PHYB2_SOYBN
ID PHYB2_SOYBN Reviewed; 1149 AA.
AC I1MGE5;
DT 10-FEB-2021, integrated into UniProtKB/Swiss-Prot.
DT 09-JAN-2013, sequence version 2.
DT 03-AUG-2022, entry version 72.
DE RecName: Full=Phytochrome B-2 {ECO:0000305};
GN ORFNames=GLYMA_15G140000 {ECO:0000312|EMBL:KRH11936.1};
OS Glycine max (Soybean) (Glycine hispida).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine;
OC Glycine subgen. Soja.
OX NCBI_TaxID=3847;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Williams 82;
RX PubMed=20075913; DOI=10.1038/nature08670;
RA Schmutz J., Cannon S.B., Schlueter J., Ma J., Mitros T., Nelson W.,
RA Hyten D.L., Song Q., Thelen J.J., Cheng J., Xu D., Hellsten U., May G.D.,
RA Yu Y., Sakurai T., Umezawa T., Bhattacharyya M.K., Sandhu D.,
RA Valliyodan B., Lindquist E., Peto M., Grant D., Shu S., Goodstein D.,
RA Barry K., Futrell-Griggs M., Abernathy B., Du J., Tian Z., Zhu L., Gill N.,
RA Joshi T., Libault M., Sethuraman A., Zhang X.-C., Shinozaki K.,
RA Nguyen H.T., Wing R.A., Cregan P., Specht J., Grimwood J., Rokhsar D.,
RA Stacey G., Shoemaker R.C., Jackson S.A.;
RT "Genome sequence of the palaeopolyploid soybean.";
RL Nature 463:178-183(2010).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) OF 85-616 IN COMPLEX WITH
RP PHYCOCYANOBILIN, AND SUBUNIT.
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: Heterodimer between subunit A and subunit B.
CC {ECO:0000269|PubMed:32366982}.
CC -!- PTM: Contains one covalently linked phytochromobilin chromophore.
CC {ECO:0000305|PubMed:32366982}.
CC -!- SIMILARITY: Belongs to the phytochrome family. {ECO:0000305}.
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DR EMBL; CM000848; KRH11936.1; -; Genomic_DNA.
DR RefSeq; XP_003546314.1; XM_003546266.3.
DR RefSeq; XP_006597696.1; XM_006597633.2.
DR RefSeq; XP_014623437.1; XM_014767951.1.
DR PDB; 6TL4; X-ray; 2.90 A; A=85-616.
DR PDBsum; 6TL4; -.
DR AlphaFoldDB; I1MGE5; -.
DR SMR; I1MGE5; -.
DR STRING; 3847.GLYMA15G14980.1; -.
DR PRIDE; I1MGE5; -.
DR EnsemblPlants; KRH11936; KRH11936; GLYMA_15G140000.
DR GeneID; 100794865; -.
DR Gramene; KRH11936; KRH11936; GLYMA_15G140000.
DR KEGG; gmx:100794865; -.
DR eggNOG; ENOG502QRNS; Eukaryota.
DR HOGENOM; CLU_010418_0_0_1; -.
DR InParanoid; I1MGE5; -.
DR OrthoDB; 59136at2759; -.
DR Proteomes; UP000008827; Chromosome 15.
DR ExpressionAtlas; I1MGE5; baseline and differential.
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:0017009; P:protein-phycocyanobilin 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; 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; 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; 3.
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..1149
FT /note="Phytochrome B-2"
FT /id="PRO_0000451872"
FT DOMAIN 267..449
FT /note="GAF"
FT /evidence="ECO:0000305"
FT DOMAIN 641..712
FT /note="PAS 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 775..846
FT /note="PAS 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 923..1143
FT /note="Histidine kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT REGION 1..48
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 12..26
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 353
FT /ligand="phytochromobilin"
FT /ligand_id="ChEBI:CHEBI:189064"
FT /note="covalent, via 1 link"
FT /evidence="ECO:0000305|PubMed:32366982"
FT HELIX 99..103
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 112..117
FT /evidence="ECO:0007829|PDB:6TL4"
FT TURN 119..121
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 123..126
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 131..135
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 165..175
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 185..190
FT /evidence="ECO:0007829|PDB:6TL4"
FT TURN 191..193
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 196..203
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 205..214
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 224..242
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 249..264
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 267..274
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 280..287
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 297..299
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 306..312
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 317..321
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 328..330
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 336..339
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 352..361
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 364..374
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 387..399
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 405..448
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 450..452
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 455..458
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 459..461
FT /evidence="ECO:0007829|PDB:6TL4"
FT TURN 463..466
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 470..476
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 479..485
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 489..502
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 504..507
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 509..512
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 514..517
FT /evidence="ECO:0007829|PDB:6TL4"
FT TURN 522..525
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 527..529
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 531..538
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 541..547
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 552..559
FT /evidence="ECO:0007829|PDB:6TL4"
FT STRAND 580..585
FT /evidence="ECO:0007829|PDB:6TL4"
FT HELIX 594..616
FT /evidence="ECO:0007829|PDB:6TL4"
SQ SEQUENCE 1149 AA; 127769 MW; 263721499E606DC6 CRC64;
MASASGAENS SVPPSPLPPP PPPQIHTSRT KLSHHHHNNN NNNNNNIDST SKAIAQYTED
ARLHAVFEQS GESGRSFDYS QSIRVTSESV PEQQITAYLL KIQRGGFIQP FGSMIAVDEP
SFRILAYSDN ARDMLGITPQ SVPSLDDKND AAFALGTDIR TLFTHSSAVL LEKAFSAREI
SLMNPIWIHS RTSGKPFYGI LHRIDVGIVI DLEPARTEDP ALSIAGAVQS QKLAVRAISQ
LQSLPGGDVK LLCDTVVESV RELTGYDRVM VYRFHEDEHG EVVAETKRPD LEPYIGLHYP
ATDIPQASRF LFKQNRVRMI VDCHASAVRV VQDEALVQPL CLVGSTLRAP HGCHAQYMAN
MGSTASLVMA VIINGNDEEG VGGRTSMRLW GLVVCHHTSA RCIPFPLRYA CEFLMQAFGL
QLNMELQLAA QSLEKRVLRT QTLLCDMLLR DSPTGIVTQS PSIMDLVKCD GAALYYQGNY
YPLGVTPTEA QIRDIIEWLL AFHRDSTGLS TDSLADAGYP GAASLGDAVC GMAVAYITEK
DFLFWFRSHT AKEIKWGGAK HHPEDKDDGQ RMHPRSSFKA FLEVVKSRSL PWENAEMDAI
HSLQLILRDS FKDAEHSNSK AVLDPRMSEL ELQGVDELSS VAREMVRLIE TATAPIFAVD
VDGRINGWNA KVSELTGLPV EEAMGKSLVR DLVFKESEET VDKLLSRALK GEEDKNVEIK
MRTFGPEHQN KAVFVVVNAC SSKDYTNNVV GVCFVGQDVT GQKIVMDKFI NIQGDYKAIV
HNPNPLIPPI FASDDNTCCL EWNTAMEKLT GWSRADVIGK MLVGEVFGSC CQLKGSDSIT
KFMIVLHNAL GGHDTDRFPF SFLDRYGKHV QAFLTANKRV NMDGQIIGAF CFLQIVSPEL
QQALKAQRQQ EKNSFARMKE LAYICQGVKN PLSGIRFTNS LLEATCLSNE QKQFLETSAA
CEKQMLKIIH DVDIESIEDG SLELEKGEFL LGNVINAVVS QVMLLLRERN LQLIRDIPEE
IKTLAVYGDQ LRIQQVLSDF LLNIVRYAPS PDGWVEIHVH PRIKQISDGL TLLHAEFRMV
CPGEGLPPEL IQNMFNNSGW GTQEGLGLSM SRKILKLMNG EVQYIREAQR CYFYVLLELP
VTRRSSKKC
