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35  structures 449  species 1  interaction 964  sequences 11  architectures

Family: KaiB (PF07689)

Summary: KaiB domain

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This is the Wikipedia entry entitled "Cyanobacterial clock proteins". More...

Cyanobacterial clock proteins Edit Wikipedia article

KaiA domain
PDB 1r8j EBI.jpg
crystal structure of circadian clock protein kaia from synechococcus elongatus
Symbol KaiA
Pfam PF07688
InterPro IPR011648
KaiB domain
PDB 1t4y EBI.jpg
solution structure of the n-terminal domain of synechococcus elongatus sasa (average minimized structure)
Symbol KaiB
Pfam PF07689
Pfam clan CL0172
InterPro IPR011649
CDD cd02978
PDB 2gbl EBI.jpg
crystal structure of full length circadian clock protein kaic with phosphorylation sites
Symbol KaiC
Pfam PF06745
Pfam clan CL0023
InterPro IPR014774
CDD cd01124

In molecular biology, the cyanobacterial clock proteins are the main circadian regulator in cyanobacteria. The cyanobacterial clock proteins comprise three proteins: KaiA, KaiB and KaiC. The kaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction.

In the complex, KaiA enhances the phosphorylation status of kaiC. In contrast, the presence of kaiB in the complex decreases the phosphorylation status of kaiC, suggesting that kaiB acts by antagonising the interaction between kaiA and kaiC. The activity of KaiA activates kaiBC expression, while KaiC represses it. The overall fold of the KaiA monomer is that of a four-helix bundle, which forms a dimer in the known structure.[1] KaiA functions as a homodimer. Each monomer is composed of three functional domains: the N-terminal amplitude-amplifier domain, the central period-adjuster domain and the C-terminal clock-oscillator domain. The N-terminal domain of KaiA, from cyanobacteria, acts as a pseudo-receiver domain, but lacks the conserved aspartyl residue required for phosphotransfer in response regulators.[2] The C-terminal domain is responsible for dimer formation, binding to KaiC, enhancing KaiC phosphorylation and generating the circadian oscillations.[3] The KaiA protein from Anabaena sp. (strain PCC 7120) lacks the N-terminal CheY-like domain.

KaiB adopts an alpha-beta meander motif and is found to be a dimer or a tetramer.[1][4]

KaiC belongs to a larger family of proteins; it performs autophosphorylation and acts as its own transcriptional repressor. It binds ATP.[5]

Also in the KaiC family is RadA/Sms, a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC.[6]


  1. ^ a b Garces RG, Wu N, Gillon W, Pai EF (April 2004). "Anabaena circadian clock proteins KaiA and KaiB reveal a potential common binding site to their partner KaiC". EMBO J. 23 (8): 1688–98. doi:10.1038/sj.emboj.7600190. PMC 394244Freely accessible. PMID 15071498. 
  2. ^ Williams SB, Vakonakis I, Golden SS, LiWang AC (November 2002). "Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism". Proc. Natl. Acad. Sci. U.S.A. 99 (24): 15357–62. doi:10.1073/pnas.232517099. PMC 137721Freely accessible. PMID 12438647. 
  3. ^ Uzumaki T, Fujita M, Nakatsu T, Hayashi F, Shibata H, Itoh N, Kato H, Ishiura M (July 2004). "Crystal structure of the C-terminal clock-oscillator domain of the cyanobacterial KaiA protein". Nat. Struct. Mol. Biol. 11 (7): 623–31. doi:10.1038/nsmb781. PMID 15170179. 
  4. ^ Hitomi K, Oyama T, Han S, Arvai AS, Getzoff ED (2005). "Tetrameric architecture of the circadian clock protein KaiB. A novel interface for intermolecular interactions and its impact on the circadian rhythm". J Biol Chem. 280 (19): 19127–35. doi:10.1074/jbc.M411284200. PMID 15716274. 
  5. ^ Pattanayek R, Wang J, Mori T, Xu Y, Johnson CH, Egli M (2004). "Visualizing a circadian clock protein: crystal structure of KaiC and functional insights". Mol Cell. 15 (3): 375–88. doi:10.1016/j.molcel.2004.07.013. PMID 15304218. 
  6. ^ Beam CE, Saveson CJ, Lovett ST (December 2002). "Role for radA/sms in recombination intermediate processing in Escherichia coli". J. Bacteriol. 184 (24): 6836–44. doi:10.1128/jb.184.24.6836-6844.2002. PMC 135464Freely accessible. PMID 12446634. 

This article incorporates text from the public domain Pfam and InterPro IPR011648

This article incorporates text from the public domain Pfam and InterPro IPR011649

This article incorporates text from the public domain Pfam and InterPro IPR014774

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

KaiB domain Provide feedback

The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. KaiB adopts an alpha-beta meander motif and is found to be a dimer [1].

Literature references

  1. Garces RG, Wu N, Gillon W, Pai EF; , EMBO J 2004;23:1688-1698.: Anabaena circadian clock proteins KaiA and KaiB reveal a potential common binding site to their partner KaiC. PUBMED:15071498 EPMC:15071498

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011649

The cyanobacterial clock proteins KaiA, KaiB and SasA are proposed as regulators of the circadian rhythm in cyanobacteria [PUBMED:12441347, PUBMED:12727878]. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. KaiB adopts an alpha-beta meander motif and is found to be a dimer [PUBMED:15313603]. KaiB was originally discovered from the cyanobacterium Synechococcus as part of the circadian clock gene cluster, kaiABC. KaiB attenuates KaiA-enhanced KaiC autokinase activity by interacting with KaiA-KaiC complexes in a circadian fashion [PUBMED:15071498, PUBMED:12727879]. KaiB is membrane-associated as well as cytosolic. The amount of membrane-associated protein peaks in the evening (at circadian time (CT) 12-16) while the cytosolic form peaks later (at CT 20). The rhythmic localization of KaiB may function in regulating the formation of Kai complexes. SasA is a sensory histidine kinase which associates with KaiC [PUBMED:10786837]. Although it is not an essential oscillator component, it is important in enhancing kaiABC expression and is important in metabolic growth control under day/night cycle conditions. SasA contains an N-terminal sensory domain with a TRX fold which is involved in the SasA-KaiC interaction [PUBMED:12449424]. This domain shows high sequence similarity with KaiB [PUBMED:15014139]. However, the KaiB structure does not show a classical TRX fold. The N-terminal half of KaiB shares the same beta-alpha-beta topology as TRX, but the topology of its C-terminal half diverges.

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Seed source: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 14
Number in full: 964
Average length of the domain: 81.50 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 46.90 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 82
Family (HMM) version: 12
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Archea Archea Eukaryota Eukaryota
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Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the KaiB domain has been found. There are 35 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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