5IUJ

Crystal structure of the DesK-DesR complex in the phosphotransfer state with low Mg2+ (20 mM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action.

Trajtenberg, F.Imelio, J.A.Machado, M.R.Larrieux, N.Marti, M.A.Obal, G.Mechaly, A.E.Buschiazzo, A.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.21422
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two-component systems (TCS) are protein machineries that enable cells to respond to input signals. Histidine kinases (HK) are the sensory component, transferring information toward downstream response regulators (RR). HKs transfer phosphoryl groups t ...

    Two-component systems (TCS) are protein machineries that enable cells to respond to input signals. Histidine kinases (HK) are the sensory component, transferring information toward downstream response regulators (RR). HKs transfer phosphoryl groups to their specific RRs, but also dephosphorylate them, overall ensuring proper signaling. The mechanisms by which HKs discriminate between such disparate directions, are yet unknown. We now disclose crystal structures of the HK:RR complex DesK:DesR from Bacillus subtilis , comprising snapshots of the phosphotransfer and the dephosphorylation reactions. The HK dictates the reactional outcome through conformational rearrangements that include the reactive histidine. The phosphotransfer center is asymmetric, poised for dissociative nucleophilic substitution. The structural bases of HK phosphatase/phosphotransferase control are uncovered, and the unexpected discovery of a dissociative reactional center, sheds light on the evolution of TCS phosphotransfer reversibility. Our findings should be applicable to a broad range of signaling systems and instrumental in synthetic TCS rewiring.


    Organizational Affiliation

    Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Biomolecular Simulations, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Département de Microbiologie, Institut Pasteur, Paris, France.,Protein Biophysics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sensor histidine kinase DesK
A, B, D, E
218Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: desK (yocF)
EC: 2.7.13.3
Find proteins for O34757 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34757
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulatory protein DesR
C, F
139Bacillus 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
C, F
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ACP
Query on ACP

Download SDF File 
Download CCD File 
A, B, D, E
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 87.820α = 90.00
b = 114.619β = 116.44
c = 91.597γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
Aimlessdata scaling
BUSTER-TNTrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Database references
  • Version 1.2: 2017-01-04
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description