5IUN

Crystal structure of the DesK-DesR complex in the phosphatase state

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    5IUJ, 5IUL, 5IUK, 5IUN, 5IUM

  • 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 to th ...

    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: 

    Département de Microbiologie, Institut Pasteur, Paris, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sensor histidine kinase DesK A, B, E224Bacillus subtilis subsp. subtilis str. 168Mutation(s): 3 
Gene Names: desK, yocF, BSU19190
EC: 2.7.13.3
Find proteins for O34757 (Bacillus subtilis (strain 168))
Explore O34757 
Go to UniProtKB:  O34757
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulatory protein DesR C, D, F139Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: desR, yocG, BSU19200
Find proteins for O34723 (Bacillus subtilis (strain 168))
Explore O34723 
Go to UniProtKB:  O34723
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP
Download Ideal Coordinates CCD File 
A, B, E
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N		 Ligand Interaction
MES
Query on MES
Download Ideal Coordinates CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
BEF
Query on BEF
Download Ideal Coordinates CCD File 
C, D, F
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 31 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/400 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.33α = 90
b = 94.33β = 90
c = 239.91γ = 120
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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