PHYB_ORYSI
ID PHYB_ORYSI Reviewed; 1171 AA.
AC A2XFW2; P25764; Q84LN8;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 2.
DT 03-AUG-2022, entry version 86.
DE RecName: Full=Phytochrome B;
GN Name=PHYB; Synonyms=PHYB1; ORFNames=OsI_010955;
OS Oryza sativa subsp. indica (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=39946;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. IR36; TISSUE=Seedling shoot;
RX PubMed=2005872; DOI=10.1007/bf00269863;
RA Dehesh K., Tepperman J., Christensen A.H., Quail P.H.;
RT "phyB is evolutionarily conserved and constitutively expressed in rice
RT seedling shoots.";
RL Mol. Gen. Genet. 225:305-313(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. 93-11;
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).
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; X57563; CAA40795.2; -; Genomic_DNA.
DR EMBL; CM000128; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; S14065; S14065.
DR AlphaFoldDB; A2XFW2; -.
DR BMRB; A2XFW2; -.
DR SMR; A2XFW2; -.
DR STRING; 39946.A2XFW2; -.
DR PRIDE; A2XFW2; -.
DR Proteomes; UP000007015; Chromosome 3.
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 3: Inferred from homology;
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_0000300860"
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"
FT CONFLICT 206
FT /note="K -> N (in Ref. 1; CAA40795)"
FT /evidence="ECO:0000305"
FT CONFLICT 245
FT /note="A -> V (in Ref. 1; CAA40795)"
FT /evidence="ECO:0000305"
FT CONFLICT 366
FT /note="A -> G (in Ref. 1; CAA40795)"
FT /evidence="ECO:0000305"
FT CONFLICT 457
FT /note="Q -> G (in Ref. 1; CAA40795)"
FT /evidence="ECO:0000305"
FT CONFLICT 540
FT /note="A -> D (in Ref. 1; CAA40795)"
FT /evidence="ECO:0000305"
FT CONFLICT 762
FT /note="S -> T (in Ref. 1; CAA40795)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1171 AA; 128451 MW; B5DFBD9D230C3A08 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 KLLCDTVVEH 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 DTMLFPFRFA CPGEGLPPEI VQDMFSNSRW TTQEGIGLSI CRKILKLMGG
EVQYIRESER SFFHIVLELP QPQQAASRGT S
