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P14713

- PHYB_ARATH

UniProt

P14713 - PHYB_ARATH

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Protein

Phytochrome B

Gene

PHYB

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

ExpressionAtlasiP14713. baseline and differential.
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

Secondary structure

1
1172
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni98 – 1003Combined sources
Helixi105 – 1095Combined sources
Beta strandi112 – 1143Combined sources
Beta strandi118 – 1236Combined sources
Turni125 – 1273Combined sources
Beta strandi129 – 1346Combined sources
Helixi137 – 1404Combined sources
Helixi163 – 1653Combined sources
Helixi169 – 18012Combined sources
Helixi184 – 1874Combined sources
Beta strandi189 – 1979Combined sources
Beta strandi200 – 2078Combined sources
Beta strandi209 – 21810Combined sources
Helixi224 – 24623Combined sources
Helixi253 – 26816Combined sources
Beta strandi271 – 2788Combined sources
Beta strandi284 – 2896Combined sources
Helixi305 – 3073Combined sources
Helixi310 – 3189Combined sources
Beta strandi321 – 3255Combined sources
Beta strandi327 – 3293Combined sources
Beta strandi332 – 3365Combined sources
Helixi356 – 36510Combined sources
Beta strandi368 – 37811Combined sources
Beta strandi394 – 40613Combined sources
Helixi412 – 44837Combined sources
Beta strandi473 – 4753Combined sources
Beta strandi477 – 4804Combined sources
Helixi496 – 50611Combined sources
Beta strandi516 – 5194Combined sources
Helixi529 – 5313Combined sources
Beta strandi538 – 5414Combined sources
Beta strandi551 – 5544Combined sources
Beta strandi561 – 5666Combined sources
Beta strandi587 – 5904Combined sources
Helixi601 – 61616Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4OURX-ray3.40A/B90-624[»]
ProteinModelPortaliP14713.
SMRiP14713. Positions 101-617.
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_C.
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

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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4OUR X-ray 3.40 A/B 90-624 [» ]
ProteinModelPortali P14713.
SMRi P14713. Positions 101-617.
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

ExpressionAtlasi P14713. baseline and differential.
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_C.
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: November 26, 2014
This is version 150 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3