5LNN

Crystal structure of D1050A mutant of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1074/jbc.M117.790212
  • Primary Citation of Related Structures:  
    5LNM, 5LNN, 5N2N

  • 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 in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1 RD ) from Arabidopsis thaliana We observed that the crystal structures of free, Mg 2+ -bound, and beryllofluoridated CKI1 RD (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 CKI1 RD variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg 2+ 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 CKI1 RD was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic β3-α3 loop of CKI1 RD , the corresponding loop of the ETR1 receiver domain (ETR1 RD ) exhibited little conformational exchange and adopted a different orientation in crystals. Biochemical data indicated that ETR1 RD 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidine kinase CKI1206Arabidopsis thalianaMutation(s): 1 
Gene Names: CKI1At2g47430T30B22.27
EC: 2.7.13.3
UniProt
Find proteins for O22267 (Arabidopsis thaliana)
Explore O22267 
Go to UniProtKB:  O22267
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO22267
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.176α = 90
b = 101.005β = 90
c = 79.464γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech RepublicGAP305/11/0756

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description