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Q79PF6

- KAIA_SYNE7

UniProt

Q79PF6 - KAIA_SYNE7

Protein

Circadian clock protein KaiA

Gene

kaiA

Organism
Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 75 (01 Oct 2014)
      Sequence version 1 (05 Jul 2004)
      Previous versions | rss
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    Functioni

    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, it 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 antagonizing the interaction between KaiA and KaiC. A KaiA dimer is sufficient to enhance KaiC hexamer phosphorylation.4 Publications

    GO - Molecular functioni

    1. identical protein binding Source: IntAct
    2. protein binding Source: IntAct

    GO - Biological processi

    1. circadian rhythm Source: InterPro
    2. entrainment of circadian clock Source: UniProtKB
    3. negative regulation of protein dephosphorylation Source: CACAO
    4. positive regulation of circadian rhythm Source: UniProtKB
    5. protein phosphorylation Source: InterPro

    Keywords - Biological processi

    Biological rhythms

    Enzyme and pathway databases

    BioCyciSYNEL:SYNPCC7942_1218-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Circadian clock protein KaiA
    Gene namesi
    Name:kaiA
    Ordered Locus Names:Synpcc7942_1218
    ORF Names:see0009
    OrganismiSynechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
    Taxonomic identifieri1140 [NCBI]
    Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
    ProteomesiUP000002717: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi9 – 91I → T: Extends the period of the circadian rhythm to 29 hours. 1 Publication
    Mutagenesisi16 – 161I → F: Extends the period of the circadian rhythm to 27 hours. 1 Publication
    Mutagenesisi31 – 311L → P: Extends the period of the circadian rhythm to 27 hours. 1 Publication
    Mutagenesisi36 – 361S → P: Extends the period of the circadian rhythm to 29 hours. 1 Publication
    Mutagenesisi53 – 531C → S: Induces an arrhythmic phenotype. 1 Publication
    Mutagenesisi76 – 761V → G: Extends the period of the circadian rhythm to 28 hours. 1 Publication
    Mutagenesisi103 – 1031E → K in kaiA1; extends the period of the circadian rhythm to 33 hours and increases the interaction with KaiB.
    Mutagenesisi113 – 1131Q → R: Extends the period of the circadian rhythm to 33 hours. 1 Publication
    Mutagenesisi117 – 1171Q → L: Extends the period of the circadian rhythm to 26 hours. 1 Publication
    Mutagenesisi119 – 1191D → E: Extends the period of the circadian rhythm to 30 hours. 1 Publication
    Mutagenesisi119 – 1191D → G: Extends the period of the circadian rhythm to 26 hours. 1 Publication
    Mutagenesisi131 – 1311V → A: Extends the period of the circadian rhythm to 28 hours. 1 Publication
    Mutagenesisi136 – 1361D → V: Extends the period of the circadian rhythm to 30 hours. 1 Publication
    Mutagenesisi136 – 1361D → Y: Extends the period of the circadian rhythm to 29 hours. 1 Publication
    Mutagenesisi166 – 1661Y → C in kaiA3; induces an arrhythmic phenotype and reduces the interaction with KaiC.
    Mutagenesisi178 – 1781F → S or I: Induces an arrhythmic phenotype. 1 Publication
    Mutagenesisi180 – 1801R → H: Extends the period of the circadian rhythm to 26 hours. 1 Publication
    Mutagenesisi194 – 1941M → T: Extends the period of the circadian rhythm to 26 hours. 1 Publication
    Mutagenesisi224 – 2241F → S: Induces an arrhythmic phenotype. 1 Publication
    Mutagenesisi225 – 2251F → S: Induces an arrhythmic phenotype. 1 Publication
    Mutagenesisi239 – 2391E → G: Extends the period of the circadian rhythm to 28 hours. 1 Publication
    Mutagenesisi241 – 2411M → T: Extends the period of the circadian rhythm to 38 hours. 1 Publication
    Mutagenesisi242 – 2421D → V or G: Extends the period of the circadian rhythm to 27 hours. 1 Publication
    Mutagenesisi243 – 2431E → A: Extends the period of the circadian rhythm to 34 hours. 1 Publication
    Mutagenesisi244 – 2441F → V: Extends the period of the circadian rhythm to 26 hours. 1 Publication
    Mutagenesisi245 – 2451A → D: Extends the period of the circadian rhythm to 26 hours. 1 Publication
    Mutagenesisi249 – 2491R → H in kaiA1; extends the period of the circadian rhythm to 30 hours.
    Mutagenesisi266 – 2661I → V: Extends the period of the circadian rhythm to 27 hours. 1 Publication
    Mutagenesisi273 – 2731C → Y: Extends the period of the circadian rhythm to 30 hours. 1 Publication
    Mutagenesisi274 – 2741E → K in kaiA3; induces an arrhythmic phenotype.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 284284Circadian clock protein KaiAPRO_0000217871Add
    BLAST

    Expressioni

    Developmental stagei

    Expressed constantly throughout the circadian cycle.1 Publication

    Interactioni

    Subunit structurei

    Homodimer. Component of the KaiABC complex, at least composed of a KaiC homohexamer, a KaiB dimer and two KaiA dimers. The KaiABC complex also interacts with SasA.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself2EBI-592281,EBI-592281
    kaiBQ79PF59EBI-592281,EBI-619150
    kaiCQ79PF417EBI-592281,EBI-592287
    ldpAQ8GLI42EBI-592281,EBI-626836

    Protein-protein interaction databases

    DIPiDIP-33329N.
    IntActiQ79PF6. 4 interactions.
    STRINGi1140.Synpcc7942_1218.

    Structurei

    Secondary structure

    1
    284
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 106
    Helixi14 – 2310
    Beta strandi29 – 346
    Helixi37 – 4610
    Turni47 – 493
    Beta strandi52 – 576
    Helixi63 – 7210
    Beta strandi79 – 835
    Beta strandi87 – 893
    Beta strandi98 – 1003
    Beta strandi104 – 1063
    Helixi108 – 1103
    Helixi111 – 1133
    Helixi114 – 12815
    Turni134 – 1363
    Beta strandi138 – 1403
    Turni144 – 1474
    Helixi149 – 1513
    Helixi152 – 16413
    Beta strandi165 – 1717
    Helixi175 – 1773
    Turni179 – 1813
    Helixi184 – 20522
    Helixi212 – 22514
    Helixi230 – 24920
    Turni250 – 2523
    Helixi257 – 2615
    Helixi262 – 27918

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1M2ENMR-A1-135[»]
    1M2FNMR-A1-135[»]
    1R8JX-ray2.03A/B2-284[»]
    4G86X-ray2.39A/B2-284[»]
    ProteinModelPortaliQ79PF6.
    SMRiQ79PF6. Positions 1-282.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ79PF6.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 164164KaiA N-terminalPROSITE-ProRule annotationAdd
    BLAST
    Domaini174 – 282109KaiA C-terminalPROSITE-ProRule annotationAdd
    BLAST

    Domaini

    The N-terminal part (1-102), which is also called pseudo-receiver domain, does not enhance KaiC autophosphorylation. It may have an amplitude-amplifier function and may be involved in transducing input signals to the KaiABC complex. This domain is not conserved in other species.1 Publication
    The KaiA domain mediates the interaction with KaiC, the homodimerization, and is responsible for the clock oscillation function.1 Publication

    Sequence similaritiesi

    Contains 1 kaiA C-terminal domain.PROSITE-ProRule annotation
    Contains 1 kaiA N-terminal domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG123092.
    HOGENOMiHOG000276784.
    KOiK08480.
    OrthoDBiEOG65QWP2.

    Family and domain databases

    Gene3Di1.10.1240.30. 1 hit.
    InterProiIPR011006. CheY-like_superfamily.
    IPR011648. Circadian_clock_KaiA.
    IPR020844. Circadian_clock_KaiA_N.
    IPR020856. Circadian_clock_protein_KaiA_C.
    IPR017944. KaiA/RbsU_helical_domain.
    [Graphical view]
    PfamiPF07688. KaiA. 1 hit.
    [Graphical view]
    SUPFAMiSSF101215. SSF101215. 1 hit.
    SSF52172. SSF52172. 1 hit.
    PROSITEiPS51431. KAIA_C. 1 hit.
    PS51430. KAIA_N. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q79PF6-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLSQIAICIW VESTAILQDC QRALSADRYQ LQVCESGEML LEYAQTHRDQ    50
    IDCLILVAAN PSFRAVVQQL CFEGVVVPAI VVGDRDSEDP DEPAKEQLYH 100
    SAELHLGIHQ LEQLPYQVDA ALAEFLRLAP VETMADHIML MGANHDPELS 150
    SQQRDLAQRL QERLGYLGVY YKRDPDRFLR NLPAYESQKL HQAMQTSYRE 200
    IVLSYFSPNS NLNQSIDNFV NMAFFADVPV TKVVEIHMEL MDEFAKKLRV 250
    EGRSEDILLD YRLTLIDVIA HLCEMYRRSI PRET 284
    Length:284
    Mass (Da):32,632
    Last modified:July 5, 2004 - v1
    Checksum:i7C4F3B79FFDF59A2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB010691 Genomic DNA. Translation: BAA37101.1.
    AY120853 Genomic DNA. Translation: AAM82684.1.
    CP000100 Genomic DNA. Translation: ABB57248.1.
    PIRiT44267.
    RefSeqiYP_400235.1. NC_007604.1.

    Genome annotation databases

    EnsemblBacteriaiABB57248; ABB57248; Synpcc7942_1218.
    GeneIDi3773506.
    KEGGisyf:Synpcc7942_1218.
    PATRICi23787743. VBISynElo51371_1400.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB010691 Genomic DNA. Translation: BAA37101.1 .
    AY120853 Genomic DNA. Translation: AAM82684.1 .
    CP000100 Genomic DNA. Translation: ABB57248.1 .
    PIRi T44267.
    RefSeqi YP_400235.1. NC_007604.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1M2E NMR - A 1-135 [» ]
    1M2F NMR - A 1-135 [» ]
    1R8J X-ray 2.03 A/B 2-284 [» ]
    4G86 X-ray 2.39 A/B 2-284 [» ]
    ProteinModelPortali Q79PF6.
    SMRi Q79PF6. Positions 1-282.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-33329N.
    IntActi Q79PF6. 4 interactions.
    STRINGi 1140.Synpcc7942_1218.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABB57248 ; ABB57248 ; Synpcc7942_1218 .
    GeneIDi 3773506.
    KEGGi syf:Synpcc7942_1218.
    PATRICi 23787743. VBISynElo51371_1400.

    Phylogenomic databases

    eggNOGi NOG123092.
    HOGENOMi HOG000276784.
    KOi K08480.
    OrthoDBi EOG65QWP2.

    Enzyme and pathway databases

    BioCyci SYNEL:SYNPCC7942_1218-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q79PF6.

    Family and domain databases

    Gene3Di 1.10.1240.30. 1 hit.
    InterProi IPR011006. CheY-like_superfamily.
    IPR011648. Circadian_clock_KaiA.
    IPR020844. Circadian_clock_KaiA_N.
    IPR020856. Circadian_clock_protein_KaiA_C.
    IPR017944. KaiA/RbsU_helical_domain.
    [Graphical view ]
    Pfami PF07688. KaiA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF101215. SSF101215. 1 hit.
    SSF52172. SSF52172. 1 hit.
    PROSITEi PS51431. KAIA_C. 1 hit.
    PS51430. KAIA_N. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria."
      Ishiura M., Kutsuna S., Aoki S., Iwasaki H., Andersson C.R., Tanabe A., Golden S.S., Johnson C.H., Kondo T.
      Science 281:1519-1523(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, MUTANTS KAIA1; KAIA2 AND KAIA3.
    2. "Synechococcus elongatus PCC7942 cosmid 7G3."
      Holtman C.K., Sandoval P., Chen Y., Socias T., Mohler B.J., McMurtry S., Gonzalez A., Salinas I., Golden S.S., Youderian P.
      Submitted (JUN-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "Complete sequence of chromosome 1 of Synechococcus elongatus PCC 7942."
      US DOE Joint Genome Institute
      Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Schmutz J., Larimer F., Land M., Kyrpides N., Lykidis A., Richardson P.
      Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: PCC 7942.
    4. "Physical interactions among circadian clock proteins KaiA, KaiB and KaiC in cyanobacteria."
      Iwasaki H., Taniguchi Y., Ishiura M., Kondo T.
      EMBO J. 18:1137-1145(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH KAIC AND KAIB, MUTANT KAIA1.
    5. "Two KaiA-binding domains of cyanobacterial circadian clock protein KaiC."
      Taniguchi Y., Yamaguchi A., Hijikata A., Iwasaki H., Kamagata K., Ishiura M., Go M., Kondo T.
      FEBS Lett. 496:86-90(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH KAIC, MUTANTS KAIA2 AND KAIA4.
    6. "Mutations in KaiA, a clock protein, extend the period of circadian rhythm in the cyanobacterium Synechococcus elongatus PCC 7942."
      Nishimura H., Nakahira Y., Imai K., Tsuruhara A., Kondo H., Hayashi H., Hirai M., Saito H., Kondo T.
      Microbiology 148:2903-2909(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ILE-9; ILE-16; LEU-31; SER-36; CYS-53; VAL-76; GLN-113; GLN-117; ASP-119; VAL-131; ASP-136; PHE-178; ARG-180; MET-194; PHE-224; PHE-225; GLU-239; MET-241; ASP-242; GLU-243; PHE-244; ALA-245; ILE-266 AND CYS-273.
    7. "KaiA-stimulated KaiC phosphorylation in circadian timing loops in cyanobacteria."
      Iwasaki H., Nishiwaki T., Kitayama Y., Nakajima M., Kondo T.
      Proc. Natl. Acad. Sci. U.S.A. 99:15788-15793(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    8. "Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC."
      Xu Y., Mori T., Johnson C.H.
      EMBO J. 22:2117-2126(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial circadian clock system."
      Kitayama Y., Iwasaki H., Nishiwaki T., Kondo T.
      EMBO J. 22:2127-2134(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DEVELOPMENTAL STAGE.
    10. "Stoichiometric interactions between cyanobacterial clock proteins KaiA and KaiC."
      Hayashi F., Ito H., Fujita M., Iwase R., Uzumaki T., Ishiura M.
      Biochem. Biophys. Res. Commun. 316:195-202(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: STOICHIOMETRY OF THE COMPLEX FORMED WITH KAIC.
    11. "Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism."
      Williams S.B., Vakonakis I., Golden S.S., LiWang A.C.
      Proc. Natl. Acad. Sci. U.S.A. 99:15357-15362(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 1-135.
    12. Erratum
      Williams S.B., Vakonakis I., Golden S.S., LiWang A.C.
      Proc. Natl. Acad. Sci. U.S.A. 100:763-763(2003)
    13. "Crystal structure of circadian clock protein KaiA from Synechococcus elongatus."
      Ye S., Vakonakis I., Ioerger T.R., LiWang A.C., Sacchettini J.C.
      J. Biol. Chem. 279:20511-20518(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.03 ANGSTROMS) OF 2-284, HOMODIMERIZATION, DOMAIN.

    Entry informationi

    Entry nameiKAIA_SYNE7
    AccessioniPrimary (citable) accession number: Q79PF6
    Secondary accession number(s): Q31NX1, Q9Z3H4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 11, 2004
    Last sequence update: July 5, 2004
    Last modified: October 1, 2014
    This is version 75 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    'Kai' means 'cycle' in Japanese.

    Caution

    PubMed:15007067 structure is derived from this sequence and not from the one of S.elongatus.Curated

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3