7SSI

CRYSTAL STRUCTURE OF THE DESK:DESR-Q10A COMPLEX IN THE PHOSPHOTRANSFER STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An allosteric switch ensures efficient unidirectional information transmission by the histidine kinase DesK from Bacillus subtilis.

Lima, S.Blanco, J.Olivieri, F.Imelio, J.A.Nieves, M.Carrion, F.Alvarez, B.Buschiazzo, A.Marti, M.A.Trajtenberg, F.

(2023) Sci Signal 16: eabo7588-eabo7588

  • DOI: https://doi.org/10.1126/scisignal.abo7588
  • Primary Citation of Related Structures:  
    7SSI, 7SSJ

  • PubMed Abstract: 

    Phosphorylation carries chemical information in biological systems. In two-component systems (TCSs), the sensor histidine kinase and the response regulator are connected through phosphoryl transfer reactions that may be uni- or bidirectional. Directionality enables the construction of complex regulatory networks that optimize signal propagation and ensure the forward flow of information. We combined x-ray crystallography, hybrid quantum mechanics/molecular mechanics (QM/MM) simulations, and systems-integrative kinetic modeling approaches to study phosphoryl flow through the Bacillus subtilis thermosensing TCS DesK-DesR. The allosteric regulation of the histidine kinase DesK was critical to avoid back transfer of phosphoryl groups and futile phosphorylation-dephosphorylation cycles by isolating phosphatase, autokinase, and phosphotransferase activities. Interactions between the kinase's ATP-binding domain and the regulator's receiver domain placed the regulator in two distinct positions in the phosphotransferase and phosphatase complexes, thereby determining whether a key glutamine residue in DesK was properly situated to assist in the dephosphorylation reaction. Moreover, an energetically unfavorable phosphotransferase conformation when DesK was not phosphorylated minimized reverse phosphoryl transfer. DesR dimerization and a dissociative phosphoryl transfer reaction also enforced the direction of phosphoryl flow. Shorter or longer distances between the phosphoryl acceptor and donor residues shifted the phosphoryl transfer equilibrium by modulating the stabilizing effect of the Mg 2+ cofactor. These mechanisms control the directionality of signal transmission and show how structure-encoded allostery stores and transmits information in signaling systems.


  • Organizational Affiliation

    Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sensor histidine kinase DesK
A, B, D, E
218Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: desKyocFBSU19190
EC: 2.7.13.3
UniProt
Find proteins for O34757 (Bacillus subtilis (strain 168))
Explore O34757 
Go to UniProtKB:  O34757
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34757
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein DesR
C, F
139Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: desRyocGBSU19200
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth D],
N [auth E]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
K [auth C]
M [auth D]
O [auth E]
H [auth A],
J [auth B],
K [auth C],
M [auth D],
O [auth E],
P [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.067α = 90
b = 115.634β = 116.74
c = 91.374γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agencia Nacional de Investigacion e Innovacion (ANII)UruguayFCE_1_2017_1_136291

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description