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246  structures 1842  species 1  interaction 5118  sequences 42  architectures

Family: ATPase (PF06745)

Summary: KaiC

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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
KaiB domain
PDB 1t4y EBI.jpg
solution structure of the n-terminal domain of synechococcus elongatus sasa (average minimized structure)
Pfam clanCL0172
PDB 2gbl EBI.jpg
crystal structure of full length circadian clock protein kaic with phosphorylation sites
Pfam clanCL0023

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]

History of Discovery

Due to the lack of a nucleus in these organisms, there was doubt as to whether or not cyanobacteria would be able to express circadian rhythms. Kondo et al. were the first to definitively demonstrate that cyanobacteria do in fact have circadian rhythms. In a 1993 experiment, they used a luciferase reporter inserted into the genetically tractable Synechococcus sp., which was grown in a 12:12 light-dark cycle to ensure “entrainment”. There were two sets of bacteria so that one was in light while the other was in darkness during this entrainment period. Once the bacteria entered the stationary phase, they were transferred into test tubes kept in constant light, except for 5-minute recording periods every 30 minutes, in which the tubes were kept in darkness to measure their levels of bioluminescence. They found that the level of bioluminescence cycled at a near 24-hour period, and that the two groups oscillated with opposite phases. This led them to conclude that the Synechococcus sp. genome was regulated by a circadian clock. (1)

Function in Vitro

The circadian oscillators in eukaryotes that have been studied function using a negative feedback loop in which proteins inhibit their own transcription in a cycle that takes approximately 24 hours. This is known as a transcription-translation-derived oscillator (TTO).(2) Without a nucleus, prokaryotic cells must have a different mechanism of keeping circadian time. In 1998, Ishiura et al. determined that the KaiABC protein complex was responsible for the circadian negative feedback loop in Synechococcus by mapping 19 clock mutants to the genes for these three proteins.(3) An experiment by Nakajima et al., in 2005, was able to demonstrate the circadian oscillation of the Synechococcus KaiABC complex in vitro. They did this by adding KaiA, KaiB, KaiC, and ATP into a test tube in the approximate ratio recorded in vivo. They then measured the levels of KaiC phosphorylation and found that it demonstrated circadian rhythmicity for three cycles without damping. This cycle was also temperature compensating. They also tested incubating mutant KaiC protein with KaiA, KaiB, and ATP. They found that the period of KaiC phosphorylation matched the intrinsic period of the cyanobacterium with the corresponding mutant genome. These results led them to conclude that KaiC phosphorylation is the basis for circadian rhythm generation in Synechococcus. (2)

Cyanobacterial Clocks as Model Systems

Cyanobacteria are the simplest organisms that have been observed demonstrating circadian rhythms.(2)(3) The primitiveness and simplicity make the KaiC phosphorylation model invaluable to circadian rhythm research. While it is much simpler than models for eukaryotic circadian rhythm generators, the principles are largely the same. In both systems the circadian period is dependent on the interactions between proteins within the cell, and when the genes for those proteins are mutated, the expressed period changes. (1)(2) This model of circadian rhythm generation also has implications for the study of circadian “evolutionary biology”. Given the simplicity of cyanobacteria and of this circadian system, it may be safe to assume that eukaryotic circadian oscillators are derived from a system similar to that present in cyanobacterium. (1)


  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 394244. 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 137721. 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 135464. 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

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KaiC Provide feedback

This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria [1].

Literature references

  1. Iwasaki H, Taniguchi Y, Ishiura M, Kondo T; , EMBO J 1999;18:1137-1145.: Physical interactions among circadian clock proteins KaiA, KaiB and KaiC in cyanobacteria. PUBMED:10064581 EPMC:10064581

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014774

This entry represents a domain found in KaiC, which is a core component of the KaiBC clock protein complex that constitutes the main circadian regulator in cyanobacteria [PUBMED:10064581]. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

Proteins containing this domain also include some eukrayotic proteins.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 229 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6 Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE Zeta_toxin Zot


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Seed source: Pfam-B_2234 (release 10.0)
Previous IDs: KaiC;
Type: Domain
Sequence Ontology: SO:0000417
Author: Vella Briffa B
Number in seed: 26
Number in full: 5118
Average length of the domain: 211.20 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 75.92 %

HMM information View help on HMM parameters

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 26.6 26.6
Trusted cut-off 26.6 26.6
Noise cut-off 26.5 26.5
Model length: 231
Family (HMM) version: 13
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Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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 ATPase domain has been found. There are 246 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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