ID   PHYA_ORYSJ              Reviewed;        1128 AA.
AC   Q10DU0; B7EKU3; P10931; Q8LLN7;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-2006, sequence version 1.
DT   03-AUG-2022, entry version 118.
DE   RecName: Full=Phytochrome A;
GN   Name=PHYA; Synonyms=PHY18; OrderedLocusNames=Os03g0719800, LOC_Os03g51030;
GN   ORFNames=B1377B10.8, OAJNBa0031O09.11, OsJ_011877;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   STRAIN=cv. Nipponbare; TISSUE=Etiolated seedling;
RX   PubMed=16278346; DOI=10.1105/tpc.105.035899;
RA   Takano M., Inagaki N., Xie X., Yuzurihara N., Hihara F., Ishizuka T.,
RA   Yano M., Nishimura M., Miyao A., Hirochika H., Shinomura T.;
RT   "Distinct and cooperative functions of phytochromes a, B, and C in the
RT   control of deetiolation and flowering in rice.";
RL   Plant Cell 17:3311-3325(2005).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16109971; DOI=10.1101/gr.3869505;
RG   The rice chromosome 3 sequencing consortium;
RA   Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA   Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA   Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA   Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA   Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA   Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA   Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA   Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA   Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA   Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA   O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA   Jin W., Lee H.R., Jiang J., Jackson S.;
RT   "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT   and diverged grass species.";
RL   Genome Res. 15:1284-1291(2005).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [5]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [7]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
RN   [8]
RP   MUTAGENESIS OF N-TERMINAL SERINES.
RX   PubMed=1459458; DOI=10.1101/gad.6.12a.2364;
RA   Stockhaus J., Nagatani A., Halfter U., Kay S., Furuya M., Chua N.-H.;
RT   "Serine-to-alanine substitutions at the amino-terminal region of
RT   phytochrome A result in an increase in biological activity.";
RL   Genes Dev. 6:2364-2372(1992).
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   -!- 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; AB109891; BAC76431.1; -; mRNA.
DR   EMBL; AC147426; AAT77854.1; -; Genomic_DNA.
DR   EMBL; AF377946; AAM47309.1; -; Genomic_DNA.
DR   EMBL; DP000009; ABF98580.1; -; Genomic_DNA.
DR   EMBL; AP008209; BAF13010.1; -; Genomic_DNA.
DR   EMBL; AP014959; BAS86112.1; -; Genomic_DNA.
DR   EMBL; CM000140; EAZ28394.1; -; Genomic_DNA.
DR   EMBL; AK072482; BAG92990.1; -; mRNA.
DR   RefSeq; XP_015630340.1; XM_015774854.1.
DR   RefSeq; XP_015630341.1; XM_015774855.1.
DR   AlphaFoldDB; Q10DU0; -.
DR   SMR; Q10DU0; -.
DR   STRING; 4530.OS03T0719800-01; -.
DR   PaxDb; Q10DU0; -.
DR   PRIDE; Q10DU0; -.
DR   EnsemblPlants; Os03t0719800-01; Os03t0719800-01; Os03g0719800.
DR   GeneID; 4333930; -.
DR   Gramene; Os03t0719800-01; Os03t0719800-01; Os03g0719800.
DR   KEGG; osa:4333930; -.
DR   eggNOG; ENOG502QRSA; Eukaryota.
DR   HOGENOM; CLU_010418_0_0_1; -.
DR   InParanoid; Q10DU0; -.
DR   OMA; YLHHIQR; -.
DR   OrthoDB; 77253at2759; -.
DR   PlantReactome; R-OSA-8933811; Circadian rhythm.
DR   Proteomes; UP000000763; Chromosome 3.
DR   Proteomes; UP000007752; Chromosome 3.
DR   Proteomes; UP000059680; Chromosome 3.
DR   Genevisible; Q10DU0; OS.
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; 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; 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   2: Evidence at transcript level;
KW   Chromophore; Photoreceptor protein; Receptor; Reference proteome; Repeat;
KW   Sensory transduction; Transcription; Transcription regulation.
FT   CHAIN           1..1128
FT                   /note="Phytochrome A"
FT                   /id="PRO_0000171977"
FT   DOMAIN          219..404
FT                   /note="GAF"
FT   DOMAIN          620..690
FT                   /note="PAS 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT   DOMAIN          750..834
FT                   /note="PAS 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT   DOMAIN          904..1124
FT                   /note="Histidine kinase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT   REGION          1..24
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         324
FT                   /ligand="phytochromobilin"
FT                   /ligand_id="ChEBI:CHEBI:189064"
FT                   /note="covalent, via 1 link"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1128 AA;  125289 MW;  7DB1823EE704E464 CRC64;
     MSSSRPTQCS SSSSRTRQSS RARILAQTTL DAELNAEYEE YGDSFDYSKL VEAQRTTGPE
     QQARSEKVIA YLHHIQRAKL IQPFGCLLAL DEKTFNVIAL SENAPEMLTT VSHAVPSVDD
     PPKLRIGTNV WSLFTDPGAT ALQKALGFAD VSLLNPILVQ CKTSGKPFYA IVHRATGCLV
     VDFEPVKPTE FPATAAGALQ SYKLAAKAIS KIQSLPGGSM EVLCNTVVKE LFDLTGYDRV
     MAYKFHEDDH GEVFAEITKP GLEPYLGLHY PATDIPQAAR FLFMKNKVRM ICDCRARSIK
     IIEDESLHLD ISLCGSTLRA PHSCHLQYME NMNSIASLVM AVVVNENEDD DEVGADQPAQ
     QQKRKKLWGL LVCHHESPRY VPFPLRYACE FLAQVFAVHV NKEFELERQV REKSILRMQT
     MLSDMLLRES SPLSIVSGTP NIMDLVKCDG AALLYGGKVW RLQNAPTESQ IRDIAFWLSD
     VHRDSTGLST DSLHDAGYPG AAALGDMICG MAVAKINSKD ILFWFRSHTA AEIRWGGAKH
     DPSDKDDSRR MHPRLSFKAF LEVVKMKSLP WNDYEMDAIH SLQLILRGTL NDDIKPTRAA
     SLDNQVGDLK LDGLAELQAV TSEMVRLMET ATVPILAVDS NGLVNGWNQK VAELTGLRVD
     EAIGRHILTV VEESSVPVVQ RMLYLALQGK EEKEVKFEVK THGSKRDDGP VILVVNACAS
     RDLHDHVVGV CFVAQDMTVH KLVMDKFTRV EGDYKAIIHN PSPLIPPIFG ADEFGWCSEW
     NAAMTKLTGW HRDEVINKML LGEVFDSTNA SCLVKNKDAF VSLCILINSA LAGDETEKAP
     FSFFDRNGKY IECLLSVNRK VNADGVITGV FCFIQVPSHE LQHALHVQQA SQQNALTKLK
     AYSYMRHAIN NPLSGMLYSR KALKNTGLNE EQMKEVNVAD SCHRQLNKIL SDLDQDSVMN
     KSSCLDLEMV EFVLQDVFVA AVSQVLITCQ GKGIRVSCNL PERYMKQTVY GDGVRLQQIL
     SDFLFVSVKF SPVGGSVEIS CSLTKNSIGE NLHLIDLELR IKHQGKGVPA DLLSQMYEDD
     NKEQSDEGMS LAVSRNLLRL MNGDVRHMRE AGMSTFILSV ELASAPAK