1VGL

Crystal structure of tetrameric KaiB from T.elongatus BP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functionally important substructures of circadian clock protein KaiB in a unique tetramer complex.

Iwase, R.Imada, K.Hayashi, F.Uzumaki, T.Morishita, M.Onai, K.Furukawa, Y.Namba, K.Ishiura, M.

(2005) J.Biol.Chem. 280: 43141-43149

  • DOI: 10.1074/jbc.M503360200

  • PubMed Abstract: 
  • KaiB is a component of the circadian clock molecular machinery in cyanobacteria, which are the simplest organisms that exhibit circadian rhythms. Here we report the x-ray crystal structure of KaiB from the thermophilic cyanobacterium Thermosynechococ ...

    KaiB is a component of the circadian clock molecular machinery in cyanobacteria, which are the simplest organisms that exhibit circadian rhythms. Here we report the x-ray crystal structure of KaiB from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. The KaiB crystal diffracts at a resolution of 2.6 A and includes four subunits organized as a dimer of dimers, each composed of two non-equivalent subunits. The overall shape of the tetramer is an elongated hexagonal plate, with a single positively charged cleft flanked by two negatively charged ridges whose surfaces includes several terminal chains. Site-directed mutagenesis of Synechococcus KaiB confirmed that alanine substitution of residues Lys-11 or Lys-43 in the cleft, or deletion of C-terminal residues 95-108, which forms part of the ridges, strongly weakens in vivo circadian rhythms. Characteristics of KaiB deduced from the x-ray crystal structure were also confirmed by physicochemical measurements of KaiB in solution. These data suggest that the positively charged cleft and flanking negatively charged ridges in KaiB are essential for the biological function of KaiB in the circadian molecular machinery in cyanobacteria.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of the circadian clock protein KaiB from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1
      Iwase, R.,Imada, K.,Hayashi, F.,Uzumaki, T.,Namba, K.,Ishiura, M.
      (2004) ACTA CRYSTALLOGR.,SECT.D 60: 727


    Organizational Affiliation

    Center for Gene Research, Nagoya University, Furo, Chikusa, Nagoya, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Circadian clock protein kaiB
A, B, C, D
108Thermosynechococcus elongatus (strain BP-1)Mutation(s): 1 
Gene Names: kaiB
Find proteins for Q79V61 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q79V61
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
A, C
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.227 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.740α = 90.00
b = 33.410β = 100.12
c = 93.740γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SOLVEphasing
CCP4data scaling
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance