Reviewed, UniProtKB/Swiss-Prot P14713 (PHYB_ARATH)

Names and origin

Protein names

Recommended name:
    Phytochrome B

Gene names

Name:	PHYB
Synonyms:	HY3
Ordered Locus Names:	At2g18790
ORF Names:	MSF3.17

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	1172 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein 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 morphogenetic 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. Involved in the flowering time regulation. Ref.6 Ref.7
Subunit structure	Homodimer. Interacts with ADO1. Stabilized by interactions with PAPP5 and FYPP3 which are enhanced in the phosphorylated Pfr form. Ref.6 Ref.7 Ref.5
Subcellular location	Cytoplasm. Nucleus › nucleoplasm. Nucleus speckle. Note: Cytoplasmic in darkness, but translocated to the nucleus upon illumination, when associated with PAPP5 into speckles. Ref.7
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 2 PAS (PER-ARNT-SIM) domains.

Ontologies

Keywords
Biological process	Phytochrome signaling pathway Sensory transduction Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Polymorphism
Domain	Repeat
Ligand	Chromophore
Molecular function	Photoreceptor protein Receptor
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	abscisic acid metabolic process Inferred from mutant phenotype. Source: TAIR circadian regulation of calcium ion oscillation Inferred from mutant phenotype. Source: TAIR entrainment of circadian clock Inferred from mutant phenotype. Source: TAIR gravitropism Inferred from mutant phenotype. Source: TAIR jasmonic acid mediated signaling pathway Inferred from mutant phenotype. Source: TAIR peptidyl-histidine phosphorylation Inferred from electronic annotation. Source: InterPro phototropism Inferred from mutant phenotype. Source: TAIR protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW protein-tetrapyrrole linkage Inferred from electronic annotation. Source: InterPro red light signaling pathway Inferred from mutant phenotype. Source: TAIR red, far-red light phototransduction Inferred from electronic annotation. Source: UniProtKB-KW regulation of defense response Inferred from mutant phenotype. Source: TAIR regulation of seed germination Inferred from mutant phenotype. Source: TAIR regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW response to cold Inferred from mutant phenotype. Source: TAIR response to low fluence red light stimulus Inferred from mutant phenotype. Source: TAIR transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell membrane Inferred from electronic annotation. Source: InterPro nuclear speck Inferred from electronic annotation. Source: UniProtKB-SubCell
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 red or far-red light photoreceptor activity Inferred from mutant phenotype. Source: TAIR two-component sensor activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ADO1	Q94BT6	1	EBI-300727,EBI-300691
ARR4	O82798	2	EBI-300727,EBI-625213
CRY2	Q96524	2	EBI-300727,EBI-531555
IAA3	Q38822	1	EBI-300727,EBI-307174
PHYC	P14714	2	EBI-300727,EBI-624366
PHYD	P42497	1	EBI-300727,EBI-624382
PHYE	P42498	2	EBI-300727,EBI-624404
PIF1	Q8GZM7	2	EBI-300727,EBI-630400
PIF3	O80536	13	EBI-300727,EBI-625701
PIF4	Q8W2F3-2	3	EBI-300727,EBI-625732
PIF5	Q84LH8	1	EBI-300727,EBI-631622
PIF6	Q8L5W7	1	EBI-300727,EBI-631639
PKS1	Q9SWI1	1	EBI-300727,EBI-626200

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1172	1172	Phytochrome B		PRO_0000171963
Regions
	Domain	252 – 433	182	GAF
	Domain	652 – 723	72	PAS 1
	Domain	786 – 857	72	PAS 2
	Domain	934 – 1153	220	Histidine kinase
	Compositional bias	3 – 25	23	Gly/Ser-rich
Sites
	Binding site	357	1	Phytochromobilin chromophore (covalent; via 1 link) By similarity
Natural variations
	Natural variant	9 – 12	4	Missing in strain: cv. Kas-1.
	Natural variant	19	1	E → K in strain: cv. Kas-1. Ref.3
	Natural variant	143	1	I → L in strain: cv. Kas-1. Ref.3
	Natural variant	980	1	V → I in strain: cv. Kas-1. Ref.3
	Natural variant	1072	1	L → V in strain: cv. Kas-1. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	P14713-1 [UniParc]. Last modified April 1, 1990. Version 1. Checksum: 7B5348CB1091B813	FASTA	1,172	129,331
	10 20 30 40 50 60 MVSGVGGSGG GRGGGRGGEE EPSSSHTPNN RRGGEQAQSS GTKSLRPRSN TESMSKAIQQ 70 80 90 100 110 120 YTVDARLHAV FEQSGESGKS FDYSQSLKTT TYGSSVPEQQ ITAYLSRIQR GGYIQPFGCM 130 140 150 160 170 180 IAVDESSFRI IGYSENAREM LGIMPQSVPT LEKPEILAMG TDVRSLFTSS SSILLERAFV 190 200 210 220 230 240 AREITLLNPV WIHSKNTGKP FYAILHRIDV GVVIDLEPAR TEDPALSIAG AVQSQKLAVR 250 260 270 280 290 300 AISQLQALPG GDIKLLCDTV VESVRDLTGY DRVMVYKFHE DEHGEVVAES KRDDLEPYIG 310 320 330 340 350 360 LHYPATDIPQ ASRFLFKQNR VRMIVDCNAT PVLVVQDDRL TQSMCLVGST LRAPHGCHSQ 370 380 390 400 410 420 YMANMGSIAS LAMAVIINGN EDDGSNVASG RSSMRLWGLV VCHHTSSRCI PFPLRYACEF 430 440 450 460 470 480 LMQAFGLQLN MELQLALQMS EKRVLRTQTL LCDMLLRDSP AGIVTQSPSI MDLVKCDGAA 490 500 510 520 530 540 FLYHGKYYPL GVAPSEVQIK DVVEWLLANH ADSTGLSTDS LGDAGYPGAA ALGDAVCGMA 550 560 570 580 590 600 VAYITKRDFL FWFRSHTAKE IKWGGAKHHP EDKDDGQRMH PRSSFQAFLE VVKSRSQPWE 610 620 630 640 650 660 TAEMDAIHSL QLILRDSFKE SEAAMNSKVV DGVVQPCRDM AGEQGIDELG AVAREMVRLI 670 680 690 700 710 720 ETATVPIFAV DAGGCINGWN AKIAELTGLS VEEAMGKSLV SDLIYKENEA TVNKLLSRAL 730 740 750 760 770 780 RGDEEKNVEV KLKTFSPELQ GKAVFVVVNA CSSKDYLNNI VGVCFVGQDV TSQKIVMDKF 790 800 810 820 830 840 INIQGDYKAI VHSPNPLIPP IFAADENTCC LEWNMAMEKL TGWSRSEVIG KMIVGEVFGS 850 860 870 880 890 900 CCMLKGPDAL TKFMIVLHNA IGGQDTDKFP FPFFDRNGKF VQALLTANKR VSLEGKVIGA 910 920 930 940 950 960 FCFLQIPSPE LQQALAVQRR QDTECFTKAK ELAYICQVIK NPLSGMRFAN SLLEATDLNE 970 980 990 1000 1010 1020 DQKQLLETSV SCEKQISRIV GDMDLESIED GSFVLKREEF FLGSVINAIV SQAMFLLRDR 1030 1040 1050 1060 1070 1080 GLQLIRDIPE EIKSIEVFGD QIRIQQLLAE FLLSIIRYAP SQEWVEIHLS QLSKQMADGF 1090 1100 1110 1120 1130 1140 AAIRTEFRMA CPGEGLPPEL VRDMFHSSRW TSPEGLGLSV CRKILKLMNG EVQYIRESER 1150 1160 1170 SYFLIILELP VPRKRPLSTA SGSGDMMLMM PY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family." Sharrock R.A., Quail P.H. Genes Dev. 3:1745-1757(1989) [PubMed: 2606345] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Columbia.
[2]	"Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development." Reed J.W., Nagpal P., Poole D.S., Furuya M., Chory J. Plant Cell 5:147-157(1993) [PubMed: 8453299] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: cv. Landsberg erecta.
[3]	"Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana." Wolyn D.J., Borevitz J.O., Loudet O., Schwartz C., Maloof J., Ecker J.R., Berry C.C., Chory J. Genetics 167:907-917(2004) [PubMed: 15238539] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS 9-GLY--ARG-12 DEL; GLU-19; ILE-143; VAL-980 AND LEU-1072. Strain: cv. Kas-1.
[4]	"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana." Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D., Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A. , Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C. Nature 402:761-768(1999) [PubMed: 10617197] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[5]	"An Arabidopsis circadian clock component interacts with both CRY1 and phyB." Jarillo J.A., Capel J., Tang R.-H., Yang H.-Q., Alonso J.M., Ecker J.R., Cashmore A.R. Nature 410:487-490(2001) [PubMed: 11260718] [Abstract] Cited for: INTERACTION WITH ADO1.
[6]	"A phytochrome-associated protein phosphatase 2A modulates light signals in flowering time control in Arabidopsis." Kim D.-H., Kang J.-G., Yang S.-S., Chung K.-S., Song P.-S., Park C.-M. Plant Cell 14:3043-3056(2002) [PubMed: 12468726] [Abstract] Cited for: FUNCTION, INTERACTION WITH FYPP3.
[7]	"Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer." Ryu J.S., Kim J.-I., Kunkel T., Kim B.C., Cho D.S., Hong S.H., Kim S.-H., Fernandez A.P., Kim Y., Alonso J.M., Ecker J.R., Nagy F., Lim P.O., Song P.-S., Schaefer E., Nam H.G. Cell 120:395-406(2005) [PubMed: 15707897] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH PAPP5.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X17342 mRNA. Translation: CAA35222.1. L09262 Genomic DNA. No translation available. AY466496 Genomic DNA. Translation: AAR32737.1. AC005724 Genomic DNA. Translation: AAD08948.1.
IPI	IPI00521343.
PIR	FKMUB. B33473.
RefSeq	NP_179469.1.
UniGene	At.96
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	P14713. 16 interactions.
Proteomic databases
PRIDE	P14713.
ProMEX	P14713.
Genome annotation databases
GeneID	816394.
GenomeReviews	Gene locus AT2G18790 in contig CT485783_GR.
KEGG	ath:AT2G18790.
NMPDR	fig|3702.1.peg.8873.
Organism-specific databases
TAIR	At2g18790.
Phylogenomic databases
OMA	P14713. GKYVQAL.
Gene expression databases
ArrayExpress	P14713.
GermOnline	AT2G18790. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR003594. ATP_bd_ATPase. IPR003018. GAF. 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]
Pfam	PF01590. GAF. 1 hit. PF02518. HATPase_c. 1 hit. PF00512. HisKA. 1 hit. PF00989. PAS. 2 hits. PF08446. PAS_2. 1 hit. PF00360. Phytochrome. 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. SM00091. PAS. 2 hits. [Graphical view]
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

PHYB_ARATH

Accession

Primary (citable) accession number: P14713
Secondary accession number(s): Q6S4P0

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	April 1, 1990
Last modified:	June 16, 2009
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)