5N2N

Crystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana complexed with Mg2+ and BeF3-


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana.

Otrusinova, O.Demo, G.Padrta, P.Jasenakova, Z.Pekarova, B.Gelova, Z.Szmitkowska, A.Kaderavek, P.Jansen, S.Zachrdla, M.Klumpler, T.Marek, J.Hritz, J.Janda, L.Iwai, H.Wimmerova, M.Hejatko, J.Zidek, L.

(2017) J. Biol. Chem. 292: 17525-17540

  • DOI: 10.1074/jbc.M117.790212
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer ...

    Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1RD) from Arabidopsis thaliana We observed that the crystal structures of free, Mg2+-bound, and beryllofluoridated CKI1RD (a stable analogue of the labile phosphorylated form) were identical and similar to the active state of receiver domains of bacterial response regulators. However, the three CKI1RD variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg2+ binding and beryllofluoridation alter the conformational equilibrium of the β3-α3 loop close to the phosphorylation site. Mutations that perturbed the conformational behavior of the β3-α3 loop while keeping the active-site aspartate intact resulted in suppression of CKI1 function. Mechanistically, homology modeling indicated that the β3-α3 loop directly interacts with the ATP-binding site of the CKI1 histidine kinase domain. The functional relevance of the conformational dynamics observed in the β3-α3 loop of CKI1RD was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic β3-α3 loop of CKI1RD, the corresponding loop of the ETR1 receiver domain (ETR1RD) exhibited little conformational exchange and adopted a different orientation in crystals. Biochemical data indicated that ETR1RD is involved in phosphorylation-independent signaling, implying a direct link between conformational behavior and the ability of eukaryotic receiver domains to participate in MSP.


    Organizational Affiliation

    From the Central European Institute of Technology and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histidine kinase CKI1
A
206Arabidopsis thalianaMutation(s): 0 
Gene Names: CKI1
EC: 2.7.13.3
Find proteins for O22267 (Arabidopsis thaliana)
Go to UniProtKB:  O22267
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 52.850α = 90.00
b = 100.152β = 90.00
c = 80.139γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech RepublicGAP305/11/0756

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references