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: 3.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.7554/eLife.21422
  • Primary Citation of Related Structures:  
    5IUJ, 5IUK, 5IUL, 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 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.


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): 0 
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 3 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
K
Query on K

Download Ideal Coordinates CCD File 
K [auth C],
P [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.82α = 90
b = 114.619β = 116.44
c = 91.597γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
Aimlessdata scaling
PHASERphasing
BUSTER-TNTrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2017-01-04
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references, Derived calculations