4TLB

Crystal structure of N-terminal C1 domain of KaiC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Circadian rhythms. Atomic-scale origins of slowness in the cyanobacterial circadian clock.

Abe, J.Hiyama, T.B.Mukaiyama, A.Son, S.Mori, T.Saito, S.Osako, M.Wolanin, J.Yamashita, E.Kondo, T.Akiyama, S.

(2015) Science 349: 312-316

  • DOI: 10.1126/science.1261040
  • Primary Citation of Related Structures:  
    4TLD, 4TLE, 4TLA, 4TLB, 4TLC, 4TL6, 4TL7, 4TL8, 4TL9

  • PubMed Abstract: 
  • Circadian clocks generate slow and ordered cellular dynamics but consist of fast-moving bio-macromolecules; consequently, the origins of the overall slowness remain unclear. We identified the adenosine triphosphate (ATP) catalytic region [adenosine t ...

    Circadian clocks generate slow and ordered cellular dynamics but consist of fast-moving bio-macromolecules; consequently, the origins of the overall slowness remain unclear. We identified the adenosine triphosphate (ATP) catalytic region [adenosine triphosphatase (ATPase)] in the amino-terminal half of the clock protein KaiC as the minimal pacemaker that controls the in vivo frequency of the cyanobacterial clock. Crystal structures of the ATPase revealed that the slowness of this ATPase arises from sequestration of a lytic water molecule in an unfavorable position and coupling of ATP hydrolysis to a peptide isomerization with high activation energy. The slow ATPase is coupled with another ATPase catalyzing autodephosphorylation in the carboxyl-terminal half of KaiC, yielding the circadian response frequency of intermolecular interactions with other clock-related proteins that influences the transcription and translation cycle.


    Organizational Affiliation

    Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. akiyamas@ims.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Circadian clock protein kinase KaiCABCDEF253Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 1 
Gene Names: kaiCSynpcc7942_1216see0011
EC: 2.7.11.1
Find proteins for Q79PF4 (Synechococcus elongatus (strain PCC 7942 / FACHB-805))
Explore Q79PF4 
Go to UniProtKB:  Q79PF4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.06α = 90
b = 133.562β = 90
c = 150.835γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Data collection, Database references, Derived calculations