Q10DU0 (PHYA_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Phytochrome A

Gene names

Name:	PHYA
Synonyms:	PHY18
Ordered Locus Names:	Os03g0719800, LOC_Os03g51030
ORF Names:	B1377B10.8, OAJNBa0031O09.11, OsJ_011877

Organism

Oryza sativa subsp. japonica (Rice)

Taxonomic identifier

39947 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza

Protein attributes

Sequence length	1128 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (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 structure	Homodimer.
Post-translational modification	Contains one covalently linked phytochromobilin chromophore By similarity.
Sequence similarities	Belongs to the phytochrome family. Contains 1 GAF domain. Contains 1 histidine kinase domain. Contains 1 PAC (PAS-associated C-terminal) domain. Contains 2 PAS (PER-ARNT-SIM) domains.

Ontologies

Keywords
Biological process	Sensory transduction Transcription Transcription regulation
Domain	Repeat
Ligand	Chromophore
Molecular function	Photoreceptor protein Receptor
Gene Ontology (GO)
Biological process	peptidyl-histidine phosphorylation Inferred from electronic annotation. Source: InterPro protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW protein-tetrapyrrole linkage Inferred from electronic annotation. Source: InterPro red, far-red light phototransduction Inferred from electronic annotation. Source: InterPro regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	membrane Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro G-protein coupled photoreceptor activity Inferred from electronic annotation. Source: InterPro protein homodimerization activity Inferred from electronic annotation. Source: InterPro two-component sensor activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1128	1128	Phytochrome A		PRO_0000171977
Regions
	Domain	219 – 404	186	GAF
	Domain	620 – 690	71	PAS 1
	Domain	750 – 834	85	PAS 2
	Domain	904 – 1124	221	Histidine kinase
Sites
	Binding site	324	1	Phytochromobilin chromophore (covalent; via 1 link) By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q10DU0 [UniParc]. Last modified August 22, 2006. Version 1. Checksum: 7DB1823EE704E464	FASTA	1,128	125,289
	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

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Distinct and cooperative functions of phytochromes a, B, and C in the control of deetiolation and flowering in rice." Takano M., Inagaki N., Xie X., Yuzurihara N., Hihara F., Ishizuka T., Yano M., Nishimura M., Miyao A., Hirochika H., Shinomura T. Plant Cell 17:3311-3325(2005) [PubMed: 16278346] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Nipponbare. Tissue: Etiolated seedling.
[2]	"Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species." 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., 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. Genome Res. 15:1284-1291(2005) [PubMed: 16109971] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[3]	"The map-based sequence of the rice genome." International rice genome sequencing project (IRGSP) Nature 436:793-800(2005) [PubMed: 16100779] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[4]	"The rice annotation project database (RAP-DB): 2008 update." The rice annotation project (RAP) Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed: 18089549] [Abstract] Cited for: GENOME REANNOTATION. Strain: cv. Nipponbare.
[5]	"The genomes of Oryza sativa: a history of duplications." 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. PLoS Biol. 3:266-281(2005) [PubMed: 15685292] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[6]	"Serine-to-alanine substitutions at the amino-terminal region of phytochrome A result in an increase in biological activity." Stockhaus J., Nagatani A., Halfter U., Kay S., Furuya M., Chua N.-H. Genes Dev. 6:2364-2372(1992) [PubMed: 1459458] [Abstract] Cited for: MUTAGENESIS OF N-TERMINAL SERINES.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB109891 mRNA. Translation: BAC76431.1. AC147426 Genomic DNA. Translation: AAT77854.1. AF377946 Genomic DNA. Translation: AAM47309.1. DP000009 Genomic DNA. Translation: ABF98580.1. AP008209 Genomic DNA. Translation: BAF13010.1. CM000140 Genomic DNA. Translation: EAZ28394.1.
RefSeq	NP_001051096.1. NM_001057631.1.
UniGene	Os.272.
3D structure databases
ProteinModelPortal	Q10DU0.
ModBase	Search...
Protein-protein interaction databases
STRING	Q10DU0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	LOC_Os03g51030.1; LOC_Os03g51030.1; LOC_Os03g51030. LOC_Os03g51030.2; LOC_Os03g51030.2; LOC_Os03g51030. LOC_Os03g51030.3; LOC_Os03g51030.3; LOC_Os03g51030.
GeneID	4333930.
KEGG	osa:4333930.
Organism-specific databases
Gramene	P10931.
Phylogenomic databases
GeneTree	EPGT00050000008838.
HOGENOM	HBG318405.
OMA	RWGGAKH.
PhylomeDB	Q10DU0.
ProtClustDB	CLSN2679275.
Family and domain databases
InterPro	IPR003594. ATPase-like_ATP-bd. 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_cen-reg. IPR003661. Sig_transdc_His_kin_sub1_dim/P. IPR005467. Sig_transdc_His_kinase_core. [Graphical view]
Gene3D	G3DSA:3.30.565.10. ATP_bd_ATPase. 1 hit.
KO	K12120.
Pfam	PF01590. GAF. 1 hit. PF02518. HATPase_c. 1 hit. PF00512. HisKA. 1 hit. PF00989. PAS. 2 hits. PF08446. PAS_2. 1 hit. PF00360. PHY. 1 hit. [Graphical view]
PIRSF	PIRSF000084. Phytochrome. 1 hit.
PRINTS	PR01033. PHYTOCHROME.
SMART	SM00065. GAF. 1 hit. SM00387. HATPase_c. 1 hit. SM00388. HisKA. 1 hit. SM00086. PAC. 1 hit. SM00091. PAS. 2 hits. [Graphical view]
SUPFAM	SSF55874. ATP_bd_ATPase. 1 hit.
TIGRFAMs	TIGR00229. Sensory_box. 1 hit.
PROSITE	PS50109. HIS_KIN. 1 hit. PS50112. PAS. 2 hits. PS00245. PHYTOCHROME_1. 1 hit. PS50046. PHYTOCHROME_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PHYA_ORYSJ

Accession

Primary (citable) accession number: Q10DU0
Secondary accession number(s): P10931, Q8LLN7

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 11, 2007
Last sequence update:	August 22, 2006
Last modified:	December 14, 2011
This is version 47 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program