4KSO

Crystal Structure of Circadian clock protein KaiB from S.Elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.622 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.279 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

CryoEM and Molecular Dynamics of the Circadian KaiB-KaiC Complex Indicates KaiB Monomers Interact with KaiC and Block ATP Binding Clefts.

Villarreal, S.A.Pattanayek, R.Williams, D.R.Mori, T.Qin, X.Johnson, C.H.Egli, M.Stewart, P.L.

(2013) J.Mol.Biol. 425: 3311-3324

  • DOI: 10.1016/j.jmb.2013.06.018

  • PubMed Abstract: 
  • The circadian control of cellular processes in cyanobacteria is regulated by a posttranslational oscillator formed by three Kai proteins. During the oscillator cycle, KaiA serves to promote autophosphorylation of KaiC while KaiB counteracts this effe ...

    The circadian control of cellular processes in cyanobacteria is regulated by a posttranslational oscillator formed by three Kai proteins. During the oscillator cycle, KaiA serves to promote autophosphorylation of KaiC while KaiB counteracts this effect. Here, we present a crystallographic structure of the wild-type Synechococcus elongatus KaiB and a cryo-electron microscopy (cryoEM) structure of a KaiBC complex. The crystal structure shows the expected dimer core structure and significant conformational variations of the KaiB C-terminal region, which is functionally important in maintaining rhythmicity. The KaiBC sample was formed with a C-terminally truncated form of KaiC, KaiC-Δ489, which is persistently phosphorylated. The KaiB-KaiC-Δ489 structure reveals that the KaiC hexamer can bind six monomers of KaiB, which form a continuous ring of density in the KaiBC complex. We performed cryoEM-guided molecular dynamics flexible fitting simulations with crystal structures of KaiB and KaiC to probe the KaiBC protein-protein interface. This analysis indicated a favorable binding mode for the KaiB monomer on the CII end of KaiC, involving two adjacent KaiC subunits and spanning an ATP binding cleft. A KaiC mutation, R468C, which has been shown to affect the affinity of KaiB for KaiC and lengthen the period in a bioluminescence rhythm assay, is found within the middle of the predicted KaiBC interface. The proposed KaiB binding mode blocks access to the ATP binding cleft in the CII ring of KaiC, which provides insight into how KaiB might influence the phosphorylation status of KaiC.


    Organizational Affiliation

    Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Circadian clock protein KaiB
C, D, A, B
102Synechococcus elongatus (strain PCC 7942)Mutation(s): 0 
Gene Names: kaiB
Find proteins for Q79PF5 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  Q79PF5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.622 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.279 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.821α = 90.00
b = 116.124β = 98.28
c = 53.228γ = 90.00
Software Package:
Software NamePurpose
CCP4model building
CCP4phasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-09-18
    Type: Database references