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UniProtKB/Swiss-Prot entry Q10DU0


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name PHYA_ORYSJ
Primary accession number Q10DU0
Secondary accession numbers P10931 Q8LLN7
Integrated into Swiss-Prot on September 11, 2007
Sequence was last modified on August 22, 2006 (Sequence version 1)
Annotations were last modified on    July 22, 2008 (Entry version 23)
Name and origin of the protein
Protein name Phytochrome A
Synonyms None
Gene name
Name: PHYA
Synonyms: PHY18
OrderedLocusNames: Os03g0719800, LOC_Os03g51030
ORFNames: B1377B10.8, OAJNBa0031O09.11, OsJ_011877
From
Oryza sativa subsp. japonica (Rice) [TaxID: 39947] 
Taxonomy Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza.
Protein existence 2: Evidence at transcript level;
References
[1]
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=cv. Nipponbare;
TISSUE=Etiolated seedling;
DOI=10.1105/tpc.105.035899; PubMed=16278346 [NCBI, ExPASy, EBI, Israel, Japan]
Takano M., Inagaki N., Xie X., Yuzurihara N., Hihara F., Ishizuka T., Yano M., Nishimura M., Miyao A., Hirochika H., Shinomura T.;
"Distinct and cooperative functions of phytochromes a, B, and C in the control of deetiolation and flowering in rice.";
Plant Cell 17:3311-3325(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Nipponbare;
DOI=10.1101/gr.3869505; PubMed=16109971 [NCBI, ExPASy, EBI, Israel, Japan]
The rice chromosome 3 sequencing consortium;
Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B., Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T., Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K., Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T., Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R., Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H.-I., Rambo T., Currie J., Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S., Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M., Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M., Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L., O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R., Jin W., Lee H.R., Jiang J., Jackson S.;
"Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.";
Genome Res. 15:1284-1291(2005).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Nipponbare;
DOI=10.1038/nature03895; PubMed=16100779 [NCBI, ExPASy, EBI, Israel, Japan]
International rice genome sequencing project (IRGSP);
"The map-based sequence of the rice genome.";
Nature 436:793-800(2005).
[4]
GENOME REANNOTATION.
STRAIN=cv. Nipponbare;
DOI=10.1101/gr.5509507; PubMed=17210932 [NCBI, ExPASy, EBI, Israel, Japan]
The rice annotation project (RAP);
"Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.";
Genome Res. 17:175-183(2007).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Nipponbare;
DOI=10.1371/journal.pbio.0030038; PubMed=15685292 [NCBI, ExPASy, EBI, Israel, Japan]
Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L., Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
"The genomes of Oryza sativa: a history of duplications.";
PLoS Biol. 3:266-281(2005).
[6]
MUTAGENESIS OF N-TERMINAL SERINES.
PubMed=1459458 [NCBI, ExPASy, EBI, Israel, Japan]
Stockhaus J., Nagatani A., Halfter U., Kay S., Furuya M., Chua N.-H.;
"Serine-to-alanine substitutions at the amino-terminal region of phytochrome A result in an increase in biological activity.";
Genes Dev. 6:2364-2372(1992).
Comments
  • FUNCTION: Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion.
  • SUBUNIT: Homodimer.
  • PTM: Contains one covalently linked phytochromobilin chromophore (By similarity).
  • SIMILARITY: Belongs to the phytochrome family.
  • SIMILARITY: Contains 1 GAF domain.
  • SIMILARITY: Contains 1 histidine kinase domain.
  • SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.
  • SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
AB109891; BAC76431.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AC147426; AAT77854.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AF377946; AAM47309.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
DP000009; ABF98580.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AP008209; BAF13010.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
CM000140; EAZ28394.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
RefSeq NP_001051096.1; -.
UniGene Os.272
3D structure databases
ModBase Q10DU0.
Organism-specific databases
Gramene P10931; -.
Family and domain databases
InterPro IPR003594; ATP_bd_ATPase.
IPR003018; GAF.
IPR001610; PAC.
IPR000014; PAS.
IPR013654; PAS_2.
IPR013767; PAS_fold.
IPR016132; Phyto_chromo_attachment.
IPR013516; Phyto_chromo_BS.
IPR001294; Phytochrome.
IPR012129; Phytochrome_A-E.
IPR013515; Phytochrome_Cr.
IPR003661; Sig_transdc_His_kin_sub1_dim/P.
IPR005467; Sig_transdc_His_kinase_core.
Graphical view of domain structure.
Gene3D G3DSA:3.30.565.10; ATP_bd_ATPase; 1.
Pfam PF01590; GAF; 1.
PF02518; HATPase_c; 1.
PF00512; HisKA; 1.
PF00989; PAS; 2.
PF08446; PAS_2; 1.
PF00360; Phytochrome; 1.
Pfam graphical view of domain structure.
PIRSF PIRSF000084; Phytochrome; 1.
PRINTS PR01033; PHYTOCHROME.
SMART SM00065; GAF; 1.
SM00387; HATPase_c; 1.
SM00388; HisKA; 1.
SM00086; PAC; 1.
SM00091; PAS; 2.
SMART graphical view of domain structure.
TIGRFAMs TIGR00229; sensory_box; 1.
PROSITE PS50109; HIS_KIN; 1.
PS50112; PAS; 2.
PS00245; PHYTOCHROME_1; 1.
PS50046; PHYTOCHROME_2; 1.
PROSITE graphical view of domain structure (profiles).
BLOCKS Q10DU0.
Genome annotation databases
GeneID 4333930; -.
KEGG osa:4333930; -.
Other
ProtoNet Q10DU0.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
Chromophore; Photoreceptor protein; Receptor; Repeat; Sensory transduction; Transcription; Transcription regulation.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
CHAIN   1   1128  1128     Phytochrome A. PRO_0000171977
DOMAIN   219    404  186     GAF. 
DOMAIN   620    690  71     PAS 1. 
DOMAIN   750    834  85     PAS 2. 
DOMAIN   904   1124  221     Histidine kinase. 
BINDING   324    324        Phytochromobilin chromophore (covalent; via 1 link) (By similarity). 
Sequence information
Length: 1128 AA [This is the length of the unprocessed precursor] Molecular weight: 125289 Da [This is the MW of the unprocessed precursor] CRC64: 7DB1823EE704E464 [This is a checksum on the sequence]
        10         20         30         40         50         60 
MSSSRPTQCS SSSSRTRQSS RARILAQTTL DAELNAEYEE YGDSFDYSKL VEAQRTTGPE 

        70         80         90        100        110        120 
QQARSEKVIA YLHHIQRAKL IQPFGCLLAL DEKTFNVIAL SENAPEMLTT VSHAVPSVDD 

       130        140        150        160        170        180 
PPKLRIGTNV WSLFTDPGAT ALQKALGFAD VSLLNPILVQ CKTSGKPFYA IVHRATGCLV 

       190        200        210        220        230        240 
VDFEPVKPTE FPATAAGALQ SYKLAAKAIS KIQSLPGGSM EVLCNTVVKE LFDLTGYDRV 

       250        260        270        280        290        300 
MAYKFHEDDH GEVFAEITKP GLEPYLGLHY PATDIPQAAR FLFMKNKVRM ICDCRARSIK 

       310        320        330        340        350        360 
IIEDESLHLD ISLCGSTLRA PHSCHLQYME NMNSIASLVM AVVVNENEDD DEVGADQPAQ 

       370        380        390        400        410        420 
QQKRKKLWGL LVCHHESPRY VPFPLRYACE FLAQVFAVHV NKEFELERQV REKSILRMQT 

       430        440        450        460        470        480 
MLSDMLLRES SPLSIVSGTP NIMDLVKCDG AALLYGGKVW RLQNAPTESQ IRDIAFWLSD 

       490        500        510        520        530        540 
VHRDSTGLST DSLHDAGYPG AAALGDMICG MAVAKINSKD ILFWFRSHTA AEIRWGGAKH 

       550        560        570        580        590        600 
DPSDKDDSRR MHPRLSFKAF LEVVKMKSLP WNDYEMDAIH SLQLILRGTL NDDIKPTRAA 

       610        620        630        640        650        660 
SLDNQVGDLK LDGLAELQAV TSEMVRLMET ATVPILAVDS NGLVNGWNQK VAELTGLRVD 

       670        680        690        700        710        720 
EAIGRHILTV VEESSVPVVQ RMLYLALQGK EEKEVKFEVK THGSKRDDGP VILVVNACAS 

       730        740        750        760        770        780 
RDLHDHVVGV CFVAQDMTVH KLVMDKFTRV EGDYKAIIHN PSPLIPPIFG ADEFGWCSEW 

       790        800        810        820        830        840 
NAAMTKLTGW HRDEVINKML LGEVFDSTNA SCLVKNKDAF VSLCILINSA LAGDETEKAP 

       850        860        870        880        890        900 
FSFFDRNGKY IECLLSVNRK VNADGVITGV FCFIQVPSHE LQHALHVQQA SQQNALTKLK 

       910        920        930        940        950        960 
AYSYMRHAIN NPLSGMLYSR KALKNTGLNE EQMKEVNVAD SCHRQLNKIL SDLDQDSVMN 

       970        980        990       1000       1010       1020 
KSSCLDLEMV EFVLQDVFVA AVSQVLITCQ GKGIRVSCNL PERYMKQTVY GDGVRLQQIL 

      1030       1040       1050       1060       1070       1080 
SDFLFVSVKF SPVGGSVEIS CSLTKNSIGE NLHLIDLELR IKHQGKGVPA DLLSQMYEDD 

      1090       1100       1110       1120 
NKEQSDEGMS LAVSRNLLRL MNGDVRHMRE AGMSTFILSV ELASAPAK 

Q10DU0 in FASTA format

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