Protein Domain : Circadian clock protein KaiA, N-terminal IPR020844

Type	Domain
Description	This entry represents the N-terminal domain of KaiA. Cyanobacteria are the most primitive organisms known to exhibit circadian rhythms. KaiA, kaiB and kaiC constitute the circadian clockmachinery in cyanobacteria, and kaiA activates kaiBC expression whereas kaiC represses it []. Apparent homologues of kaiB and kaiC are found amongnoncyanobacterial eubacteria and the archaea. However kaiA appears confined within the cyanobacteria, which are the only prokaryotes with demonstratedcircadian rhythms [ ].There are at least two types of kaiA proteins: long and short [ ]. The longversions consist of ~300 aminoacyl residues. There is limited sequence conservation in the amino-terminal 200 residues of these proteins but a highdegree 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 (beta1 to beta5) parallel β-sheet flanked by two groups of α-helices (alpha1,alpha4 and alpha2, alpha3) packed on either side of the β-sheet and an additional alpha helix (alpha5) lying near the amino terminus of the centralβ-strand [ , ]. The structure of the N-terminal domain ofkaiA 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, the primary sequence is dissimilar, and it lacks theconserved aspartate residue necessary for phosphorylation. KaiA activation most likely involves direct protein-protein interactions of the N-terminaldomain 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[ , , , ]. 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.
Short Name	Circadian_clock_KaiA_N