Circadian Clock Protein KaiC

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Structure of KaiC complex with ATP (PDB entry 1tf7)

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Biological Importance and Evolutionary Complementarity

Secondary Structure of Monomers
Secondary Structure of Monomers

In cyanobacteria, the KaiC system is vital to survival because of it's role in global gene regulation: nearly all promoters in a cyanobacteria are under circadian control. Correlating with a circadian clock system enhances fitness of any organism in a rhythmic environment [3]. Structure similarity exists between KaiC and RecA and DnaB. RecA is a DNA recombinase and DnaB is a DNA helicase, so the observation that there is similarity between these molecules imply possible direct interactions with DNA. The folds of each monomer resemble those of RecA, where eight α-helices surround the twisted β-sheet made up of seven strands (shown in the figure on the right). The similarity indicates nucleotide binding on the carboxy side of the β-sheet [2]. The entire hexamer also has structural similarities to proteins that do not bind DNA, such as F1-ATPase. This is consistent with the fact that KaiC has phosphotransferase activity, so it is capable of generating ATP. Yet there is more indication that KaiC acts on DNA, especially single stranded DNA, rather than pumps any small molecule through the pore. Inside the CI domain of the channel, the electrostatic potential is mostly negative, while inside the more constricted CII domain of the channel, the electrostatic potential is mostly positive. The biological activity of KaiC is still a mystery. It may mediate changes in chromosomal torsion or interact directly with nucleic acids [2]. It has also been shown to cause changes in DNA topology and transcription factor activity [1]. Based on the amount of KaiC molecules per cell (~10,000) and its DNA interaction properties, scientists are strongly persuaded that the protein regulates global gene expression by a direct mechanism that changes DNA structure.

Defining the mechanism of a biological oscillator is a powerful key to the future. Although biological clock system in bacteria differs vastly from the complex network of molecules that make up eukaryotic biological clocks, it can still be useful to the understanding of circadian rhythms in general. Knowing the mechanism of KaiC can help us eradicate or reduce the harm of certain bacteria by altering their biological rhythm and therefore decreasing their fitness. On the other hand, we can enhance the fitness of other bacteria in order to exploit them for positive changes in the atmosphere, such as bioremedial techniques. The possibilities are endless with such a vital function as circadian rhythms.


  1. 1.0 1.1 PMCID: PMC2585598
  2. 2.0 2.1 2.2 2.3 2.4 2.5 Pattanayek R, Wang J, Mori T, Xu Y, Johnson CH, Egli M. Visualizing a circadian clock protein: crystal structure of KaiC and functional insights. Mol Cell. 2004 Aug 13;15(3):375-88. PMID:15304218 doi:10.1016/j.molcel.2004.07.013
  3. 3.0 3.1 3.2 PMCID: PMC518856

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