PHYB_SORBI
ID PHYB_SORBI Reviewed; 1178 AA.
AC P93527; Q6S527;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 10-FEB-2021, sequence version 3.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Phytochrome B;
GN Name=PHYB; Synonyms=MA3;
GN ORFNames=SORBI_3001G394400 {ECO:0000312|EMBL:EER94971.1};
OS Sorghum bicolor (Sorghum) (Sorghum vulgare).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade;
OC Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum.
OX NCBI_TaxID=4558;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=10723737; DOI=10.1093/oxfordjournals.molbev.a026316;
RA Alba R., Kelmenson P.M., Cordonnier-Pratt M.-M., Pratt L.H.;
RT "The phytochrome gene family in tomato and the rapid differential evolution
RT of this family in angiosperms.";
RL Mol. Biol. Evol. 17:362-373(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=14963106; DOI=10.1093/molbev/msh067;
RA White G.M., Hamblin M.T., Kresovich S.;
RT "Molecular evolution of the phytochrome gene family in sorghum: changing
RT rates of synonymous and replacement evolution.";
RL Mol. Biol. Evol. 21:716-723(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. BTx623;
RX PubMed=19189423; DOI=10.1038/nature07723;
RA Paterson A.H., Bowers J.E., Bruggmann R., Dubchak I., Grimwood J.,
RA Gundlach H., Haberer G., Hellsten U., Mitros T., Poliakov A., Schmutz J.,
RA Spannagl M., Tang H., Wang X., Wicker T., Bharti A.K., Chapman J.,
RA Feltus F.A., Gowik U., Grigoriev I.V., Lyons E., Maher C.A., Martis M.,
RA Narechania A., Otillar R.P., Penning B.W., Salamov A.A., Wang Y., Zhang L.,
RA Carpita N.C., Freeling M., Gingle A.R., Hash C.T., Keller B., Klein P.,
RA Kresovich S., McCann M.C., Ming R., Peterson D.G., Mehboob-ur-Rahman M.,
RA Ware D., Westhoff P., Mayer K.F.X., Messing J., Rokhsar D.S.;
RT "The Sorghum bicolor genome and the diversification of grasses.";
RL Nature 457:551-556(2009).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 208-1178.
RC STRAIN=cv. 58M;
RX PubMed=9046599; DOI=10.1104/pp.113.2.611;
RA Childs K.L., Miller F.R., Cordonnier-Pratt M.-M., Pratt L.H., Morgan P.W.,
RA Mullet J.E.;
RT "The Sorghum bicolor photoperiod sensitivity gene, Ma3, encodes a
RT phytochrome B.";
RL Plant Physiol. 113:611-619(1997).
RN [5]
RP COMPLEX WITH PHYTOCHROMOBILIN.
RX PubMed=28376244; DOI=10.1002/1873-3468.12642;
RA Velazquez Escobar F., Buhrke D., Fernandez Lopez M., Shenkutie S.M.,
RA von Horsten S., Essen L.O., Hughes J., Hildebrandt P.;
RT "Structural communication between the chromophore-binding pocket and the N-
RT terminal extension in plant phytochrome phyB.";
RL FEBS Lett. 591:1258-1265(2017).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 113-459 IN COMPLEX WITH
RP PHYCOCYANOBILIN AND PHYTOCHROMOBILIN.
RX PubMed=32366982; DOI=10.1038/s41477-020-0638-y;
RA Nagano S., Guan K., Shenkutie S.M., Feiler C., Weiss M., Kraskov A.,
RA Buhrke D., Hildebrandt P., Hughes J.;
RT "Structural insights into photoactivation and signalling in plant
RT phytochromes.";
RL Nat. Plants 6:581-588(2020).
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. {ECO:0000250|UniProtKB:P14713}.
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P14713}.
CC -!- PTM: Contains one covalently linked phytochromobilin chromophore.
CC {ECO:0000269|PubMed:28376244, ECO:0000269|PubMed:32366982}.
CC -!- SIMILARITY: Belongs to the phytochrome family. {ECO:0000305}.
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DR EMBL; AF182394; AAB41398.2; -; Genomic_DNA.
DR EMBL; AY466084; AAR30900.1; -; Genomic_DNA.
DR EMBL; AY466085; AAR30901.1; -; Genomic_DNA.
DR EMBL; AY466086; AAR30902.1; -; Genomic_DNA.
DR EMBL; AY466088; AAR30904.1; -; Genomic_DNA.
DR EMBL; CM000760; EER94971.1; -; Genomic_DNA.
DR PIR; T14802; T14802.
DR RefSeq; XP_002467973.1; XM_002467928.1.
DR PDB; 6TBY; X-ray; 1.80 A; AAA=113-451.
DR PDB; 6TC5; X-ray; 2.10 A; AAA=113-459.
DR PDBsum; 6TBY; -.
DR PDBsum; 6TC5; -.
DR AlphaFoldDB; P93527; -.
DR SMR; P93527; -.
DR STRING; 4558.Sb01g037340.1; -.
DR EnsemblPlants; EER94971; EER94971; SORBI_3001G394400.
DR GeneID; 8081072; -.
DR Gramene; EER94971; EER94971; SORBI_3001G394400.
DR KEGG; sbi:8081072; -.
DR eggNOG; ENOG502QRNS; Eukaryota.
DR HOGENOM; CLU_010418_0_0_1; -.
DR OMA; STACEKQ; -.
DR OrthoDB; 59136at2759; -.
DR Proteomes; UP000000768; Chromosome 1.
DR ExpressionAtlas; P93527; baseline and differential.
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:0017012; P:protein-phytochromobilin linkage; IDA:UniProtKB.
DR GO; GO:0009585; P:red, far-red light phototransduction; IEA:UniProtKB-KW.
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; 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; 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 1: Evidence at protein level;
KW 3D-structure; Chromophore; Photoreceptor protein;
KW Phytochrome signaling pathway; Receptor; Reference proteome; Repeat;
KW Sensory transduction; Transcription; Transcription regulation.
FT CHAIN 1..1178
FT /note="Phytochrome B"
FT /id="PRO_0000171988"
FT DOMAIN 267..449
FT /note="GAF"
FT /evidence="ECO:0000305"
FT DOMAIN 668..739
FT /note="PAS 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 802..873
FT /note="PAS 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 950..1170
FT /note="Histidine kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT REGION 1..58
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 372
FT /ligand="phytochromobilin"
FT /ligand_id="ChEBI:CHEBI:189064"
FT /note="covalent, via 1 link"
FT /evidence="ECO:0000269|PubMed:32366982,
FT ECO:0007744|PDB:6TC5"
FT CONFLICT 990
FT /note="K -> E (in Ref. 1; AAB41398)"
FT CONFLICT 1107..1108
FT /note="AC -> TY (in Ref. 1; AAB41398)"
SQ SEQUENCE 1178 AA; 129047 MW; 248501C936B9AAFE CRC64;
MASGSRATPT RSPSSARPEA PRHAHHHHHH HSQSSGGSTS RAGGGGGGGG GGGGTAATAT
ATATESVSKA VAQYTLDARL HAVFEQSGAS GRSFDYSQSL RAPPTPSSEQ QIAAYLSRIQ
RGGHIQPFGC TLAVADDSSF RLLAFSENAA DLLDLSPHHS VPSLDSAAPP PVSLGADARL
LFSPSSAVLL ERAFAAREIS LLNPLWIHSR VSSKPFYAIL HRIDVGVVID LEPARTEDPA
LSIAGAVQSQ KLAVRAISRL QALPGGDIKL LCDTVVEHVR ELTGYDRVMV YRFHEDEHGE
VVAESRRDNL EPYLGLHYPA TDIPQASRFL FRQNRVRMIA DCHATPVRVI QDPGMSQPLC
LVGSTLRAPH GCHAQYMANM GSIASLVMAV IISSGGDDEQ TGRGGISSAM KLWGLVVCHH
TSPRCIPFPL RYACEFLMQA FGLQLNMELQ LAHQLSEKHI LRTQTLLCDM LLRDSPTGIV
TQSPSIMDLV KCDGAALYYH GKYYPLGVTP TESQIKDIIE WLTVCHGDST GLSTDSLADA
GYLGAAALGD AVCGMAVAYI TPSDYLFWFR SHTAKEIKWG GAKHHPEDKD DGQRMHPRSS
FKAFLEVVKS RSLPWENAEM DAIHSLQLIL RDSFRDAAEG TSNSKAIVNG QVQLGELELR
GINELSSVAR EMVRLIETAT VPIFAVDTDG CINGWNAKIA ELTGLSVEEA MGKSLVNDLI
FKESEEIVEK LLSRALRGEE DKNVEIKLKT FGSEQSNGAI FVIVNACSSR DYTQNIVGVC
FVGQDVTGQK VVMDKFINIQ GDYKAIVHNP NPLIPPIFAS DENTSCSEWN TAMEKLTGWS
RGEVVGKFLI GEVFGSFCRL KGPDALTKFM VVIHNAIGGQ DYEKFPFSFF DKNGKYVQAL
LTANTRSKMD GKSIGAFCFL QIASAEIQQA FEIQRQQEKK CYARMKELAY ICQEIKNPLS
GIRFTNSLLQ MTDLNDDQRQ FLETCSACEK QMSKIVKDAT LQSIEDGSLV LEKSEFSFGD
VMNAVVSQAM LLLRERDLQL IRDIPDEIKD ASAYGDQFRI QQVLADFLLS MVRSAPSENG
WVEIQVRPNV KQNSDGTDTE LFIFRFACPG EGLPADIVQD MFSNSQWSTQ EGVGLSTCRK
ILKLMGGEVQ YIRESERSFF LIVLELPQPR PAADREIS
