PHYB1_SOLLC
ID PHYB1_SOLLC Reviewed; 1131 AA.
AC Q9ZS62; Q9ZS57; Q9ZS58; Q9ZS59; Q9ZS60; Q9ZS61;
DT 15-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Phytochrome B1;
GN Name=PHYB1 {ECO:0000312|EMBL:CAA05293.1};
OS Solanum lycopersicum (Tomato) (Lycopersicon esculentum).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum;
OC Solanum subgen. Lycopersicon.
OX NCBI_TaxID=4081;
RN [1] {ECO:0000305, ECO:0000312|EMBL:CAA05293.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1), NUCLEOTIDE SEQUENCE [MRNA]
RP (ISOFORMS 2; 3; 4; 5 AND 6), AND MUTANT TRI3.
RX PubMed=9869419; DOI=10.1023/a:1006068305454;
RA Lazarova G.I., Kubota T., Frances S., Peters J.L., Hughes M.J.G.,
RA Brandstaedter J., Szell M., Matsui M., Kendrick R.E.,
RA Cordonnier-Pratt M.-M., Pratt L.H.;
RT "Characterization of tomato PHYB1 and identification of molecular defects
RT in four mutant alleles.";
RL Plant Mol. Biol. 38:1137-1146(1998).
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:0000305}.
CC -!- SUBUNIT: Homodimer. {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=6;
CC Name=1 {ECO:0000269|PubMed:9869419};
CC IsoId=Q9ZS62-1; Sequence=Displayed;
CC Name=2 {ECO:0000269|PubMed:9869419};
CC IsoId=Q9ZS62-2; Sequence=VSP_051666;
CC Name=3 {ECO:0000269|PubMed:9869419};
CC IsoId=Q9ZS62-3; Sequence=VSP_051667, VSP_051668;
CC Name=4 {ECO:0000269|PubMed:9869419};
CC IsoId=Q9ZS62-4; Sequence=VSP_051669;
CC Name=5 {ECO:0000269|PubMed:9869419};
CC IsoId=Q9ZS62-5; Sequence=VSP_051672, VSP_051673;
CC Name=6 {ECO:0000269|PubMed:9869419};
CC IsoId=Q9ZS62-6; Sequence=VSP_051670, VSP_051671;
CC -!- PTM: Contains one covalently linked phytochromobilin chromophore.
CC {ECO:0000250}.
CC -!- MISCELLANEOUS: [Isoform 3]: May be produced at very low levels due to a
CC premature stop codon in the mRNA, leading to nonsense-mediated mRNA
CC decay. {ECO:0000305}.
CC -!- MISCELLANEOUS: [Isoform 5]: May be produced at very low levels due to a
CC premature stop codon in the mRNA, leading to nonsense-mediated mRNA
CC decay. {ECO:0000305}.
CC -!- MISCELLANEOUS: [Isoform 6]: May be produced at very low levels due to a
CC premature stop codon in the mRNA, leading to nonsense-mediated mRNA
CC decay. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the phytochrome family. {ECO:0000255}.
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DR EMBL; AJ002281; CAA05293.1; -; Genomic_DNA.
DR EMBL; AJ002282; CAA05294.1; -; mRNA.
DR EMBL; AJ002283; CAA05295.1; -; mRNA.
DR EMBL; AJ002284; CAA05296.1; -; mRNA.
DR EMBL; AJ002285; CAA05297.1; -; mRNA.
DR EMBL; AJ002287; CAA05298.1; -; mRNA.
DR RefSeq; NP_001293131.1; NM_001306202.1. [Q9ZS62-1]
DR AlphaFoldDB; Q9ZS62; -.
DR SMR; Q9ZS62; -.
DR STRING; 4081.Solyc01g059870.2.1; -.
DR PaxDb; Q9ZS62; -.
DR PRIDE; Q9ZS62; -.
DR EnsemblPlants; Solyc01g059870.3.1; Solyc01g059870.3.1; Solyc01g059870.3. [Q9ZS62-1]
DR GeneID; 101262847; -.
DR Gramene; Solyc01g059870.3.1; Solyc01g059870.3.1; Solyc01g059870.3. [Q9ZS62-1]
DR KEGG; sly:101262847; -.
DR eggNOG; ENOG502QRNS; Eukaryota.
DR HOGENOM; CLU_010418_0_0_1; -.
DR InParanoid; Q9ZS62; -.
DR OMA; STACEKQ; -.
DR OrthoDB; 59136at2759; -.
DR PhylomeDB; Q9ZS62; -.
DR Proteomes; UP000004994; Chromosome 1.
DR ExpressionAtlas; Q9ZS62; baseline and differential.
DR GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProt.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0051740; F:ethylene binding; IEA:UniProt.
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:0010105; P:negative regulation of ethylene-activated signaling pathway; IEA:UniProt.
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 Alternative splicing; Chromophore; Photoreceptor protein; Receptor;
KW Reference proteome; Repeat; Sensory transduction; Transcription;
KW Transcription regulation.
FT CHAIN 1..1131
FT /note="Phytochrome B1"
FT /id="PRO_0000171974"
FT DOMAIN 229..408
FT /note="GAF"
FT DOMAIN 622..693
FT /note="PAS 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 756..808
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..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 334
FT /ligand="phytochromobilin"
FT /ligand_id="ChEBI:CHEBI:189064"
FT /note="covalent, via 1 link"
FT /evidence="ECO:0000250"
FT VAR_SEQ 23..691
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:9869419"
FT /id="VSP_051666"
FT VAR_SEQ 23..24
FT /note="GT -> VH (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:9869419"
FT /id="VSP_051667"
FT VAR_SEQ 25..1131
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:9869419"
FT /id="VSP_051668"
FT VAR_SEQ 54..691
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:9869419"
FT /id="VSP_051669"
FT VAR_SEQ 54..55
FT /note="GE -> VH (in isoform 6)"
FT /evidence="ECO:0000303|PubMed:9869419"
FT /id="VSP_051670"
FT VAR_SEQ 55..77
FT /note="ESGKSFDYSQSVKTTTQSVPERQ -> CGRGLWVCISILCSISNLLPFRI
FT (in isoform 5)"
FT /evidence="ECO:0000303|PubMed:9869419"
FT /id="VSP_051672"
FT VAR_SEQ 56..1131
FT /note="Missing (in isoform 6)"
FT /evidence="ECO:0000303|PubMed:9869419"
FT /id="VSP_051671"
FT VAR_SEQ 78..1131
FT /note="Missing (in isoform 5)"
FT /evidence="ECO:0000303|PubMed:9869419"
FT /id="VSP_051673"
FT VARIANT 238
FT /note="V -> F (in mutant tri3; temporarily insensitive to
FT red light)"
FT /evidence="ECO:0000269|PubMed:9869419"
SQ SEQUENCE 1131 AA; 125581 MW; F45727804AADC9BA CRC64;
MASGSRTKHS YHNSSQGQAQ SSGTSNMNYK DSISKAIAQY TADARLHAVF EQSGESGKSF
DYSQSVKTTT QSVPERQITA YLTKIQRGGH IQPFGCMIAV DEASFRIIAY SENACEMLSL
TPQSVPSLDK SEILTVGTDV RTLFTPSSSV LLERAFGARE ITLLNPIWIH SKNSGKPFYA
ILHRVDVGIV IDLEPARTED PALSIAGAVQ SQKLAVRAIS HLQSLPGGDI KLLCDTVVES
VRELTGYDRV MVYKFHEDEH GEVVAESKRS DLEPYIGLHY PATDIPQASR FLFKQNRVRM
IVDCHATPVR VTQDESLMQP LCLVGSTLRA PHGCHAQYMA NMGSIASLTL AVIINGNDEE
AVGGGRNSMR LWGLVVGHHT SVRSIPFPLR YACEFLMQAF GLQLNMELQL ASQLSEKHVL
RTQTLLCDML LRDSPPGIVT QSPSIMDLVK CDGAALYYQR KYYPLGVTPT EAQIKDIVEW
LLAYHGDSTG LSTDSLADAG YPGAASLGDA VCGMAVAYIT SKDFLFWFRS HTAKEIKWGG
AKHHPEDKDD GQRMHPRSSF KAFLEVVKSR SSPWENAEMD AIHSLQLILR DSFKDAEASN
SKAIVHALGE MELQGIDELS SVAREMVRLI ETATAPIFGV DVNGRINGWN EKVVELTGLS
AEEAKGKSLV HDLLYKESQE SAEKLLYNAL RGVEGKNVEI KLRTFGAEQV EKAVFLVVNA
CSSRDYTNSI VGVSFVGQDV TGEKIVMDKF IHIQGDYKAI VHSPNPLIPP IFASDENTSC
SEWNTAMEKL SGWSREEIVG KMLVGEIFGS CCRLKGPDAM TKFMIVLHNA IGGQDTDKFP
FSFFDRNGKY VQALLTANKR VNMEGDTIGA FCFIQIASPE LQQALRVQRQ QEKKCYSQMK
ELAYICQEVK SPLNGIRFTN SLLEATNLTE YQKQYLETSA ACERQMSKII RDVDLENIED
GSLTLEKEDF FLGSVIDAVV SQVMLLLREK GVQLIRDIPE EIKTLTVHGD QVRIQQVLAD
FLLNMVRYAP SPDGWVEIQL RPSMMPISDG ATVVHIELRI ICPGEGLPPE LVQDMFHSSR
WVTQEGLGLS MCRKMLKLMN GEIQYIRESE RCYFMIILDL PMTRKGPKSV G
