4KSO

Crystal Structure of Circadian clock protein KaiB from S.Elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.281 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.jmb.2013.06.018
  • Primary Citation of Related Structures:  
    4KSO

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Circadian clock protein KaiBA [auth C],
B [auth D],
C [auth A],
D [auth B]
102Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: kaiB
UniProt
Find proteins for Q79PF5 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q79PF5 
Go to UniProtKB:  Q79PF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79PF5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.281 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.821α = 90
b = 116.124β = 98.28
c = 53.228γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CCP4model building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description