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Q6R0H1

- LHY_ARATH

UniProt

Q6R0H1 - LHY_ARATH

Protein

Protein LHY

Gene

LHY

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 88 (01 Oct 2014)
      Sequence version 2 (24 Nov 2009)
      Previous versions | rss
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    Functioni

    Transcription factor involved in the circadian clock. Binds to the promoter region of APRR1/TOC1 and TCP21/CHE to repress their transcription. Represses both CCA1 and itself.4 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi46 – 6924H-T-H motifPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. chromatin binding Source: InterPro
    2. sequence-specific DNA binding transcription factor activity Source: UniProtKB
    3. transcription regulatory region DNA binding Source: UniProtKB

    GO - Biological processi

    1. circadian rhythm Source: TAIR
    2. long-day photoperiodism, flowering Source: TAIR
    3. negative regulation of circadian rhythm Source: TAIR
    4. negative regulation of sequence-specific DNA binding transcription factor activity Source: UniProtKB
    5. regulation of circadian rhythm Source: UniProtKB
    6. regulation of transcription, DNA-templated Source: TAIR
    7. response to abscisic acid Source: TAIR
    8. response to auxin Source: TAIR
    9. response to cadmium ion Source: TAIR
    10. response to cold Source: TAIR
    11. response to ethylene Source: TAIR
    12. response to gibberellin Source: TAIR
    13. response to jasmonic acid Source: TAIR
    14. response to salicylic acid Source: TAIR
    15. response to salt stress Source: TAIR
    16. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Biological processi

    Biological rhythms, Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein LHY
    Alternative name(s):
    MYB-related transcription factor LHY
    Protein LATE ELONGATED HYPOCOTYL
    Gene namesi
    Name:LHY
    Ordered Locus Names:At1g01060
    ORF Names:T25K16.6
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 1

    Organism-specific databases

    TAIRiAT1G01060.

    Subcellular locationi

    Nucleus 1 PublicationPROSITE-ProRule annotation

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Shorter circadian oscillations.2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 645645Protein LHYPRO_0000388998Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei6 – 61PhosphoserineBy similarity

    Post-translational modificationi

    Phosphorylated by CK2.1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiQ6R0H1.
    PRIDEiQ6R0H1.

    Expressioni

    Tissue specificityi

    Expressed in leaves, roots, stems, flowers and siliques.2 Publications

    Inductioni

    Circadian-regulation with peak levels occurring around 1 hour after dawn. Up-regulated by APRR1/TOC1 and transiently by light treatment. Down-regulated by APRR5, APRR7 and APRR9.6 Publications

    Gene expression databases

    ArrayExpressiQ6R0H1.

    Interactioni

    Subunit structurei

    Homodimer or heterodimer with CCA1. Interacts with CCA1 (via internal domain); independently of photoperiod. Functions probably as part of a large complex. Interacts with CKB1 and CKB3.3 Publications

    Protein-protein interaction databases

    BioGridi24576. 13 interactions.
    IntActiQ6R0H1. 2 interactions.
    STRINGi3702.AT1G01060.3-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ6R0H1.
    SMRiQ6R0H1. Positions 22-75.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini19 – 7355HTH myb-typePROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi310 – 36051Ala-richAdd
    BLAST

    Sequence similaritiesi

    Contains 1 HTH myb-type DNA-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG269073.
    HOGENOMiHOG000084594.
    InParanoidiQ6R0H1.
    KOiK12133.
    OMAiMDEPRAS.
    PhylomeDBiQ6R0H1.

    Family and domain databases

    Gene3Di1.10.10.60. 1 hit.
    InterProiIPR009057. Homeodomain-like.
    IPR017930. Myb_dom.
    IPR006447. Myb_dom_plants.
    IPR001005. SANT/Myb.
    [Graphical view]
    PfamiPF00249. Myb_DNA-binding. 1 hit.
    [Graphical view]
    SMARTiSM00717. SANT. 1 hit.
    [Graphical view]
    SUPFAMiSSF46689. SSF46689. 1 hit.
    TIGRFAMsiTIGR01557. myb_SHAQKYF. 1 hit.
    PROSITEiPS51294. HTH_MYB. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    This entry describes 1 isoform i produced by alternative splicing. Align

    Note: A number of isoforms are produced. According to EST sequences.

    Isoform 1 (identifier: Q6R0H1-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MDTNTSGEEL LAKARKPYTI TKQRERWTED EHERFLEALR LYGRAWQRIE    50
    EHIGTKTAVQ IRSHAQKFFT KLEKEAEVKG IPVCQALDIE IPPPRPKRKP 100
    NTPYPRKPGN NGTSSSQVSS AKDAKLVSSA SSSQLNQAFL DLEKMPFSEK 150
    TSTGKENQDE NCSGVSTVNK YPLPTKQVSG DIETSKTSTV DNAVQDVPKK 200
    NKDKDGNDGT TVHSMQNYPW HFHADIVNGN IAKCPQNHPS GMVSQDFMFH 250
    PMREETHGHA NLQATTASAT TTASHQAFPA CHSQDDYRSF LQISSTFSNL 300
    IMSTLLQNPA AHAAATFAAS VWPYASVGNS GDSSTPMSSS PPSITAIAAA 350
    TVAAATAWWA SHGLLPVCAP APITCVPFST VAVPTPAMTE MDTVENTQPF 400
    EKQNTALQDQ NLASKSPASS SDDSDETGVT KLNADSKTND DKIEEVVVTA 450
    AVHDSNTAQK KNLVDRSSCG SNTPSGSDAE TDALDKMEKD KEDVKETDEN 500
    QPDVIELNNR KIKMRDNNSN NNATTDSWKE VSEEGRIAFQ ALFARERLPQ 550
    SFSPPQVAEN VNRKQSDTSM PLAPNFKSQD SCAADQEGVV MIGVGTCKSL 600
    KTRQTGFKPY KRCSMEVKES QVGNINNQSD EKVCKRLRLE GEAST 645
    Length:645
    Mass (Da):70,438
    Last modified:November 24, 2009 - v2
    Checksum:iDC327F40AB75AAF5
    GO

    Sequence cautioni

    The sequence AAF26474.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti98 – 981R → Q in BAH19541. (PubMed:19423640)Curated
    Sequence conflicti408 – 4081Q → R in AAS09977. (PubMed:16463103)Curated
    Sequence conflicti411 – 4111N → T in CAA07004. (PubMed:9657154)Curated
    Sequence conflicti537 – 5371I → V in BAH19541. (PubMed:19423640)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ006404 mRNA. Translation: CAA07004.1.
    AY519507 mRNA. Translation: AAS09977.1.
    AC007323 Genomic DNA. Translation: AAF26474.1. Sequence problems.
    CP002684 Genomic DNA. Translation: AEE27223.1.
    CP002684 Genomic DNA. Translation: AEE27224.1.
    CP002684 Genomic DNA. Translation: AEE27225.1.
    AK316728 mRNA. Translation: BAH19454.1.
    AK316829 mRNA. Translation: BAH19541.1.
    RefSeqiNP_001030924.1. NM_001035847.1. [Q6R0H1-1]
    NP_171614.1. NM_099988.3. [Q6R0H1-1]
    NP_849568.1. NM_179237.1. [Q6R0H1-1]
    UniGeneiAt.25466.

    Genome annotation databases

    EnsemblPlantsiAT1G01060.1; AT1G01060.1; AT1G01060. [Q6R0H1-1]
    AT1G01060.2; AT1G01060.2; AT1G01060. [Q6R0H1-1]
    AT1G01060.3; AT1G01060.3; AT1G01060. [Q6R0H1-1]
    GeneIDi839341.
    KEGGiath:AT1G01060.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ006404 mRNA. Translation: CAA07004.1 .
    AY519507 mRNA. Translation: AAS09977.1 .
    AC007323 Genomic DNA. Translation: AAF26474.1 . Sequence problems.
    CP002684 Genomic DNA. Translation: AEE27223.1 .
    CP002684 Genomic DNA. Translation: AEE27224.1 .
    CP002684 Genomic DNA. Translation: AEE27225.1 .
    AK316728 mRNA. Translation: BAH19454.1 .
    AK316829 mRNA. Translation: BAH19541.1 .
    RefSeqi NP_001030924.1. NM_001035847.1. [Q6R0H1-1 ]
    NP_171614.1. NM_099988.3. [Q6R0H1-1 ]
    NP_849568.1. NM_179237.1. [Q6R0H1-1 ]
    UniGenei At.25466.

    3D structure databases

    ProteinModelPortali Q6R0H1.
    SMRi Q6R0H1. Positions 22-75.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 24576. 13 interactions.
    IntActi Q6R0H1. 2 interactions.
    STRINGi 3702.AT1G01060.3-P.

    Proteomic databases

    PaxDbi Q6R0H1.
    PRIDEi Q6R0H1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT1G01060.1 ; AT1G01060.1 ; AT1G01060 . [Q6R0H1-1 ]
    AT1G01060.2 ; AT1G01060.2 ; AT1G01060 . [Q6R0H1-1 ]
    AT1G01060.3 ; AT1G01060.3 ; AT1G01060 . [Q6R0H1-1 ]
    GeneIDi 839341.
    KEGGi ath:AT1G01060.

    Organism-specific databases

    GeneFarmi 1653. 100.
    TAIRi AT1G01060.

    Phylogenomic databases

    eggNOGi NOG269073.
    HOGENOMi HOG000084594.
    InParanoidi Q6R0H1.
    KOi K12133.
    OMAi MDEPRAS.
    PhylomeDBi Q6R0H1.

    Gene expression databases

    ArrayExpressi Q6R0H1.

    Family and domain databases

    Gene3Di 1.10.10.60. 1 hit.
    InterProi IPR009057. Homeodomain-like.
    IPR017930. Myb_dom.
    IPR006447. Myb_dom_plants.
    IPR001005. SANT/Myb.
    [Graphical view ]
    Pfami PF00249. Myb_DNA-binding. 1 hit.
    [Graphical view ]
    SMARTi SM00717. SANT. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46689. SSF46689. 1 hit.
    TIGRFAMsi TIGR01557. myb_SHAQKYF. 1 hit.
    PROSITEi PS51294. HTH_MYB. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering."
      Schaffer R., Ramsay N., Samach A., Corden S., Putterill J., Carre I.A., Coupland G.
      Cell 93:1219-1229(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INDUCTION.
    2. "The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family."
      Chen Y., Yang X., He K., Liu M., Li J., Gao Z., Lin Z., Zhang Y., Wang X., Qiu X., Shen Y., Zhang L., Deng X., Luo J., Deng X.-W., Chen Z., Gu H., Qu L.-J.
      Plant Mol. Biol. 60:107-124(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY.
    3. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
      Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
      , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
      Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    4. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    5. "Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
      Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
      DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    6. "The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis."
      Sugano S., Andronis C., Ong M.S., Green R.M., Tobin E.M.
      Proc. Natl. Acad. Sci. U.S.A. 96:12362-12366(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION, INTERACTION WITH CKB1 AND CKB3.
    7. "LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis."
      Mizoguchi T., Wheatley K., Hanzawa Y., Wright L., Mizoguchi M., Song H.-R., Carre I.A., Coupland G.
      Dev. Cell 2:629-641(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    8. "Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY."
      Kim J.Y., Song H.R., Taylor B.L., Carre I.A.
      EMBO J. 22:935-944(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION BY LIGHT.
    9. "The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots."
      James A.B., Monreal J.A., Nimmo G.A., Kelly C.L., Herzyk P., Jenkins G.I., Nimmo H.G.
      Science 322:1832-1835(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY, INDUCTION.
    10. "CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis."
      Lu S.X., Knowles S.M., Andronis C., Ong M.S., Tobin E.M.
      Plant Physiol. 150:834-843(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INDUCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, SUBUNIT, INTERACTION WITH CCA1, DNA-BINDING, DISRUPTION PHENOTYPE.
    11. "Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the circadian oscillator of Arabidopsis."
      Yakir E., Hilman D., Kron I., Hassidim M., Melamed-Book N., Green R.M.
      Plant Physiol. 150:844-857(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH CCA1.
    12. "A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock."
      Pruneda-Paz J.L., Breton G., Para A., Kay S.A.
      Science 323:1481-1485(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    13. "PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock."
      Nakamichi N., Kiba T., Henriques R., Mizuno T., Chua N.H., Sakakibara H.
      Plant Cell 22:594-605(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.

    Entry informationi

    Entry nameiLHY_ARATH
    AccessioniPrimary (citable) accession number: Q6R0H1
    Secondary accession number(s): B9DFD7
    , B9DFM4, O81713, Q9MAM8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 24, 2009
    Last sequence update: November 24, 2009
    Last modified: October 1, 2014
    This is version 88 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    CCA1 and LHY are only partially redundant, but they bind to the same region of the promoters.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3