Summary: KaiA domain
This is the Wikipedia entry entitled "Cyanobacterial clock proteins". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Cyanobacterial clock proteins Edit Wikipedia article
|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): 1688â98. doi:10.1038/sj.emboj.7600190. PMC 394244. PMID 15071498. //www.ncbi.nlm.nih.gov/pmc/articles/PMC394244/.
- 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): 15357â62. doi:10.1073/pnas.232517099. PMC 137721. PMID 12438647. //www.ncbi.nlm.nih.gov/pmc/articles/PMC137721/.
- 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): 623â31. 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): 19127â35. doi:10.1074/jbc.M411284200. PMID 15716274. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=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): 375â88. doi:10.1016/j.molcel.2004.07.013. PMID 15304218. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=15304218.
- Beam CE, Saveson CJ, Lovett ST (December 2002). "Role for radA/sms in recombination intermediate processing in Escherichia coli". J. Bacteriol. 184 (24): 6836â44. PMC 135464. PMID 12446634. //www.ncbi.nlm.nih.gov/pmc/articles/PMC135464/.
KaiA domain Provide feedback
The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. The overall fold of the KaiA monomer is that of a four-helix bundle, which forms a dimer in the known structure .
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 IPR011648
KaiA is a component of the kaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. 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 [PUBMED:15071498]. 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-termianl clock-oscillator domain. The N-terminal domain of KaiA, from cyanobacteria, acts as a psuedo-receiver domain, but lacks the conserved aspartyl residue required for phosphotransfer in response regulators [PUBMED:12438647]. The C-terminal domain is responsible for dimer formation, binding to KaiC, enhancing KaiC phosphorylation and generating the circadian oscillations [PUBMED:15170179]. The KaiA protein from Anabaena sp. (strain PCC 7120) lacks the N-terminal CheY-like domain.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||circadian rhythm (GO:0007623)|
|protein phosphorylation (GO:0006468)|
- 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
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Bateman A|
|Number in seed:||3|
|Number in full:||66|
|Average length of the domain:||249.20 aa|
|Average identity of full alignment:||44 %|
|Average coverage of the sequence by the domain:||92.72 %|
|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|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
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 KaiA domain has been found. There are 14 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.
Loading structure mapping...