PHYC_ORYSJ
ID PHYC_ORYSJ Reviewed; 1137 AA.
AC Q10CQ8; P93429; Q10CQ9; Q7FUM6; Q9M7A9; Q9ZWI9;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=Phytochrome C;
GN Name=PHYC; OrderedLocusNames=Os03g0752100, LOC_Os03g54084;
GN ORFNames=OJ1112_G08.5, OsJ_012088, OSJNBa0032E21.08, OSJNBa0047E24.9;
OS Oryza sativa subsp. japonica (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=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Nipponbare;
RA Tahir M., Kanegae H., Takano M.;
RT "Phytochrome C (PHYC) gene in rice: isolation and characterization of a
RT complete coding sequence.";
RL (er) Plant Gene Register PGR98-210(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
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).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 275-378.
RX PubMed=8865668; DOI=10.1093/oxfordjournals.molbev.a025677;
RA Mathews S., Sharrock R.A.;
RT "The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence
RT that grasses have a subset of the loci found in dicot angiosperms.";
RL Mol. Biol. Evol. 13:1141-1150(1996).
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. {ECO:0000250}.
CC -!- PTM: Contains one covalently linked phytochromobilin chromophore.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the phytochrome family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABF98917.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB018442; BAA74448.1; -; mRNA.
DR EMBL; AC092556; AAR87239.1; -; Genomic_DNA.
DR EMBL; AC135225; AAP68360.1; -; Genomic_DNA.
DR EMBL; AF377947; AAM34402.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF98915.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF98917.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008209; BAF13210.1; -; Genomic_DNA.
DR EMBL; AP014959; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CM000140; EAZ28605.1; -; Genomic_DNA.
DR EMBL; U61207; AAB41996.1; -; Genomic_DNA.
DR PIR; T04149; T04149.
DR RefSeq; XP_015630523.1; XM_015775037.1.
DR AlphaFoldDB; Q10CQ8; -.
DR SMR; Q10CQ8; -.
DR STRING; 4530.OS03T0752100-01; -.
DR PaxDb; Q10CQ8; -.
DR PRIDE; Q10CQ8; -.
DR EnsemblPlants; Os03t0752100-01; Os03t0752100-01; Os03g0752100.
DR GeneID; 4334135; -.
DR Gramene; Os03t0752100-01; Os03t0752100-01; Os03g0752100.
DR KEGG; osa:4334135; -.
DR eggNOG; ENOG502QT1B; Eukaryota.
DR InParanoid; Q10CQ8; -.
DR OrthoDB; 77253at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
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: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; 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; 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 Chromophore; Photoreceptor protein; Receptor; Reference proteome; Repeat;
KW Sensory transduction; Transcription; Transcription regulation.
FT CHAIN 1..1137
FT /note="Phytochrome C"
FT /id="PRO_0000171979"
FT DOMAIN 217..400
FT /note="GAF"
FT DOMAIN 620..690
FT /note="PAS 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 750..824
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..27
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..24
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 322
FT /ligand="phytochromobilin"
FT /ligand_id="ChEBI:CHEBI:189064"
FT /note="covalent, via 1 link"
FT /evidence="ECO:0000250"
FT CONFLICT 279
FT /note="F -> S (in Ref. 7; AAB41996)"
FT /evidence="ECO:0000305"
FT CONFLICT 292
FT /note="C -> S (in Ref. 7; AAB41996)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1137 AA; 125983 MW; F2A520181CFE7B32 CRC64;
MSSSRSNNRA TCSRSSSARS KHSARVVAQT PMDAQLHAEF EGSQRHFDYS SSVGAANRSG
ATTSNVSAYL QNMQRGRFVQ PFGCLLAVHP ETFALLAYSE NAAEMLDLTP HAVPTIDQRE
ALAVGTDVRT LFRSHSFVAL QKAATFGDVN LLNPILVHAR TSGKPFYAIM HRIDVGLVID
LEPVNPVDLP VTATGAIKSY KLAARAIARL QSLPSGNLSL LCDVLVREVS ELTGYDRVMA
YKFHEDEHGE VIAECKRSDL EPYLGLHYPA TDIPQASRFL FMKNKVRMIC DCSATPVKII
QDDSLTQPIS ICGSTLRAPH GCHAQYMASM GSVASLVMSV TINEDEDDDG DTGSDQQPKG
RKLWGLMVCH HTSPRFVPFP LRYACEFLLQ VFGIQINKEV ELAAQAKERH ILRTQTLLCD
MLLRDAPVGI FTQSPNVMDL VKCDGAALYY QNQLWVLGST PSEAEIKNIV AWLQEYHDGS
TGLSTDSLVE AGYPGAAALG DVVCGMAAIK ISSKDFIFWF RSHTAKEIKW GGAKHEPIDA
DDNGRKMHPR SSFKAFLEVV KWRSVPWEDV EMDAIHSLQL ILRGSLQDED ANKNNNAKSI
VTAPSDDMKK IQGLLELRTV TNEMVRLIET ATAPILAVDI TGSINGWNNK AAELTGLPVM
EAIGKPLVDL VIDDSVEVVK QILNSALQGI EEQNLQIKLK TFNHQENNGP VILMVNACCS
RDLSEKVVGV CFVAQDMTGQ NIIMDKYTRI QGDYVAIVKN PSELIPPIFM INDLGSCLEW
NEAMQKITGI KREDAVDKLL IGEVFTHHEY GCRVKDHGTL TKLSILMNTV ISGQDPEKLL
FGFFNTDGKY IESLMTATKR TDAEGKITGA LCFLHVASPE LQHALQVQKM SEQAAMNSFK
ELTYIRQELR NPLNGMQFTR NLLEPSDLTE EQRKLLASNV LCQEQLKKIL HDTDLESIEQ
CYTEMSTVDF NLEEALNTVL MQAMPQSKEK QISIDRDWPA EVSCMHLCGD NLRLQQVLAD
FLACMLQFTQ PAEGPIVLQV IPRMENIGSG MQIAHLEFRL VHPAPGVPEA LIQEMFRHSP
GASREGLGLY ISQKLVKTMS GTVQYLRESE SSSFIVLVEF PVAQLSTKRC KASTSKF
