PHYB_ORYSJ
ID PHYB_ORYSJ Reviewed; 1171 AA.
AC Q10MG9; P25764; Q84LN8;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Phytochrome B;
GN Name=PHYB; Synonyms=PHYB1; OrderedLocusNames=Os03g0309200, LOC_Os03g19590;
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 [GENOMIC DNA / MRNA].
RC STRAIN=cv. Nipponbare, and cv. Nohrin 8; 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).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF11824.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AB109892; BAC76432.1; -; mRNA.
DR EMBL; AB183525; BAD86669.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF95558.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF11824.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014959; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_015631282.1; XM_015775796.1.
DR AlphaFoldDB; Q10MG9; -.
DR BMRB; Q10MG9; -.
DR SMR; Q10MG9; -.
DR IntAct; Q10MG9; 1.
DR STRING; 4530.OS03T0309200-01; -.
DR PaxDb; Q10MG9; -.
DR PRIDE; Q10MG9; -.
DR EnsemblPlants; Os03t0309200-02; Os03t0309200-02; Os03g0309200.
DR GeneID; 4332623; -.
DR Gramene; Os03t0309200-02; Os03t0309200-02; Os03g0309200.
DR KEGG; osa:4332623; -.
DR eggNOG; ENOG502QRNS; Eukaryota.
DR HOGENOM; CLU_010418_0_0_1; -.
DR InParanoid; Q10MG9; -.
DR OrthoDB; 59136at2759; -.
DR PlantReactome; R-OSA-8933811; Circadian rhythm.
DR PlantReactome; R-OSA-8934036; Long day regulated expression of florigens.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR ExpressionAtlas; Q10MG9; baseline and differential.
DR Genevisible; Q10MG9; 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; 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; IPR036097; HisK_dim/P_sf.
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; SSF47384; SSF47384; 1.
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..1171
FT /note="Phytochrome B"
FT /id="PRO_0000171978"
FT DOMAIN 259..442
FT /note="GAF"
FT DOMAIN 661..732
FT /note="PAS 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 795..866
FT /note="PAS 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 943..1161
FT /note="Histidine kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT REGION 1..53
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..17
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 364
FT /ligand="phytochromobilin"
FT /ligand_id="ChEBI:CHEBI:189064"
FT /note="covalent, via 1 link"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1171 AA; 128493 MW; DEE981FC89D46FDC CRC64;
MASGSRATPT RSPSSARPAA PRHQHHHSQS SGGSTSRAGG GGGGGGGGGG GAAAAESVSK
AVAQYTLDAR LHAVFEQSGA SGRSFDYTQS LRASPTPSSE QQIAAYLSRI QRGGHIQPFG
CTLAVADDSS FRLLAYSENT ADLLDLSPHH SVPSLDSSAV PPPVSLGADA RLLFAPSSAV
LLERAFAARE ISLLNPLWIH SRVSSKPFYA ILHRIDVGVV IDLEPARTED PALSIAGAVQ
SQKLAVRAIS RLQALPGGDV KLLCDTVVEY VRELTGYDRV MVYRFHEDEH GEVVAESRRN
NLEPYIGLHY PATDIPQASR FLFRQNRVRM IADCHAAPVR VIQDPALTQP LCLVGSTLRS
PHGCHAQYMA NMGSIASLVM AVIISSGGDD DHNISRGSIP SAMKLWGLVV CHHTSPRCIP
FPLRYACEFL MQAFGLQLNM ELQLAHQLSE KHILRTQTLL CDMLLRDSPT GIVTQSPSIM
DLVKCDGAAL YYHGKYYPLG VTPTEVQIKD IIEWLTMCHG DSTGLSTDSL ADAGYPGAAA
LGDAVSGMAV AYITPSDYLF WFRSHTAKEI KWGGAKHHPE DKDDGQRMHP RSSFKAFLEV
VKSRSLPWEN AEMDAIHSLQ LILRDSFRDS AEGTSNSKAI VNGQVQLGEL ELRGIDELSS
VAREMVRLIE TATVPIFAVD TDGCINGWNA KVAELTGLSV EEAMGKSLVN DLIFKESEET
VNKLLSRALR GDEDKNVEIK LKTFGPEQSK GPIFVIVNAC SSRDYTKNIV GVCFVGQDVT
GQKVVMDKFI NIQGDYKAIV HNPNPLIPPI FASDENTCCS EWNTAMEKLT GWSRGEVVGK
LLVGEVFGNC CRLKGPDALT KFMIVLHNAI GGQDCEKFPF SFFDKNGKYV QALLTANTRS
RMDGEAIGAF CFLQIASPEL QQAFEIQRHH EKKCYARMKE LAYIYQEIKN PLNGIRFTNS
LLEMTDLKDD QRQFLETSTA CEKQMSKIVK DASLQSIEDG SLVLEKGEFS LGSVMNAVVS
QVMIQLRERD LQLIRDIPDE IKEASAYGDQ YRIQQVLCDF LLSMVRFAPA ENGWVEIQVR
PNIKQNSDGT DTMLFLFRFA CPGEGLPPEI VQDMFSNSRW TTQEGIGLSI CRKILKLMGG
EVQYIRESER SFFHIVLELP QPQQAASRGT S
