PROSITE documentation PDOC51430
KaiA N- and C-terminal domain profiles


Cyanobacteria are the most primitive organisms known to exhibit circadian rhythms. KaiA, kaiB and kaiC (see <PDOC51146>) constitute the circadian clock machinery in cyanobacteria, and kaiA activates kaiBC expression whereas kaiC represses it [1]. Apparent homologues of kaiB and kaiC are found among noncyanobacterial eubacteria and the archaea. However kaiA appears confined within the cyanobacteria, which are the only prokaryotes with demonstrated circadian rhythms [2].

There are at least two types of kaiA proteins: long and short [2]. The long versions consist of ~300 aminoacyl residues. There is limited sequence conservation in the amino-terminal 200 residues of these proteins but a high degree of conservation in the carboxyl-terminal 100 residues. They thus appear to contain two independently folded domains, the amino and carboxyl regions, connected by a canonical linker. The short versions are essentially independent carboxyl-terminal domains.

The kaiA N-terminal domain consists of a central five-stranded (β1 to β5) parallel β-sheet flanked by two groups of α-helices (α1, α4 and α2, α3) packed on either side of the β-sheet and an additional α helix (α5) lying near the amino terminus of the central β-strand (see <PDB:1R8J>) [2,3]. The structure of the N-terminal domain of kaiA is that of a pseudo-receiver domain, similar to those found in bacterial response regulators. Although the fold is that of a canonical receiver domain (see <PDOC50110>), the primary sequence is dissimilar, and it lacks the conserved aspartate residue necessary for phosphorylation. KaiA activation most likely involves direct protein-protein interactions of the N-terminal domain that result in functional modulation of the C-terminal effector domain. The C-terminal kaiA domain is reponsible for dimer formation, binding to kaiC, enhancing kaiC phosphorylation and generating the circadian oscillations. It adopts a novel all α-helical homodimeric structure (see <PDB:1Q6A>) [1,3,4,5]. The kaiA C-terminal domain contains two parallel helix-hairpin-helix motifs that form a four helix bundle, which represents a new protein folding motif.

The profiles we developed cover the entire kaiA N- and C-terminal domains.

Last update:

January 2009 / First entry.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

KAIA_C, PS51431; KaiA C-terminal domain profile  (MATRIX)

KAIA_N, PS51430; KaiA N-terminal domain profile  (MATRIX)


1AuthorsUzumaki T. Fujita M. Nakatsu T. Hayashi F. Shibata H. Itoh N. Kato H. Ishiura M.
TitleCrystal structure of the C-terminal clock-oscillator domain of the cyanobacterial KaiA protein.
SourceNat. Struct. Mol. Biol. 11:623-631(2004).
PubMed ID15170179

2AuthorsWilliams S.B. Vakonakis I. Golden S.S. LiWang A.C.
TitleStructure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism.
SourceProc. Natl. Acad. Sci. U.S.A. 99:15357-15362(2002).
PubMed ID12438647

3AuthorsYe S. Vakonakis I. Ioerger T.R. LiWang A.C. Sacchettini J.C.
TitleCrystal structure of circadian clock protein KaiA from Synechococcus elongatus.
SourceJ. Biol. Chem. 279:20511-20518(2004).
PubMed ID15007067

4AuthorsVakonakis I. Sun J. Wu T. Holzenburg A. Golden S.S. LiWang A.C.
TitleNMR structure of the KaiC-interacting C-terminal domain of KaiA, a circadian clock protein: implications for KaiA-KaiC interaction.
SourceProc. Natl. Acad. Sci. U.S.A. 101:1479-1484(2004).
PubMed ID14749515

5AuthorsVakonakis I. LiWang A.C.
TitleStructure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation.
SourceProc. Natl. Acad. Sci. U.S.A. 101:10925-10930(2004).
PubMed ID15256595

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