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Protein

Phytochrome B

Gene

PHYB

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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. Involved in light-regulated circadian phase control that triggers stomatal aperture, stomatal conductance, and CO2 assimilation. Implicated in red light perception, and, to a lower extent, in blue light signaling (PubMed:12177480). Regulates temperature responses by associating with the promoters of key target genes in a temperature-dependent manner and subsequently repressing their expression probably in a PIF4-dependent manner. Thermal timer that integrates temperature information over the course of the night (PubMed:27789797).4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei357Phytochromobilin chromophore (covalent; via 1 link)Combined sources1

GO - Molecular functioni

  • far-red light photoreceptor activity Source: TAIR
  • identical protein binding Source: IntAct
  • phosphorelay sensor kinase activity Source: InterPro
  • promoter-specific chromatin binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB
  • red light photoreceptor activity Source: TAIR
  • red or far-red light photoreceptor activity Source: TAIR
  • sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

  • abscisic acid metabolic process Source: TAIR
  • chromatin organization Source: TAIR
  • circadian regulation of calcium ion oscillation Source: TAIR
  • detection of visible light Source: InterPro
  • entrainment of circadian clock Source: TAIR
  • gravitropism Source: TAIR
  • jasmonic acid mediated signaling pathway Source: TAIR
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • photomorphogenesis Source: TAIR
  • photosynthesis Source: TAIR
  • phototropism Source: TAIR
  • protein-chromophore linkage Source: UniProtKB-KW
  • protein-phytochromobilin linkage Source: UniProtKB
  • red light signaling pathway Source: TAIR
  • regulation of defense response Source: TAIR
  • regulation of photoperiodism, flowering Source: TAIR
  • regulation of seed germination Source: TAIR
  • response to cold Source: TAIR
  • response to far red light Source: TAIR
  • response to low fluence blue light stimulus by blue low-fluence system Source: UniProtKB
  • response to low fluence red light stimulus Source: TAIR
  • response to temperature stimulus Source: UniProtKB
  • stomatal complex development Source: TAIR
  • transcription, DNA-templated Source: UniProtKB-KW
  • transpiration Source: TAIR

Keywordsi

Molecular functionDNA-binding, Photoreceptor protein, Receptor, Repressor
Biological processPhytochrome signaling pathway, Sensory transduction, Transcription, Transcription regulation
LigandChromophore

Names & Taxonomyi

Protein namesi
Recommended name:
Phytochrome B1 Publication
Alternative name(s):
Protein LONG HYPOCOTYL 31 Publication
Protein OUT OF PHASE 11 Publication
Gene namesi
Name:PHYB1 Publication
Synonyms:HY31 Publication, OOP11 Publication
Ordered Locus Names:At2g18790Imported
ORF Names:MSF3.17Imported
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRilocus:2005515. AT2G18790.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: TAIR
  • nuclear body Source: TAIR
  • nuclear speck Source: UniProtKB-SubCell
  • nucleus Source: TAIR

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

In oop1, defects in circadian timing with altered phase; early timing of the peak (acrophase) of multiple circadian rhythms such as leaf movement, CO2 assimilation and light-induced gene expression. Strong photoperception defect in red light leading to long hypocotyls; this phenotype is increased when blue lights are combined to red lights. Increased sensitivity to SO2. Elongated internodes before the transition to flowering when grown in short day conditions.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi276Y → H in YHB; constitutively active and stronger interaction with PTAC12/HMR in the dark. Constitutive warm-temperature response with the warm-temperature transcriptome derepressed at low temperatures. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001719631 – 1172Phytochrome BAdd BLAST1172

Post-translational modificationi

Contains one covalently linked phytochromobilin chromophore.1 Publication

Proteomic databases

PaxDbiP14713.

PTM databases

iPTMnetiP14713.

Expressioni

Inductioni

Inactivation is proportional to temperature in the dark.1 Publication

Gene expression databases

ExpressionAtlasiP14713. baseline and differential.
GenevisibleiP14713. AT.

Interactioni

Subunit structurei

Homodimer (PubMed:24982198). 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 (PubMed:11260718, PubMed:12468726, PubMed:15707897, PubMed:18390804, PubMed:22904146). Binds, via its photosensory domain, to PTAC12/HMR when photoactivated; this interaction stimulates its localization to photobodies (PubMed:22895253). Interacts with CRY1 specifically when in the dark/far-red (Pr) state, but not when red light-activated (Pfr) (PubMed:22577138). Interacts with PIF4 AND PIF5 in response to low blue light (LBL) (PubMed:26724867).9 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • identical protein binding Source: IntAct
  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi1751. 68 interactors.
DIPiDIP-31742N.
IntActiP14713. 16 interactors.
MINTiMINT-192399.
STRINGi3702.AT2G18790.1.

Structurei

Secondary structure

11172
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni98 – 100Combined sources3
Helixi105 – 109Combined sources5
Beta strandi112 – 114Combined sources3
Beta strandi118 – 123Combined sources6
Turni125 – 127Combined sources3
Beta strandi129 – 134Combined sources6
Helixi137 – 140Combined sources4
Helixi163 – 165Combined sources3
Helixi169 – 180Combined sources12
Helixi184 – 187Combined sources4
Beta strandi189 – 197Combined sources9
Beta strandi200 – 207Combined sources8
Beta strandi209 – 218Combined sources10
Helixi224 – 246Combined sources23
Helixi253 – 268Combined sources16
Beta strandi271 – 278Combined sources8
Beta strandi284 – 289Combined sources6
Helixi305 – 307Combined sources3
Helixi310 – 318Combined sources9
Beta strandi321 – 325Combined sources5
Beta strandi327 – 329Combined sources3
Beta strandi332 – 336Combined sources5
Helixi356 – 365Combined sources10
Beta strandi368 – 378Combined sources11
Beta strandi394 – 406Combined sources13
Helixi412 – 448Combined sources37
Beta strandi473 – 475Combined sources3
Beta strandi477 – 480Combined sources4
Helixi496 – 506Combined sources11
Beta strandi516 – 519Combined sources4
Helixi529 – 531Combined sources3
Beta strandi538 – 541Combined sources4
Beta strandi551 – 554Combined sources4
Beta strandi561 – 566Combined sources6
Beta strandi587 – 590Combined sources4
Helixi601 – 616Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4OURX-ray3.40A/B90-624[»]
ProteinModelPortaliP14713.
SMRiP14713.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini252 – 433GAFCuratedAdd BLAST182
Domaini652 – 723PAS 1PROSITE-ProRule annotationAdd BLAST72
Domaini786 – 857PAS 2PROSITE-ProRule annotationAdd BLAST72
Domaini934 – 1153Histidine kinasePROSITE-ProRule annotationAdd BLAST220

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi3 – 25Gly/Ser-richPROSITE-ProRule annotationAdd BLAST23

Sequence similaritiesi

Belongs to the phytochrome family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410IJ3B. Eukaryota.
COG4251. LUCA.
HOGENOMiHOG000272703.
InParanoidiP14713.
KOiK12121.
OMAiKTFGPEQ.
OrthoDBiEOG09360112.
PhylomeDBiP14713.

Family and domain databases

CDDicd00130. PAS. 2 hits.
Gene3Di3.30.450.40. 1 hit.
3.30.565.10. 1 hit.
InterProiView protein in InterPro
IPR003018. GAF.
IPR029016. GAF_dom-like.
IPR003594. HATPase_C.
IPR005467. His_kinase_dom.
IPR003661. HisK_dim/P.
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.
PfamiView protein in 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.
PIRSFiPIRSF000084. Phytochrome. 1 hit.
PRINTSiPR01033. PHYTOCHROME.
SMARTiView protein in SMART
SM00065. GAF. 1 hit.
SM00387. HATPase_c. 1 hit.
SM00388. HisKA. 1 hit.
SM00091. PAS. 2 hits.
SUPFAMiSSF55781. SSF55781. 2 hits.
SSF55785. SSF55785. 3 hits.
SSF55874. SSF55874. 1 hit.
TIGRFAMsiTIGR00229. sensory_box. 1 hit.
PROSITEiView protein in PROSITE
PS50109. HIS_KIN. 1 hit.
PS50112. PAS. 2 hits.
PS00245. PHYTOCHROME_1. 1 hit.
PS50046. PHYTOCHROME_2. 1 hit.

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)DescriptionActionsGraphical viewLength
Natural varianti9 – 12Missing in strain: cv. Kas-1. 1 Publication4
Natural varianti19E → K in strain: cv. Kas-1. 1 Publication1
Natural varianti143I → L in strain: cv. Kas-1. 1 Publication1
Natural varianti980V → I in strain: cv. Kas-1. 1 Publication1
Natural varianti1072L → V in strain: cv. Kas-1. 1 Publication1

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_127435.4.
UniGeneiAt.96.

Genome annotation databases

EnsemblPlantsiAT2G18790.1; AT2G18790.1; AT2G18790.
GeneIDi816394.
GrameneiAT2G18790.1; AT2G18790.1; AT2G18790.
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.
PIRiB33473. FKMUB.
RefSeqiNP_179469.1. NM_127435.4.
UniGeneiAt.96.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4OURX-ray3.40A/B90-624[»]
ProteinModelPortaliP14713.
SMRiP14713.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1751. 68 interactors.
DIPiDIP-31742N.
IntActiP14713. 16 interactors.
MINTiMINT-192399.
STRINGi3702.AT2G18790.1.

PTM databases

iPTMnetiP14713.

Proteomic databases

PaxDbiP14713.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G18790.1; AT2G18790.1; AT2G18790.
GeneIDi816394.
GrameneiAT2G18790.1; AT2G18790.1; AT2G18790.
KEGGiath:AT2G18790.

Organism-specific databases

AraportiAT2G18790.
TAIRilocus:2005515. AT2G18790.

Phylogenomic databases

eggNOGiENOG410IJ3B. Eukaryota.
COG4251. LUCA.
HOGENOMiHOG000272703.
InParanoidiP14713.
KOiK12121.
OMAiKTFGPEQ.
OrthoDBiEOG09360112.
PhylomeDBiP14713.

Miscellaneous databases

PROiPR:P14713.

Gene expression databases

ExpressionAtlasiP14713. baseline and differential.
GenevisibleiP14713. AT.

Family and domain databases

CDDicd00130. PAS. 2 hits.
Gene3Di3.30.450.40. 1 hit.
3.30.565.10. 1 hit.
InterProiView protein in InterPro
IPR003018. GAF.
IPR029016. GAF_dom-like.
IPR003594. HATPase_C.
IPR005467. His_kinase_dom.
IPR003661. HisK_dim/P.
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.
PfamiView protein in 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.
PIRSFiPIRSF000084. Phytochrome. 1 hit.
PRINTSiPR01033. PHYTOCHROME.
SMARTiView protein in SMART
SM00065. GAF. 1 hit.
SM00387. HATPase_c. 1 hit.
SM00388. HisKA. 1 hit.
SM00091. PAS. 2 hits.
SUPFAMiSSF55781. SSF55781. 2 hits.
SSF55785. SSF55785. 3 hits.
SSF55874. SSF55874. 1 hit.
TIGRFAMsiTIGR00229. sensory_box. 1 hit.
PROSITEiView protein in PROSITE
PS50109. HIS_KIN. 1 hit.
PS50112. PAS. 2 hits.
PS00245. PHYTOCHROME_1. 1 hit.
PS50046. PHYTOCHROME_2. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPHYB_ARATH
AccessioniPrimary (citable) accession number: P14713
Secondary accession number(s): Q6S4P0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: April 1, 1990
Last modified: April 12, 2017
This is version 174 of the entry and version 1 of the sequence. See 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.