using a combination of complementary approaches, including determination of the crystal structures of active and inactive forms of the response regulator DesR, we unveil novel molecular mechanisms of DesR's activation switch. In particular, we show that the association of the cognate histidine kinase DesK triggers DesR activation beyond the transfer of the phosphoryl group. On the basis of sequence and structural analyses of other two-component systems, this activation mechanism appears to be used in a wide range of sensory systems, contributing a further level of specificity control among different signaling pathways.

  • Organizational Affiliation

    Institut Pasteur de Montevideo, Unit of Protein Crystallography, Montevideo, Uruguay.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein DesR
A, B
203Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: desRyocGBSU19200
Find proteins for O34723 (Bacillus subtilis (strain 168))
Explore O34723 
Go to UniProtKB:  O34723
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34723
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
C3 H8 O3
Query on BEF

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
Be F3
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.612α = 90
b = 77.646β = 90
c = 139.751γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations