ID   PHYE_ARATH              Reviewed;        1112 AA.
AC   P42498; Q56Y99;
DT   01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT   03-MAY-2011, sequence version 2.
DT   03-AUG-2022, entry version 180.
DE   RecName: Full=Phytochrome E;
GN   Name=PHYE; OrderedLocusNames=At4g18130; ORFNames=F15J5.100;
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].
RC   STRAIN=cv. Landsberg erecta;
RX   PubMed=8049367; DOI=10.1007/bf00043870;
RA   Clack T., Mathews S., Sharrock R.A.;
RT   "The phytochrome apoprotein family in Arabidopsis is encoded by five genes:
RT   the sequences and expression of PHYD and PHYE.";
RL   Plant Mol. Biol. 25:413-427(1994).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10617198; DOI=10.1038/47134;
RA   Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA   Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA   Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA   de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA   Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA   Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA   Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA   Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA   Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA   Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA   Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA   Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA   Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA   Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA   Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA   Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA   Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA   Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA   Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA   Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA   Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA   Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA   Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA   Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA   Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA   Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA   Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA   de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA   Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA   Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA   Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA   Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA   Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA   Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA   Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA   Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA   Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA   O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA   Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA   Martienssen R., McCombie W.R.;
RT   "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL   Nature 402:769-777(1999).
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] OF 1-316.
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 (MAR-2005) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Regulatory photoreceptor which exists in two forms that are
CC       reversibly interconvertible by light: the Pr form that absorbs
CC       maximally in the red region of the spectrum and the Pfr form that
CC       absorbs maximally in the far-red region. Photoconversion of Pr to Pfr
CC       induces an array of morphogenic responses, whereas reconversion of Pfr
CC       to Pr cancels the induction of those responses. Pfr controls the
CC       expression of a number of nuclear genes including those encoding the
CC       small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B
CC       binding protein, protochlorophyllide reductase, rRNA, etc. It also
CC       controls the expression of its own gene(s) in a negative feedback
CC       fashion.
CC   -!- SUBUNIT: Homodimer.
CC   -!- INTERACTION:
CC       P42498; P14713: PHYB; NbExp=5; IntAct=EBI-624404, EBI-300727;
CC       P42498; P42497: PHYD; NbExp=4; IntAct=EBI-624404, EBI-624382;
CC   -!- PTM: Contains one covalently linked phytochromobilin chromophore.
CC       {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the phytochrome family. {ECO:0000305}.
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DR   EMBL; X76610; CAA54075.1; -; Genomic_DNA.
DR   EMBL; AL110123; CAB53654.1; -; Genomic_DNA.
DR   EMBL; AL161548; CAB78815.1; -; Genomic_DNA.
DR   EMBL; CP002687; AEE84000.1; -; Genomic_DNA.
DR   EMBL; AK221424; BAD94419.1; -; mRNA.
DR   PIR; S46313; S46313.
DR   RefSeq; NP_193547.4; NM_117923.8.
DR   AlphaFoldDB; P42498; -.
DR   SMR; P42498; -.
DR   BioGRID; 12831; 6.
DR   IntAct; P42498; 2.
DR   STRING; 3702.AT4G18130.1; -.
DR   iPTMnet; P42498; -.
DR   PaxDb; P42498; -.
DR   PRIDE; P42498; -.
DR   ProteomicsDB; 236755; -.
DR   EnsemblPlants; AT4G18130.1; AT4G18130.1; AT4G18130.
DR   GeneID; 827538; -.
DR   Gramene; AT4G18130.1; AT4G18130.1; AT4G18130.
DR   KEGG; ath:AT4G18130; -.
DR   Araport; AT4G18130; -.
DR   TAIR; locus:2005536; AT4G18130.
DR   eggNOG; ENOG502R3WG; Eukaryota.
DR   HOGENOM; CLU_010418_0_0_1; -.
DR   InParanoid; P42498; -.
DR   OMA; GGKCWLL; -.
DR   OrthoDB; 59136at2759; -.
DR   PRO; PR:P42498; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; P42498; baseline and differential.
DR   Genevisible; P42498; AT.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0000155; F:phosphorelay sensor kinase activity; IEA:InterPro.
DR   GO; GO:0009881; F:photoreceptor activity; IEA:UniProtKB-KW.
DR   GO; GO:0042803; F:protein homodimerization activity; IEA:InterPro.
DR   GO; GO:0009584; P:detection of visible light; IEA:InterPro.
DR   GO; GO:0017006; P:protein-tetrapyrrole linkage; IEA:InterPro.
DR   GO; GO:0009585; P:red, far-red light phototransduction; IEA:InterPro.
DR   GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
DR   CDD; cd16932; HATPase_Phy-like; 1.
DR   CDD; cd00082; HisKA; 1.
DR   CDD; cd00130; PAS; 2.
DR   Gene3D; 3.30.450.270; -; 1.
DR   Gene3D; 3.30.450.40; -; 1.
DR   Gene3D; 3.30.565.10; -; 1.
DR   InterPro; IPR003018; GAF.
DR   InterPro; IPR029016; GAF-like_dom_sf.
DR   InterPro; IPR003594; HATPase_C.
DR   InterPro; IPR036890; HATPase_C_sf.
DR   InterPro; IPR005467; His_kinase_dom.
DR   InterPro; IPR003661; HisK_dim/P.
DR   InterPro; IPR000014; PAS.
DR   InterPro; IPR035965; PAS-like_dom_sf.
DR   InterPro; IPR013654; PAS_2.
DR   InterPro; IPR013767; PAS_fold.
DR   InterPro; IPR044767; Phy_HATPase-like.
DR   InterPro; IPR016132; Phyto_chromo_attachment.
DR   InterPro; IPR013516; Phyto_chromo_BS.
DR   InterPro; IPR001294; Phytochrome.
DR   InterPro; IPR012129; Phytochrome_A-E.
DR   InterPro; IPR013515; Phytochrome_cen-reg.
DR   InterPro; IPR043150; Phytochrome_PHY.
DR   Pfam; PF01590; GAF; 1.
DR   Pfam; PF02518; HATPase_c; 1.
DR   Pfam; PF00512; HisKA; 1.
DR   Pfam; PF00989; PAS; 2.
DR   Pfam; PF08446; PAS_2; 1.
DR   Pfam; PF00360; PHY; 1.
DR   PIRSF; PIRSF000084; Phytochrome; 1.
DR   PRINTS; PR01033; PHYTOCHROME.
DR   SMART; SM00065; GAF; 1.
DR   SMART; SM00387; HATPase_c; 1.
DR   SMART; SM00388; HisKA; 1.
DR   SMART; SM00091; PAS; 2.
DR   SUPFAM; SSF55785; SSF55785; 3.
DR   SUPFAM; SSF55874; SSF55874; 1.
DR   TIGRFAMs; TIGR00229; sensory_box; 1.
DR   PROSITE; PS50109; HIS_KIN; 1.
DR   PROSITE; PS50112; PAS; 2.
DR   PROSITE; PS00245; PHYTOCHROME_1; 1.
DR   PROSITE; PS50046; PHYTOCHROME_2; 1.
PE   1: Evidence at protein level;
KW   Chromophore; Photoreceptor protein; Receptor; Reference proteome; Repeat;
KW   Sensory transduction; Transcription; Transcription regulation.
FT   CHAIN           1..1112
FT                   /note="Phytochrome E"
FT                   /id="PRO_0000171966"
FT   DOMAIN          217..387
FT                   /note="GAF"
FT   DOMAIN          595..666
FT                   /note="PAS 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT   DOMAIN          732..803
FT                   /note="PAS 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT   DOMAIN          877..1096
FT                   /note="Histidine kinase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT   REGION          1..20
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         322
FT                   /ligand="phytochromobilin"
FT                   /ligand_id="ChEBI:CHEBI:189064"
FT                   /note="covalent, via 1 link"
FT                   /evidence="ECO:0000250"
FT   CONFLICT        498
FT                   /note="G -> E (in Ref. 1; CAA54075 and 2; CAB53654/
FT                   CAB78815)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1112 AA;  122516 MW;  2E06677039213B57 CRC64;
     MGFESSSSAA SNMKPQPQKS NTAQYSVDAA LFADFAQSIY TGKSFNYSKS VISPPNHVPD
     EHITAYLSNI QRGGLVQPFG CLIAVEEPSF RILGLSDNSS DFLGLLSLPS TSHSGEFDKV
     KGLIGIDART LFTPSSGASL SKAASFTEIS LLNPVLVHSR TTQKPFYAIL HRIDAGIVMD
     LEPAKSGDPA LTLAGAVQSQ KLAVRAISRL QSLPGGDIGA LCDTVVEDVQ RLTGYDRVMV
     YQFHEDDHGE VVSEIRRSDL EPYLGLHYPA TDIPQAARFL FKQNRVRMIC DCNATPVKVV
     QSEELKRPLC LVNSTLRAPH GCHTQYMANM GSVASLALAI VVKGKDSSKL WGLVVGHHCS
     PRYVPFPLRY ACEFLMQAFG LQLQMELQLA SQLAEKKAMR TQTLLCDMLL RDTVSAIVTQ
     SPGIMDLVKC DGAALYYKGK CWLVGVTPNE SQVKDLVNWL VENHGDDSTG LTTDSLVDAG
     YPGAISLGDA VCGVAAAGFS SKDYLLWFRS NTASAIKWGG AKHHPKDKDD AGRMHPRSSF
     TAFLEVAKSR SLPWEISEID AIHSLRLIMR ESFTSSRPVL SGNGVARDAN ELTSFVCEMV
     RVIETATAPI FGVDSSGCIN GWNKKTAEMT GLLASEAMGK SLADEIVQEE SRAALESLLC
     KALQGEEEKS VMLKLRKFGQ NNHPDYSSDV CVLVNSCTSR DYTENIIGVC FVGQDITSEK
     AITDRFIRLQ GDYKTIVQSL NPLIPPIFAS DENACCSEWN AAMEKLTGWS KHEVIGKMLP
     GEVFGVFCKV KCQDSLTKFL ISLYQGIAGD NVPESSLVEF FNKEGKYIEA SLTANKSTNI
     EGKVIRCFFF LQIINKESGL SCPELKESAQ SLNELTYVRQ EIKNPLNGIR FAHKLLESSE
     ISASQRQFLE TSDACEKQIT TIIESTDLKS IEEGKLQLET EEFRLENILD TIISQVMIIL
     RERNSQLRVE VAEEIKTLPL NGDRVKLQLI LADLLRNIVN HAPFPNSWVG ISISPGQELS
     RDNGRYIHLQ FRMIHPGKGL PSEMLSDMFE TRDGWVTPDG LGLKLSRKLL EQMNGRVSYV
     REDERCFFQV DLQVKTMLGV ESRGTEGSSS IK