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P14713

- PHYB_ARATH

UniProt

P14713 - PHYB_ARATH

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Protein

Phytochrome B

Gene
PHYB, HY3, At2g18790, MSF3.17
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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

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
Complete GO annotation...

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.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini252 – 433182GAFAdd
BLAST
Domaini652 – 72372PAS 1Add
BLAST
Domaini786 – 85772PAS 2Add
BLAST
Domaini934 – 1153220Histidine kinaseAdd
BLAST

Compositional bias

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

Sequence similaritiesi

Belongs to the phytochrome family.
Contains 1 GAF domain.

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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 147 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

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