PHYA2_SOYBN
ID PHYA2_SOYBN Reviewed; 1123 AA.
AC B4YB07;
DT 10-FEB-2021, integrated into UniProtKB/Swiss-Prot.
DT 23-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Phytochrome A-2 {ECO:0000305};
DE Short=GmphyA2 {ECO:0000303|PubMed:18780733};
GN Name=PHYA2 {ECO:0000303|PubMed:18780733};
GN ORFNames=GLYMA_20G090000 {ECO:0000312|EMBL:KRG90417.1};
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 [GENOMIC DNA].
RX PubMed=18780733; DOI=10.1534/genetics.108.092742;
RA Liu B., Kanazawa A., Matsumura H., Takahashi R., Harada K., Abe J.;
RT "Genetic redundancy in soybean photoresponses associated with duplication
RT of the phytochrome A gene.";
RL Genetics 180:995-1007(2008).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Tsubokura Y., Matsumura H., Liu B., Nakashima H., Anai T., Xu M., Kong F.,
RA Kanamori H., Katayose Y., Takahashi R., Harada K., Abe J.;
RT "Genetic variation in the soybean maturity locus E4 involved in adaptation
RT to high latitudes.";
RL Submitted (JUN-2011) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Wu F., Lin C., Fu Y.;
RL Submitted (JAN-2012) to the EMBL/GenBank/DDBJ databases.
RN [4]
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 [5]
RP X-RAY CRYSTALLOGRAPHY (2.13 ANGSTROMS) OF 51-402 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; AB370253; BAG72095.1; -; Genomic_DNA.
DR EMBL; AB643572; BAL45569.1; -; Genomic_DNA.
DR EMBL; EU428746; ACE79195.1; -; mRNA.
DR EMBL; CM000853; KRG90417.1; -; Genomic_DNA.
DR RefSeq; NP_001241532.1; NM_001254603.3.
DR RefSeq; XP_006605349.1; XM_006605286.2.
DR PDB; 6TC7; X-ray; 2.13 A; AAA/BBB=51-402.
DR PDBsum; 6TC7; -.
DR AlphaFoldDB; B4YB07; -.
DR SMR; B4YB07; -.
DR STRING; 3847.GLYMA20G22160.1; -.
DR PRIDE; B4YB07; -.
DR EnsemblPlants; KRG90417; KRG90417; GLYMA_20G090000.
DR GeneID; 100790763; -.
DR Gramene; KRG90417; KRG90417; GLYMA_20G090000.
DR KEGG; gmx:100790763; -.
DR eggNOG; ENOG502QRSA; Eukaryota.
DR HOGENOM; CLU_010418_0_0_1; -.
DR InParanoid; B4YB07; -.
DR OrthoDB; 77253at2759; -.
DR Proteomes; UP000008827; Chromosome 20.
DR ExpressionAtlas; B4YB07; 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; 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; IPR000700; PAS-assoc_C.
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; 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; SSF55785; SSF55785; 3.
DR SUPFAM; SSF55874; SSF55874; 1.
DR TIGRFAMs; TIGR00229; sensory_box; 1.
DR PROSITE; PS50109; HIS_KIN; 1.
DR PROSITE; PS50113; PAC; 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..1123
FT /note="Phytochrome A-2"
FT /id="PRO_0000451873"
FT DOMAIN 267..449
FT /note="GAF"
FT /evidence="ECO:0000305"
FT DOMAIN 616..686
FT /note="PAS 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 689..745
FT /note="PAC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00141"
FT DOMAIN 749..823
FT /note="PAS 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 900..1119
FT /note="Histidine kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..18
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 323
FT /ligand="phytochromobilin"
FT /ligand_id="ChEBI:CHEBI:189064"
FT /note="covalent, via 1 link"
FT /evidence="ECO:0000305|PubMed:32366982"
SQ SEQUENCE 1123 AA; 124209 MW; B17ED2C2BDDB121D CRC64;
MSTSRPSQSS SNSGRSRRSA RAMALATVDA KLHATFEESG SSFDYSSSVR ISGTADGVNQ
PRHDKVTTAY LHHMQKGKMI QPFGCLLALD EKTCKVIAYS ENAPEMLTMV SHAVPSVGDH
PALGIGTDIK TLFTAPSASA LQKALGFAEV LLLNPVLIHC KTSGKPFYAI IHRVTGSMII
DFEPVKPYEV PMTAAGALQS YKLAAKAITR LQSLPSGSME RLCDTMVQEV FELTGYDRVM
AYKFHEDDHG EVIAEITKPG LEPYLGLHYP ATDIPQASRF LFMKNKVRMI VDCHAKHVRV
LQDEKLPFDL TLCGSTLRAP HSCHAQYMAN MDSIASLVMA VVVNDNEEDG DTDAIQPQKR
KRLWGLVVCH NTTPRFVPFP LRYACEFLAQ VFAIHVNKEI ELEYQIIEKN ILRTQTLLCD
LVMRDAPLGI VSESPNIMDL VKCDGAALIY KNKVWRLGVT PSESQIREIA FWLSEYHMDS
TGFSTDSLSD AGFPSALSLG DVVCGMAAVR VTAKDVVFWF RSHTAAEIRW GGAKHEAGEK
DDGRRMHPRS SFKVFLDVVK ARSLPWKEYE IDAMHSLQLI LRNAFKDTES MDLNTKAINT
RLSDLKIEGM QELEAVTSEI VRLIETATVP ILAVDVDGLV NGWNIKIAEL TGLPVGEAMG
KHLLTLVEDS STDRVKKMLN LALLGEEEKN VQFEIKTHGS KMDSGPISLV VNACASRDLR
DNVVGVCFVA HDITAQKNVM DKFTRIEGDY KAIVQNRNPL IPPIFGTDEF GWCCEWNPAM
TKLTGWKREE VMDKMLLGEL FGTHMAACRL KNQEAFVNLG VVLNKAMTGL ETEKVPFGFF
ARNGKYVECL LSVSKKLDVE GLVTGVFCFL QLASPELQQA LHIQRLSEQT ALKRLNALSY
MKRQIRNPLC GIIFSRKMLE GTALGTEQKQ LLRTSAQCQQ QLSKILDDSD LDSIIDGYLD
LEMAEFTLHE VLVTSLSQVM TKSNGKSIRI VNDVAEQIVM ETLYGDSLRL QQVLADFLLI
SINFTPNGGQ VVVAGTLTKE QLGKSVHLVK LELSITHGGS GVPEALLNQM FGNNGLESEE
GISLLISRKL LKLMNGDVRY LREAGKSAFI LSAELAAAHN LKG
