7DYE

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.282 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Regulation mechanisms of the dual ATPase in KaiC.

Furuike, Y.Mukaiyama, A.Koda, S.I.Simon, D.Ouyang, D.Ito-Miwa, K.Saito, S.Yamashita, E.Nishiwaki-Ohkawa, T.Terauchi, K.Kondo, T.Akiyama, S.

(2022) Proc Natl Acad Sci U S A 119: e2119627119-e2119627119

  • DOI: https://doi.org/10.1073/pnas.2119627119
  • Primary Citation of Related Structures:  
    7DY1, 7DYE

  • PubMed Abstract: 

    KaiC is a dual adenosine triphosphatase (ATPase), with one active site in its N-terminal domain and another in its C-terminal domain, that drives the circadian clock system of cyanobacteria through sophisticated coordination of the two sites. To elucidate the coordination mechanism, we studied the contribution of the dual-ATPase activities in the ring-shaped KaiC hexamer and these structural bases for activation and inactivation. At the N-terminal active site, a lytic water molecule is sequestered between the N-terminal domains, and its reactivity to adenosine triphosphate (ATP) is controlled by the quaternary structure of the N-terminal ring. The C-terminal ATPase activity is regulated mostly by water-incorporating voids between the C-terminal domains, and the size of these voids is sensitive to phosphoryl modification of S431. The up-regulatory effect on the N-terminal ATPase activity inversely correlates with the affinity of KaiC for KaiB, a clock protein constitutes the circadian oscillator together with KaiC and KaiA, and the complete dissociation of KaiB from KaiC requires KaiA-assisted activation of the dual ATPase. Delicate interactions between the N-terminal and C-terminal rings make it possible for the components of the dual ATPase to work together, thereby driving the assembly and disassembly cycle of KaiA and KaiB.


  • Organizational Affiliation

    Research Center of Integrative Molecular Systems, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Circadian clock protein kinase KaiC
A, B
519Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 2 
Gene Names: kaiCSynpcc7942_1216see0011
EC: 2.7.11.1 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for Q79PF4 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q79PF4 
Go to UniProtKB:  Q79PF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79PF4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.282 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.906α = 90
b = 94.906β = 90
c = 276.523γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description