PROSITE documentation PDOC51430KaiA 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.
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PROSITE methods (with tools and information) covered by this documentation:
| 1 | Authors | Uzumaki T. Fujita M. Nakatsu T. Hayashi F. Shibata H. Itoh N. Kato H. Ishiura M. |
| Title | Crystal structure of the C-terminal clock-oscillator domain of the cyanobacterial KaiA protein. | |
| Source | Nat. Struct. Mol. Biol. 11:623-631(2004). | |
| PubMed ID | 15170179 | |
| DOI | 10.1038/nsmb781 |
| 2 | Authors | Williams S.B. Vakonakis I. Golden S.S. LiWang A.C. |
| Title | Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 99:15357-15362(2002). | |
| PubMed ID | 12438647 | |
| DOI | 10.1073/pnas.232517099 |
| 3 | Authors | Ye S. Vakonakis I. Ioerger T.R. LiWang A.C. Sacchettini J.C. |
| Title | Crystal structure of circadian clock protein KaiA from Synechococcus elongatus. | |
| Source | J. Biol. Chem. 279:20511-20518(2004). | |
| PubMed ID | 15007067 | |
| DOI | 10.1074/jbc.M400077200 |
| 4 | Authors | Vakonakis I. Sun J. Wu T. Holzenburg A. Golden S.S. LiWang A.C. |
| Title | NMR structure of the KaiC-interacting C-terminal domain of KaiA, a circadian clock protein: implications for KaiA-KaiC interaction. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 101:1479-1484(2004). | |
| PubMed ID | 14749515 | |
| DOI | 10.1073/pnas.0305516101 |
| 5 | Authors | Vakonakis I. LiWang A.C. |
| Title | Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 101:10925-10930(2004). | |
| PubMed ID | 15256595 | |
| DOI | 10.1073/pnas.0403037101 |
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