Summary: KaiB domain
This is the Wikipedia entry entitled "Cyanobacterial clock proteins". More...
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Cyanobacterial clock proteins Edit Wikipedia article
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crystal structure of circadian clock protein kaia from synechococcus elongatus
solution structure of the n-terminal domain of synechococcus elongatus sasa (average minimized structure)
crystal structure of full length circadian clock protein kaic with phosphorylation sites
In molecular biology, the cyanobacterial clock proteins are the main circadian regulator in cyanobacteria. The cyanobacterial clock proteins comprise three proteins: kiaA, kiaB and kiaC. 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. 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. The C-terminal domain is responsible for dimer formation, binding to KaiC, enhancing KaiC phosphorylation and generating the circadian oscillations. The KaiA protein from Anabaena sp. (strain PCC 7120) lacks the N-terminal CheY-like domain.
Also in the KiaC 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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. PMC 135464. PMID 12446634.
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 .
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
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR011649The 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 [PUBMED:15071498].
|Biological process||rhythmic process (GO:0048511)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This clan contains families related to the thioredoxin family. Thioredoxins are small enzymes that are involved in redox reactions via the reversible oxidation of an active centre disulfide bond. The thioredoxin fold consists of a 3 layer alpha/beta/alpha sandwich and a central beta sheet.
The clan contains the following 45 members:2Fe-2S_thioredx AhpC-TSA AhpC-TSA_2 ArsC ArsD Calsequestrin DIM1 DSBA DUF1525 DUF1687 DUF2703 DUF4174 DUF836 DUF899 DUF953 ERp29_N Glutaredoxin GSHPx GST_N GST_N_2 GST_N_3 HyaE KaiB MRP-S23 MRP-S25 OST3_OST6 Phosducin Redoxin SCO1-SenC SelP_N SH3BGR T4_deiodinase Thioredox_DsbH Thioredoxin Thioredoxin_2 Thioredoxin_3 Thioredoxin_4 Thioredoxin_5 Thioredoxin_6 Thioredoxin_7 Thioredoxin_8 Thioredoxin_9 Tom37 TraF YtfJ_HI0045
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||16|
|Number in full:||352|
|Average length of the domain:||80.00 aa|
|Average identity of full alignment:||41 %|
|Average coverage of the sequence by the domain:||45.47 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 18 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 seqence.
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