PCL1_ARATH
ID PCL1_ARATH Reviewed; 323 AA.
AC Q9SNB4; B9DI71;
DT 24-JUL-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Transcription factor LUX;
DE AltName: Full=Protein LUX ARRHYTHMO;
DE AltName: Full=Protein PHYTOCLOCK 1;
GN Name=LUX; Synonyms=PCL1; OrderedLocusNames=At3g46640; ORFNames=F12A12.160;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBCELLULAR LOCATION,
RP INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=16164597; DOI=10.1111/j.1365-2443.2005.00892.x;
RA Onai K., Ishiura M.;
RT "PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis
RT circadian clock.";
RL Genes Cells 10:963-972(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP FUNCTION, INDUCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF PRO-171.
RX PubMed=16006522; DOI=10.1073/pnas.0503029102;
RA Hazen S.P., Schultz T.F., Pruneda-Paz J.L., Borevitz J.O., Ecker J.R.,
RA Kay S.A.;
RT "LUX ARRHYTHMO encodes a Myb domain protein essential for circadian
RT rhythms.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:10387-10392(2005).
RN [8]
RP INDUCTION.
RX PubMed=17132630; DOI=10.1093/pcp/pcl043;
RA Murakami M., Tago Y., Yamashino T., Mizuno T.;
RT "Comparative overviews of clock-associated genes of Arabidopsis thaliana
RT and Oryza sativa.";
RL Plant Cell Physiol. 48:110-121(2007).
RN [9]
RP FUNCTION.
RX PubMed=21236673; DOI=10.1016/j.cub.2010.12.021;
RA Helfer A., Nusinow D.A., Chow B.Y., Gehrke A.R., Bulyk M.L., Kay S.A.;
RT "LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression
RT in the Arabidopsis core clock.";
RL Curr. Biol. 21:126-133(2011).
RN [10]
RP FUNCTION, INTERACTION WITH ELF3, AND INDUCTION.
RX PubMed=21753751; DOI=10.1038/nature10182;
RA Nusinow D.A., Helfer A., Hamilton E.E., King J.J., Imaizumi T.,
RA Schultz T.F., Farre E.M., Kay S.A.;
RT "The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of
RT hypocotyl growth.";
RL Nature 475:398-402(2011).
RN [11]
RP INTERACTION WITH ELF3.
RX PubMed=22307044; DOI=10.4161/psb.18766;
RA Chow B.Y., Helfer A., Nusinow D.A., Kay S.A.;
RT "ELF3 recruitment to the PRR9 promoter requires other Evening Complex
RT members in the Arabidopsis circadian clock.";
RL Plant Signal. Behav. 7:170-173(2012).
RN [12]
RP FUNCTION.
RX PubMed=22311777; DOI=10.1093/mp/ssr122;
RA Sellaro R., Pacin M., Casal J.J.;
RT "Diurnal dependence of growth responses to shade in Arabidopsis: role of
RT hormone, clock, and light signaling.";
RL Mol. Plant 5:619-628(2012).
RN [13]
RP SUBCELLULAR LOCATION.
RX PubMed=22327739; DOI=10.1105/tpc.111.093807;
RA Herrero E., Kolmos E., Bujdoso N., Yuan Y., Wang M., Berns M.C.,
RA Uhlworm H., Coupland G., Saini R., Jaskolski M., Webb A., Goncalves J.,
RA Davis S.J.;
RT "EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains
RT the Arabidopsis circadian clock.";
RL Plant Cell 24:428-443(2012).
CC -!- FUNCTION: Transcription factor that is essential for the generation of
CC the circadian clock oscillation. Is necessary for activation of CCA1
CC and LHY expression. Is coregulated with TOC1 and seems to be repressed
CC by CCA1 and LHY by direct binding of these proteins to the evening
CC element in the LUX promoter. Directly regulates the expression of PRR9,
CC a major component of the morning transcriptional feedback circuit, by
CC binding specific sites on PRR9 promoter. Binds to its own promoter,
CC inducing a negative auto-regulatory feedback loop within the core
CC clock. Binds to ELF3 and associates with ELF4 in a diurnal complex
CC which is required for the expression of the growth-promoting
CC transcription factors PIF4 and PIF5 and subsequent hypocotyl growth in
CC the early evening. {ECO:0000269|PubMed:16006522,
CC ECO:0000269|PubMed:16164597, ECO:0000269|PubMed:21236673,
CC ECO:0000269|PubMed:21753751, ECO:0000269|PubMed:22311777}.
CC -!- SUBUNIT: Interacts with ELF3 and forms a complex with ELF3 and ELF4.
CC {ECO:0000269|PubMed:21753751, ECO:0000269|PubMed:22307044}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00625,
CC ECO:0000269|PubMed:16164597, ECO:0000269|PubMed:22327739}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9SNB4-1; Sequence=Displayed;
CC -!- INDUCTION: Circadian oscillation with peaks at subjective dusk.
CC {ECO:0000269|PubMed:16006522, ECO:0000269|PubMed:16164597,
CC ECO:0000269|PubMed:17132630, ECO:0000269|PubMed:21753751}.
CC -!- DISRUPTION PHENOTYPE: Mutant plant flowering lacks a photoperiodic
CC response. {ECO:0000269|PubMed:16006522, ECO:0000269|PubMed:16164597}.
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DR EMBL; AB206576; BAE16277.1; -; Genomic_DNA.
DR EMBL; AL133314; CAB62334.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78186.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78187.1; -; Genomic_DNA.
DR EMBL; BT006425; AAP21233.1; -; mRNA.
DR EMBL; AK319175; BAH20438.1; -; mRNA.
DR EMBL; AK227686; BAE99673.1; -; mRNA.
DR PIR; T45601; T45601.
DR RefSeq; NP_001030823.1; NM_001035746.2. [Q9SNB4-1]
DR RefSeq; NP_190248.1; NM_114531.3. [Q9SNB4-1]
DR PDB; 5LXU; X-ray; 2.14 A; A=144-200.
DR PDB; 6QEC; X-ray; 1.90 A; A=139-200.
DR PDBsum; 5LXU; -.
DR PDBsum; 6QEC; -.
DR AlphaFoldDB; Q9SNB4; -.
DR SMR; Q9SNB4; -.
DR BioGRID; 9137; 8.
DR ComplexPortal; CPX-1291; Evening Complex.
DR IntAct; Q9SNB4; 5.
DR STRING; 3702.AT3G46640.3; -.
DR iPTMnet; Q9SNB4; -.
DR PaxDb; Q9SNB4; -.
DR PRIDE; Q9SNB4; -.
DR ProteomicsDB; 236384; -. [Q9SNB4-1]
DR EnsemblPlants; AT3G46640.1; AT3G46640.1; AT3G46640. [Q9SNB4-1]
DR EnsemblPlants; AT3G46640.2; AT3G46640.2; AT3G46640. [Q9SNB4-1]
DR GeneID; 823817; -.
DR Gramene; AT3G46640.1; AT3G46640.1; AT3G46640. [Q9SNB4-1]
DR Gramene; AT3G46640.2; AT3G46640.2; AT3G46640. [Q9SNB4-1]
DR KEGG; ath:AT3G46640; -.
DR Araport; AT3G46640; -.
DR eggNOG; ENOG502RIEW; Eukaryota.
DR HOGENOM; CLU_055357_1_0_1; -.
DR OMA; RMSDYDV; -.
DR PhylomeDB; Q9SNB4; -.
DR PRO; PR:Q9SNB4; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SNB4; baseline and differential.
DR Genevisible; Q9SNB4; AT.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0005667; C:transcription regulator complex; IDA:ComplexPortal.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IBA:GO_Central.
DR GO; GO:0007623; P:circadian rhythm; IEP:UniProtKB.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:ComplexPortal.
DR GO; GO:0042753; P:positive regulation of circadian rhythm; IMP:UniProtKB.
DR GO; GO:0042752; P:regulation of circadian rhythm; IDA:ComplexPortal.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR044841; LUX/BOA-like.
DR InterPro; IPR017930; Myb_dom.
DR InterPro; IPR006447; Myb_dom_plants.
DR PANTHER; PTHR31442; PTHR31442; 1.
DR Pfam; PF00249; Myb_DNA-binding; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR TIGRFAMs; TIGR01557; myb_SHAQKYF; 1.
DR PROSITE; PS51294; HTH_MYB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Biological rhythms; DNA-binding;
KW Nucleus; Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..323
FT /note="Transcription factor LUX"
FT /id="PRO_0000422983"
FT DNA_BIND 139..200
FT /note="Myb-like GARP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00625"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 53..139
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 267..298
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 53..106
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 171
FT /note="P->L: In lux-5; compromised circadian clock."
FT /evidence="ECO:0000269|PubMed:16006522"
FT CONFLICT 177
FT /note="L -> V (in Ref. 5; BAH20438)"
FT /evidence="ECO:0000305"
FT CONFLICT 275
FT /note="H -> R (in Ref. 5; BAH20438)"
FT /evidence="ECO:0000305"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:6QEC"
FT HELIX 151..163
FT /evidence="ECO:0007829|PDB:6QEC"
FT HELIX 166..168
FT /evidence="ECO:0007829|PDB:6QEC"
FT HELIX 171..178
FT /evidence="ECO:0007829|PDB:6QEC"
FT HELIX 185..199
FT /evidence="ECO:0007829|PDB:6QEC"
SQ SEQUENCE 323 AA; 34649 MW; A4CF9244F858CE9F CRC64;
MGEEVQMSDY DVSGDGDRVS EWEMGLPSDE DLASLSYSLI PPNLAMAFSI TPERSRTIQD
VNRASETTLS SLRGGSSGPN TSSSNNNVEE EDRVGSSSPG SDSKKQKTSN GDGDDGGGVD
PDSAMAAEEG DSGTEDLSGK TLKRPRLVWT PQLHKRFVDV VAHLGIKNAV PKTIMQLMNV
EGLTRENVAS HLQKYRLYLK RMQGLTNEGP SASDKLFSST PVPPQSFQDI GGGGGSSGNV
GVPIPGAYGT QQMMQMPVYA HHMGMQGYHH QNHNHDPYHQ NHRHHHGAGG NGAFESNPYM
MQQNKFGSMA SYPSVGGGSA NEN
