Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.19 kDa 
• Atom Count: 957 
• Modelled Residue Count: 106 
• Deposited Residue Count: 111 
• Unique protein chains: 1

1V2Z

Crystal structure of the C-terminal domain of Thermosynechococcus elongatus BP-1 KaiA

• PDB DOI: 10.2210/pdb1V2Z/pdb

• Classification: CIRCADIAN CLOCK PROTEIN
• Organism(s): Thermosynechococcus vestitus BP-1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-10-20 Released: 2004-06-01 
• Deposition Author(s): Uzumaki, T., Fujita, M., Nakatsu, T., Hayashi, F., Shibata, H., Itoh, N., Kato, H., Ishiura, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Literature

Crystal structure of the C-terminal clock-oscillator domain of the cyanobacterial KaiA protein

Uzumaki, T., Fujita, M., Nakatsu, T., Hayashi, F., Shibata, H., Itoh, N., Kato, H., Ishiura, M.

(2004) Nat Struct Mol Biol 11: 623-631

• PubMed: 15170179 
• DOI: 10.1038/nsmb781
• Primary Citation of Related Structures:  
  1V2Z


• PubMed Abstract: 
  

KaiA, KaiB and KaiC constitute the circadian clock machinery in cyanobacteria, and KaiA activates kaiBC expression whereas KaiC represses it. Here we show that KaiA is composed of three functional domains, the N-terminal amplitude-amplifier domain, the central period-adjuster domain and the C-terminal clock-oscillator domain. The C-terminal domain is responsible for dimer formation, binding to KaiC, enhancing KaiC phosphorylation and generating the circadian oscillations. The X-ray crystal structure at a resolution of 1.8 A of the C-terminal clock-oscillator domain of KaiA from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 shows that residue His270, located at the center of a KaiA dimer concavity, is essential to KaiA function. KaiA binding to KaiC probably occurs via the concave surface. On the basis of the structure, we predict the structural roles of the residues that affect circadian oscillations.

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Organizational Affiliation: 

Center for Gene Research, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
circadian clock protein KaiA homolog	A	111	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Gene Names: kaiA, tlr0481
UniProt
Find proteins for Q79V62 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q79V62  Go to UniProtKB:  Q79V62

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.467	α = 90
b = 61.467	β = 90
c = 57.305	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-20 
• Released Date: 2004-06-01 
Deposition Author(s): Uzumaki, T., Fujita, M., Nakatsu, T., Hayashi, F., Shibata, H., Itoh, N., Kato, H., Ishiura, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-06-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance