PHYD_ARATH
ID PHYD_ARATH Reviewed; 1164 AA.
AC P42497; O23472;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2000, sequence version 2.
DT 03-AUG-2022, entry version 182.
DE RecName: Full=Phytochrome D;
GN Name=PHYD; OrderedLocusNames=At4g16250; ORFNames=dl4165c;
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=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [3]
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 [4]
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).
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 P42497; P14713: PHYB; NbExp=6; IntAct=EBI-624382, EBI-300727;
CC P42497; P14714: PHYC; NbExp=2; IntAct=EBI-624382, EBI-624366;
CC P42497; P42497: PHYD; NbExp=2; IntAct=EBI-624382, EBI-624382;
CC P42497; P42498: PHYE; NbExp=4; IntAct=EBI-624382, EBI-624404;
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; X76609; CAA54072.1; -; Genomic_DNA.
DR EMBL; Z97340; CAB10404.1; -; Genomic_DNA.
DR EMBL; AL161543; CAB78667.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE83721.1; -; Genomic_DNA.
DR PIR; B71429; B71429.
DR RefSeq; NP_193360.1; NM_117721.2.
DR AlphaFoldDB; P42497; -.
DR SMR; P42497; -.
DR BioGRID; 12613; 9.
DR IntAct; P42497; 4.
DR STRING; 3702.AT4G16250.1; -.
DR iPTMnet; P42497; -.
DR PaxDb; P42497; -.
DR PRIDE; P42497; -.
DR ProteomicsDB; 235020; -.
DR EnsemblPlants; AT4G16250.1; AT4G16250.1; AT4G16250.
DR GeneID; 827319; -.
DR Gramene; AT4G16250.1; AT4G16250.1; AT4G16250.
DR KEGG; ath:AT4G16250; -.
DR Araport; AT4G16250; -.
DR TAIR; locus:2005535; AT4G16250.
DR eggNOG; ENOG502QPNJ; Eukaryota.
DR HOGENOM; CLU_010418_0_0_1; -.
DR InParanoid; P42497; -.
DR OMA; ERTEFFI; -.
DR OrthoDB; 59136at2759; -.
DR PhylomeDB; P42497; -.
DR PRO; PR:P42497; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; P42497; baseline and differential.
DR Genevisible; P42497; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
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..1164
FT /note="Phytochrome D"
FT /id="PRO_0000171965"
FT DOMAIN 255..437
FT /note="GAF"
FT DOMAIN 656..727
FT /note="PAS 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 790..861
FT /note="PAS 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 938..1157
FT /note="Histidine kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT REGION 1..55
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..16
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 27..55
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 360
FT /ligand="phytochromobilin"
FT /ligand_id="ChEBI:CHEBI:189064"
FT /note="covalent, via 1 link"
FT /evidence="ECO:0000250"
FT CONFLICT 425
FT /note="L -> F (in Ref. 1; CAA54072)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1164 AA; 129268 MW; BB7CFE19C50ACBAB CRC64;
MVSGGGSKTS GGEAASSGHR RSRHTSAAEQ AQSSANKALR SQNQQPQNHG GGTESTNKAI
QQYTVDARLH AVFEQSGESG KSFDYSQSLK TAPYDSSVPE QQITAYLSRI QRGGYTQPFG
CLIAVEESTF TIIGYSENAR EMLGLMSQSV PSIEDKSEVL TIGTDLRSLF KSSSYLLLER
AFVAREITLL NPIWIHSNNT GKPFYAILHR VDVGILIDLE PARTEDPALS IAGAVQSQKL
AVRAISHLQS LPSGDIKLLC DTVVESVRDL TGYDRVMVYK FHEDEHGEVV AESKRNDLEP
YIGLHYPATD IPQASRFLFK QNRVRMIVDC YASPVRVVQD DRLTQFICLV GSTLRAPHGC
HAQYMTNMGS IASLAMAVII NGNEEDGNGV NTGGRNSMRL WGLVVCHHTS ARCIPFPLRY
ACEFLMQAFG LQLNMELQLA LQVSEKRVLR MQTLLCDMLL RDSPAGIVTQ RPSIMDLVKC
NGAAFLYQGK YYPLGVTPTD SQINDIVEWL VANHSDSTGL STDSLGDAGY PRAAALGDAV
CGMAVACITK RDFLFWFRSH TEKEIKWGGA KHHPEDKDDG QRMNPRSSFQ TFLEVVKSRC
QPWETAEMDA IHSLQLILRD SFKESEAMDS KAAAAGAVQP HGDDMVQQGM QEIGAVAREM
VRLIETATVP IFAVDIDGCI NGWNAKIAEL TGLSVEDAMG KSLVRELIYK EYKETVDRLL
SCALKGDEGK NVEVKLKTFG SELQGKAMFV VVNACSSKDY LNNIVGVCFV GQDVTGHKIV
MDKFINIQGD YKAIIHSPNP LIPPIFAADE NTCCLEWNTA MEKLTGWPRS EVIGKLLVRE
VFGSYCRLKG PDALTKFMIV LHNAIGGQDT DKFPFPFFDR KGEFIQALLT LNKRVSIDGK
IIGAFCFLQI PSPELQQALE VQRRQESEYF SRRKELAYIF QVIKNPLSGL RFTNSLLEDM
DLNEDQKQLL ETSVSCEKQI SKIVGDMDVK SIDDGSFLLE RTEFFIGNVT NAVVSQVMLV
VRERNLQLIR NIPTEVKSMA VYGDQIRLQQ VLAEFLLSIV RYAPMEGSVE LHLCPTLNQM
ADGFSAVRLE FRMACAGEGV PPEKVQDMFH SSRWTSPEGL GLSVCRKILK LMNGGVQYIR
EFERSYFLIV IELPVPLMMM MPSS
