6QRJ

Crystal structure of ShkA full-length in complex with AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Hybrid histidine kinase activation by cyclic di-GMP-mediated domain liberation.

Dubey, B.N.Agustoni, E.Bohm, R.Kaczmarczyk, A.Mangia, F.von Arx, C.Jenal, U.Hiller, S.Plaza-Menacho, I.Schirmer, T.

(2020) Proc Natl Acad Sci U S A 117: 1000-1008

  • DOI: 10.1073/pnas.1911427117
  • Primary Citation of Related Structures:  
    6QRJ, 6QRL

  • PubMed Abstract: 
  • Cytosolic hybrid histidine kinases (HHKs) constitute major signaling nodes that control various biological processes, but their input signals and how these are processed are largely unknown. In Caulobacter crescentus , the HHK ShkA is essential for accurate timing of the G1-S cell cycle transition and is regulated by the corresponding increase in the level of the second messenger c-di-GMP ...

    Cytosolic hybrid histidine kinases (HHKs) constitute major signaling nodes that control various biological processes, but their input signals and how these are processed are largely unknown. In Caulobacter crescentus , the HHK ShkA is essential for accurate timing of the G1-S cell cycle transition and is regulated by the corresponding increase in the level of the second messenger c-di-GMP. Here, we use a combination of X-ray crystallography, NMR spectroscopy, functional analyses, and kinetic modeling to reveal the regulatory mechanism of ShkA. In the absence of c-di-GMP, ShkA predominantly adopts a compact domain arrangement that is catalytically inactive. C-di-GMP binds to the dedicated pseudoreceiver domain Rec1, thereby liberating the canonical Rec2 domain from its central position where it obstructs the large-scale motions required for catalysis. Thus, c-di-GMP cannot only stabilize domain interactions, but also engage in domain dissociation to allosterically invoke a downstream effect. Enzyme kinetics data are consistent with conformational selection of the ensemble of active domain constellations by the ligand and show that autophosphorylation is a reversible process.


    Organizational Affiliation

    Structural Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland; tilman.schirmer@unibas.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hybrid kinaseA484Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: shkACC_0138CC0138
EC: 2.7.13.3
Find proteins for Q9ABT2 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Explore Q9ABT2 
Go to UniProtKB:  Q9ABT2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.504α = 90
b = 64.504β = 90
c = 260.209γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_166652

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references