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P14713

- PHYB_ARATH

UniProt

P14713 - PHYB_ARATH

Protein

Phytochrome B

Gene

PHYB

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 148 (01 Oct 2014)
      Sequence version 1 (01 Apr 1990)
      Previous versions | rss
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    Functioni

    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.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei357 – 3571Phytochromobilin chromophore (covalent; via 1 link)By similarity

    GO - Molecular functioni

    1. ATP binding Source: InterPro
    2. far-red light photoreceptor activity Source: TAIR
    3. identical protein binding Source: IntAct
    4. phosphorelay sensor kinase activity Source: InterPro
    5. protein binding Source: IntAct
    6. red light photoreceptor activity Source: TAIR
    7. red or far-red light photoreceptor activity Source: TAIR

    GO - Biological processi

    1. abscisic acid metabolic process Source: TAIR
    2. chromatin organization Source: TAIR
    3. circadian regulation of calcium ion oscillation Source: TAIR
    4. detection of visible light Source: InterPro
    5. entrainment of circadian clock Source: TAIR
    6. far-red light signaling pathway Source: GOC
    7. gravitropism Source: TAIR
    8. jasmonic acid mediated signaling pathway Source: TAIR
    9. photomorphogenesis Source: TAIR
    10. photosynthesis Source: TAIR
    11. phototropism Source: TAIR
    12. protein-chromophore linkage Source: UniProtKB-KW
    13. protein-tetrapyrrole linkage Source: InterPro
    14. red light signaling pathway Source: TAIR
    15. regulation of defense response Source: TAIR
    16. regulation of seed germination Source: TAIR
    17. regulation of transcription, DNA-templated Source: UniProtKB-KW
    18. response to cold Source: TAIR
    19. response to far red light Source: TAIR
    20. response to low fluence red light stimulus Source: TAIR
    21. stomatal complex development Source: TAIR
    22. transcription, DNA-templated Source: UniProtKB-KW
    23. transpiration Source: TAIR

    Keywords - Molecular functioni

    Photoreceptor protein, Receptor

    Keywords - Biological processi

    Phytochrome signaling pathway, Sensory transduction, Transcription, Transcription regulation

    Keywords - Ligandi

    Chromophore

    Enzyme and pathway databases

    BioCyciARA:GQT-616-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phytochrome B
    Gene namesi
    Name:PHYB
    Synonyms:HY3
    Ordered Locus Names:At2g18790
    ORF Names:MSF3.17
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 2

    Organism-specific databases

    TAIRiAT2G18790.

    Subcellular locationi

    Cytoplasm 1 Publication. Nucleusnucleoplasm 1 Publication. Nucleus speckle 1 Publication
    Note: Cytoplasmic in darkness, but translocated to the nucleus upon illumination, when associated with PAPP5 into speckles.

    GO - Cellular componenti

    1. cytosol Source: TAIR
    2. membrane Source: InterPro
    3. nuclear body Source: TAIR
    4. nuclear speck Source: UniProtKB-SubCell
    5. nucleus Source: TAIR

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 11721172Phytochrome BPRO_0000171963Add
    BLAST

    Post-translational modificationi

    Contains one covalently linked phytochromobilin chromophore.By similarity

    Proteomic databases

    PaxDbiP14713.
    PRIDEiP14713.

    Expressioni

    Gene expression databases

    GenevestigatoriP14713.

    Interactioni

    Subunit structurei

    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 VOZ2.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-300727,EBI-300727
    ARR4O827983EBI-300727,EBI-625213
    CRY2Q965243EBI-300727,EBI-531555
    PHYCP147145EBI-300727,EBI-624366
    PHYDP424976EBI-300727,EBI-624382
    PHYEP424985EBI-300727,EBI-624404
    PIF1Q8GZM73EBI-300727,EBI-630400
    PIF3O8053619EBI-300727,EBI-625701
    PIF4Q8W2F3-23EBI-300727,EBI-625732
    PKS1Q9SWI12EBI-300727,EBI-626200
    VOZ1Q9SGQ04EBI-300727,EBI-6306928
    VOZ2Q9SLB94EBI-300727,EBI-6306942

    Protein-protein interaction databases

    BioGridi1751. 39 interactions.
    DIPiDIP-31742N.
    IntActiP14713. 16 interactions.
    MINTiMINT-192399.

    Structurei

    3D structure databases

    ProteinModelPortaliP14713.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini252 – 433182GAFAdd
    BLAST
    Domaini652 – 72372PAS 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini786 – 85772PAS 2PROSITE-ProRule annotationAdd
    BLAST
    Domaini934 – 1153220Histidine kinasePROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi3 – 2523Gly/Ser-richAdd
    BLAST

    Sequence similaritiesi

    Belongs to the phytochrome family.Curated
    Contains 1 GAF domain.Curated
    Contains 1 histidine kinase domain.PROSITE-ProRule annotation
    Contains 2 PAS (PER-ARNT-SIM) domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiCOG4251.
    HOGENOMiHOG000272703.
    InParanoidiP14713.
    KOiK12121.
    OMAiDCHATPV.
    PhylomeDBiP14713.

    Family and domain databases

    Gene3Di3.30.450.40. 1 hit.
    3.30.565.10. 1 hit.
    InterProiIPR003661. 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]
    PfamiPF01590. 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]
    PIRSFiPIRSF000084. Phytochrome. 1 hit.
    PRINTSiPR01033. PHYTOCHROME.
    SMARTiSM00065. GAF. 1 hit.
    SM00387. HATPase_c. 1 hit.
    SM00388. HisKA. 1 hit.
    SM00091. PAS. 2 hits.
    [Graphical view]
    SUPFAMiSSF55781. SSF55781. 2 hits.
    SSF55785. SSF55785. 3 hits.
    SSF55874. SSF55874. 1 hit.
    TIGRFAMsiTIGR00229. sensory_box. 1 hit.
    PROSITEiPS50109. HIS_KIN. 1 hit.
    PS50112. PAS. 2 hits.
    PS00245. PHYTOCHROME_1. 1 hit.
    PS50046. PHYTOCHROME_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P14713-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVSGVGGSGG GRGGGRGGEE EPSSSHTPNN RRGGEQAQSS GTKSLRPRSN     50
    TESMSKAIQQ YTVDARLHAV FEQSGESGKS FDYSQSLKTT TYGSSVPEQQ 100
    ITAYLSRIQR GGYIQPFGCM IAVDESSFRI IGYSENAREM LGIMPQSVPT 150
    LEKPEILAMG TDVRSLFTSS SSILLERAFV AREITLLNPV WIHSKNTGKP 200
    FYAILHRIDV GVVIDLEPAR TEDPALSIAG AVQSQKLAVR AISQLQALPG 250
    GDIKLLCDTV VESVRDLTGY DRVMVYKFHE DEHGEVVAES KRDDLEPYIG 300
    LHYPATDIPQ ASRFLFKQNR VRMIVDCNAT PVLVVQDDRL TQSMCLVGST 350
    LRAPHGCHSQ YMANMGSIAS LAMAVIINGN EDDGSNVASG RSSMRLWGLV 400
    VCHHTSSRCI PFPLRYACEF LMQAFGLQLN MELQLALQMS EKRVLRTQTL 450
    LCDMLLRDSP AGIVTQSPSI MDLVKCDGAA FLYHGKYYPL GVAPSEVQIK 500
    DVVEWLLANH ADSTGLSTDS LGDAGYPGAA ALGDAVCGMA VAYITKRDFL 550
    FWFRSHTAKE IKWGGAKHHP EDKDDGQRMH PRSSFQAFLE VVKSRSQPWE 600
    TAEMDAIHSL QLILRDSFKE SEAAMNSKVV DGVVQPCRDM AGEQGIDELG 650
    AVAREMVRLI ETATVPIFAV DAGGCINGWN AKIAELTGLS VEEAMGKSLV 700
    SDLIYKENEA TVNKLLSRAL RGDEEKNVEV KLKTFSPELQ GKAVFVVVNA 750
    CSSKDYLNNI VGVCFVGQDV TSQKIVMDKF INIQGDYKAI VHSPNPLIPP 800
    IFAADENTCC LEWNMAMEKL TGWSRSEVIG KMIVGEVFGS CCMLKGPDAL 850
    TKFMIVLHNA IGGQDTDKFP FPFFDRNGKF VQALLTANKR VSLEGKVIGA 900
    FCFLQIPSPE LQQALAVQRR QDTECFTKAK ELAYICQVIK NPLSGMRFAN 950
    SLLEATDLNE DQKQLLETSV SCEKQISRIV GDMDLESIED GSFVLKREEF 1000
    FLGSVINAIV SQAMFLLRDR GLQLIRDIPE EIKSIEVFGD QIRIQQLLAE 1050
    FLLSIIRYAP SQEWVEIHLS QLSKQMADGF AAIRTEFRMA CPGEGLPPEL 1100
    VRDMFHSSRW TSPEGLGLSV CRKILKLMNG EVQYIRESER SYFLIILELP 1150
    VPRKRPLSTA SGSGDMMLMM PY 1172
    Length:1,172
    Mass (Da):129,331
    Last modified:April 1, 1990 - v1
    Checksum:i7B5348CB1091B813
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti9 – 124Missing in strain: cv. Kas-1.
    Natural varianti19 – 191E → K in strain: cv. Kas-1.
    Natural varianti143 – 1431I → L in strain: cv. Kas-1.
    Natural varianti980 – 9801V → I in strain: cv. Kas-1.
    Natural varianti1072 – 10721L → V in strain: cv. Kas-1.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    PIRiB33473. FKMUB.
    RefSeqiNP_179469.1. NM_127435.3.
    UniGeneiAt.96.

    Genome annotation databases

    EnsemblPlantsiAT2G18790.1; AT2G18790.1; AT2G18790.
    GeneIDi816394.
    KEGGiath:AT2G18790.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    PIRi B33473. FKMUB.
    RefSeqi NP_179469.1. NM_127435.3.
    UniGenei At.96.

    3D structure databases

    ProteinModelPortali P14713.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 1751. 39 interactions.
    DIPi DIP-31742N.
    IntActi P14713. 16 interactions.
    MINTi MINT-192399.

    Proteomic databases

    PaxDbi P14713.
    PRIDEi P14713.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT2G18790.1 ; AT2G18790.1 ; AT2G18790 .
    GeneIDi 816394.
    KEGGi ath:AT2G18790.

    Organism-specific databases

    TAIRi AT2G18790.

    Phylogenomic databases

    eggNOGi COG4251.
    HOGENOMi HOG000272703.
    InParanoidi P14713.
    KOi K12121.
    OMAi DCHATPV.
    PhylomeDBi P14713.

    Enzyme and pathway databases

    BioCyci ARA:GQT-616-MONOMER.

    Gene expression databases

    Genevestigatori P14713.

    Family and domain databases

    Gene3Di 3.30.450.40. 1 hit.
    3.30.565.10. 1 hit.
    InterProi IPR003661. 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 ]
    Pfami 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 ]
    PIRSFi PIRSF000084. Phytochrome. 1 hit.
    PRINTSi PR01033. PHYTOCHROME.
    SMARTi SM00065. GAF. 1 hit.
    SM00387. HATPase_c. 1 hit.
    SM00388. HisKA. 1 hit.
    SM00091. PAS. 2 hits.
    [Graphical view ]
    SUPFAMi SSF55781. SSF55781. 2 hits.
    SSF55785. SSF55785. 3 hits.
    SSF55874. SSF55874. 1 hit.
    TIGRFAMsi TIGR00229. sensory_box. 1 hit.
    PROSITEi PS50109. HIS_KIN. 1 hit.
    PS50112. PAS. 2 hits.
    PS00245. PHYTOCHROME_1. 1 hit.
    PS50046. PHYTOCHROME_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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. 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.

    Entry informationi

    Entry nameiPHYB_ARATH
    AccessioniPrimary (citable) accession number: P14713
    Secondary accession number(s): Q6S4P0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1990
    Last sequence update: April 1, 1990
    Last modified: October 1, 2014
    This is version 148 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3