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P14713 (PHYB_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 147. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Phytochrome B
Gene names
Name:PHYB
Synonyms:HY3
Ordered Locus Names:At2g18790
ORF Names:MSF3.17
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length1172 AA.
Sequence statusComplete.
Protein existenceEvidence 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. Nucleusnucleoplasm. 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 processPhytochrome signaling pathway
Sensory transduction
Transcription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityPolymorphism
   DomainRepeat
   LigandChromophore
   Molecular functionPhotoreceptor protein
Receptor
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processabscisic 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

far-red light signaling pathway

Inferred from direct assay PubMed 23321421. Source: GOC

gravitropism

Inferred from mutant phenotype PubMed 15695459. Source: TAIR

jasmonic acid mediated signaling pathway

Inferred from mutant phenotype PubMed 19251652. Source: TAIR

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

red light signaling pathway

Inferred from mutant phenotype PubMed 17076805. Source: TAIR

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-templated

Inferred from electronic annotation. Source: UniProtKB-KW

response to cold

Inferred from mutant phenotype PubMed 12148528. Source: TAIR

response to far red light

Inferred from mutant phenotype PubMed 23371951. Source: TAIR

response to low fluence red light stimulus

Inferred from mutant phenotype PubMed 9351250. Source: TAIR

stomatal complex development

Inferred from mutant phenotype PubMed 19363093. Source: TAIR

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

transpiration

Inferred from mutant phenotype PubMed 19363093. Source: TAIR

   Cellular_componentcytosol

Inferred from direct assay PubMed 23321421. Source: TAIR

membrane

Inferred from electronic annotation. Source: InterPro

nuclear body

Inferred from direct assay PubMed 23321421PubMed 23371951. Source: TAIR

nuclear speck

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from direct assay PubMed 10225946PubMed 15823535PubMed 23371951. Source: TAIR

   Molecular_functionATP binding

Inferred from electronic annotation. Source: InterPro

far-red light photoreceptor activity

Inferred from direct assay PubMed 23321421. Source: TAIR

identical protein binding

Inferred from physical interaction PubMed 15273290PubMed 19286967. Source: IntAct

phosphorelay sensor kinase activity

Inferred from electronic annotation. Source: InterPro

protein binding

Inferred from physical interaction PubMed 10348744PubMed 10466729PubMed 10995393PubMed 11069292PubMed 11089975PubMed 11691995PubMed 12006496PubMed 15155879PubMed 15273290PubMed 15448264PubMed 15486100PubMed 15486102PubMed 19286967PubMed 21928113Ref.10PubMed 9845368. Source: IntAct

red light photoreceptor activity

Inferred from direct assay PubMed 23321421. Source: TAIR

red or far-red light photoreceptor activity

Inferred from mutant phenotype PubMed 12177480. Source: TAIR

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 11721172Phytochrome B
PRO_0000171963

Regions

Domain252 – 433182GAF
Domain652 – 72372PAS 1
Domain786 – 85772PAS 2
Domain934 – 1153220Histidine kinase
Compositional bias3 – 2523Gly/Ser-rich

Sites

Binding site3571Phytochromobilin chromophore (covalent; via 1 link) By similarity

Natural variations

Natural variant9 – 124Missing in strain: cv. Kas-1.
Natural variant191E → K in strain: cv. Kas-1.
Natural variant1431I → L in strain: cv. Kas-1.
Natural variant9801V → I in strain: cv. Kas-1.
Natural variant10721L → V in strain: cv. Kas-1.

Sequences

Sequence LengthMass (Da)Tools
P14713 [UniParc].

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

FASTA1,172129,331
        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' 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. expand/collapse author list , 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] [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.
PIRFKMUB. B33473.
RefSeqNP_179469.1. NM_127435.3.
UniGeneAt.96.

3D structure databases

ProteinModelPortalP14713.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid1751. 39 interactions.
DIPDIP-31742N.
IntActP14713. 16 interactions.
MINTMINT-192399.

Proteomic databases

PaxDbP14713.
PRIDEP14713.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT2G18790.1; AT2G18790.1; AT2G18790.
GeneID816394.
KEGGath:AT2G18790.

Organism-specific databases

TAIRAT2G18790.

Phylogenomic databases

eggNOGCOG4251.
HOGENOMHOG000272703.
InParanoidP14713.
KOK12121.
OMADCHATPV.
PhylomeDBP14713.

Enzyme and pathway databases

BioCycARA:GQT-616-MONOMER.

Gene expression databases

GenevestigatorP14713.

Family and domain databases

Gene3D3.30.450.40. 1 hit.
3.30.565.10. 1 hit.
InterProIPR003661. EnvZ-like_dim/P.
IPR003018. GAF.
IPR029016. GAF_dom_like.
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.
IPR005467. Sig_transdc_His_kinase_core.
[Graphical view]
PfamPF01590. 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]
PIRSFPIRSF000084. Phytochrome. 1 hit.
PRINTSPR01033. PHYTOCHROME.
SMARTSM00065. GAF. 1 hit.
SM00387. HATPase_c. 1 hit.
SM00388. HisKA. 1 hit.
SM00091. PAS. 2 hits.
[Graphical view]
SUPFAMSSF55781. SSF55781. 2 hits.
SSF55785. SSF55785. 3 hits.
SSF55874. SSF55874. 1 hit.
TIGRFAMsTIGR00229. sensory_box. 1 hit.
PROSITEPS50109. HIS_KIN. 1 hit.
PS50112. PAS. 2 hits.
PS00245. PHYTOCHROME_1. 1 hit.
PS50046. PHYTOCHROME_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePHYB_ARATH
AccessionPrimary (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: July 9, 2014
This is version 147 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names