Phytochrome B - Arabidopsis thaliana (Mouse-ear cress)

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P14713 (PHYB_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 135. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	1172 AA.
Sequence status	Complete.
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.7 Ref.8
Subunit structure	Homodimer. Interacts with ADO1 and PKS4. Stabilized by interactions with PAPP5 and FYPP3 which are enhanced in the phosphorylated Pfr form. Interacts with VOZ1 and VOZ2. Ref.6 Ref.7 Ref.8 Ref.9 Ref.10
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.8
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 Reference proteome
Gene Ontology (GO)
Biological_process	abscisic acid metabolic process Inferred from mutant phenotype PubMed 17010113. Source: TAIR chromatin organization Inferred from mutant phenotype PubMed 20935177. Source: TAIR circadian regulation of calcium ion oscillation Inferred from mutant phenotype PubMed 17982000. Source: TAIR detection of visible light Inferred from electronic annotation. Source: InterPro entrainment of circadian clock Inferred from mutant phenotype PubMed 12177480. Source: TAIR gravitropism Inferred from mutant phenotype PubMed 15695459. Source: TAIR jasmonic acid mediated signaling pathway Inferred from mutant phenotype PubMed 19251652. Source: TAIR phosphorelay signal transduction system Inferred from electronic annotation. Source: GOC photomorphogenesis Inferred from mutant phenotype PubMed 23321421. Source: TAIR photosynthesis Inferred from mutant phenotype PubMed 19363093. Source: TAIR phototropism Inferred from mutant phenotype PubMed 14686433. Source: TAIR protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW protein-tetrapyrrole linkage Inferred from electronic annotation. Source: InterPro regulation of defense response Inferred from mutant phenotype PubMed 19251652. Source: TAIR regulation of seed germination Inferred from mutant phenotype PubMed 17010113. Source: TAIR regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW response to cold Inferred from mutant phenotype PubMed 12148528. Source: TAIR response to low fluence red light stimulus Inferred from mutant phenotype PubMed 9351250. Source: TAIR signal transduction by phosphorylation Inferred from electronic annotation. Source: GOC stomatal complex development Inferred from mutant phenotype PubMed 19363093. Source: TAIR transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transpiration Inferred from mutant phenotype PubMed 19363093. Source: TAIR
Cellular_component	cytosol Inferred from direct assay PubMed 23321421. Source: TAIR membrane Inferred from electronic annotation. Source: InterPro nuclear body Inferred from direct assay PubMed 23321421 PubMed 23371951. Source: TAIR nuclear speck Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: InterPro far-red light photoreceptor activity Inferred from direct assay PubMed 23321421. Source: TAIR phosphorelay sensor kinase activity Inferred from electronic annotation. Source: InterPro red light photoreceptor activity Inferred from direct assay PubMed 23321421. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
itself		3	EBI-300727,EBI-300727
ADO1	Q94BT6	2	EBI-300727,EBI-300691
ARR4	O82798	3	EBI-300727,EBI-625213
CRY2	Q96524	3	EBI-300727,EBI-531555
PHYC	P14714	5	EBI-300727,EBI-624366
PHYD	P42497	6	EBI-300727,EBI-624382
PHYE	P42498	5	EBI-300727,EBI-624404
PIF1	Q8GZM7	3	EBI-300727,EBI-630400
PIF3	O80536	19	EBI-300727,EBI-625701
PIF4	Q8W2F3-2	3	EBI-300727,EBI-625732
PKS1	Q9SWI1	2	EBI-300727,EBI-626200
VOZ1	Q9SGQ0	4	EBI-300727,EBI-6306928
VOZ2	Q9SLB9	4	EBI-300727,EBI-6306942

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

PAS 1

Domain

786 – 857

PAS 2

Domain

934 – 1153

220

Histidine kinase

Compositional bias

3 – 25

Gly/Ser-rich

Sites

Binding site

357

Phytochromobilin chromophore (covalent; via 1 link) By similarity

Natural variations

Natural variant

9 – 12

Missing in strain: cv. Kas-1.

Natural variant

E → K in strain: cv. Kas-1.

Natural variant

143

I → L in strain: cv. Kas-1.

Natural variant

980

V → I in strain: cv. Kas-1.

Natural variant

1072

L → V in strain: cv. Kas-1.

Sequences

Sequence

Length

Mass (Da)

Tools

P14713 [UniParc].

Last modified April 1, 1990. Version 1.
Checksum: 7B5348CB1091B813
Show »

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

« Hide

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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. Venter J.C. Nature 402:761-768(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[5]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[6]	"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] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ADO1.
[7]	"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] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH FYPP3.
[8]	"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] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH PAPP5.
[9]	"PHYTOCHROME KINASE SUBSTRATE4 modulates phytochrome-mediated control of hypocotyl growth orientation." Schepens I., Boccalandro H.E., Kami C., Casal J.J., Fankhauser C. Plant Physiol. 147:661-671(2008) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PKS4.
[10]	"The phytochrome-interacting VASCULAR PLANT ONE-ZINC FINGER1 and VOZ2 redundantly regulate flowering in Arabidopsis." Yasui Y., Mukougawa K., Uemoto M., Yokofuji A., Suzuri R., Nishitani A., Kohchi T. Plant Cell 24:3248-3263(2012) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH VOZ1 AND VOZ2.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X17342 mRNA. Translation: CAA35222.1. L09262 Genomic DNA. No translation available. AY466496 Genomic DNA. Translation: AAR32737.1. AC005724 Genomic DNA. Translation: AAD08948.1. CP002685 Genomic DNA. Translation: AEC06808.1.
IPI	IPI00521343.
PIR	FKMUB. B33473.
RefSeq	NP_179469.1. NM_127435.3.
UniGene	At.96.
3D structure databases
ProteinModelPortal	P14713.
SMR	P14713. Positions 108-617.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-31742N.
IntAct	P14713. 17 interactions.
MINT	MINT-192399.
Proteomic databases
PaxDb	P14713.
PRIDE	P14713.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT2G18790.1; AT2G18790.1; AT2G18790.
GeneID	816394.
KEGG	ath:AT2G18790.
Organism-specific databases
TAIR	At2g18790.
Phylogenomic databases
eggNOG	COG4251.
HOGENOM	HOG000272703.
InParanoid	P14713.
KO	K12121.
OMA	AVAYITK.
PhylomeDB	P14713.
ProtClustDB	CLSN2679275.
Gene expression databases
ArrayExpress	P14713.
Genevestigator	P14713.
GermOnline	AT2G18790. Arabidopsis thaliana.
Family and domain databases
Gene3D	3.30.565.10. 1 hit.
InterPro	IPR003018. GAF. IPR003594. HATPase_ATP-bd. 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]
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. 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

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:	May 1, 2013
This is version 135 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Natural variations

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents