5IDJ

Bifunctional histidine kinase CckA (domains DHp-CA) in complex with ADP/Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.

Dubey, B.N.Lori, C.Ozaki, S.Fucile, G.Plaza-Menacho, I.Jenal, U.Schirmer, T.

(2016) Sci Adv 2: e1600823-e1600823

  • DOI: 10.1126/sciadv.1600823
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Histidine kinases are key components of regulatory networks in bacteria. Although many of these enzymes are bifunctional, mediating both phosphorylation and dephosphorylation of downstream targets, the molecular details of this central regulatory swi ...

    Histidine kinases are key components of regulatory networks in bacteria. Although many of these enzymes are bifunctional, mediating both phosphorylation and dephosphorylation of downstream targets, the molecular details of this central regulatory switch are unclear. We showed recently that the universal second messenger cyclic di-guanosine monophosphate (c-di-GMP) drives Caulobacter crescentus cell cycle progression by forcing the cell cycle kinase CckA from its default kinase into phosphatase mode. We use a combination of structure determination, modeling, and functional analysis to demonstrate that c-di-GMP reciprocally regulates the two antagonistic CckA activities through noncovalent cross-linking of the catalytic domain with the dimerization histidine phosphotransfer (DHp) domain. We demonstrate that both c-di-GMP and ADP (adenosine diphosphate) promote phosphatase activity and propose that c-di-GMP stabilizes the ADP-bound quaternary structure, which allows the receiver domain to access the dimeric DHp stem for dephosphorylation. In silico analyses predict that c-di-GMP control is widespread among bacterial histidine kinases, arguing that it can replace or modulate canonical transmembrane signaling.


    Organizational Affiliation

    Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell cycle histidine kinase CckA
A
242Caulobacter vibrioidesMutation(s): 0 
Gene Names: cckA
Find proteins for Q9X688 (Caulobacter vibrioides)
Go to UniProtKB:  Q9X688
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.212 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 164.856α = 90.00
b = 164.856β = 90.00
c = 48.001γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
SAINTdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A-138414

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Advisory, Author supporting evidence
  • Version 1.2: 2018-10-24
    Type: Advisory, Data collection, Derived calculations