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Protein

Phytochrome E

Gene

PHYE

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 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 morphogenic 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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei322 – 3221Phytochromobilin chromophore (covalent; via 1 link)By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Photoreceptor protein, Receptor

Keywords - Biological processi

Sensory transduction, Transcription, Transcription regulation

Keywords - Ligandi

Chromophore

Enzyme and pathway databases

BioCyciARA:GQT-1963-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Phytochrome E
Gene namesi
Name:PHYE
Ordered Locus Names:At4g18130
ORF Names:F15J5.100
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G18130.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11121112Phytochrome EPRO_0000171966Add
BLAST

Post-translational modificationi

Contains one covalently linked phytochromobilin chromophore.By similarity

Proteomic databases

PaxDbiP42498.
PRIDEiP42498.

Expressioni

Gene expression databases

GenevisibleiP42498. AT.

Interactioni

Subunit structurei

Homodimer.

Binary interactionsi

WithEntry#Exp.IntActNotes
PHYBP147135EBI-624404,EBI-300727
PHYDP424974EBI-624404,EBI-624382

Protein-protein interaction databases

BioGridi12831. 3 interactions.
IntActiP42498. 2 interactions.
STRINGi3702.AT4G18130.1.

Structurei

3D structure databases

ProteinModelPortaliP42498.
SMRiP42498. Positions 63-572.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini217 – 387171GAFAdd
BLAST
Domaini595 – 66672PAS 1PROSITE-ProRule annotationAdd
BLAST
Domaini732 – 80372PAS 2PROSITE-ProRule annotationAdd
BLAST
Domaini877 – 1096220Histidine kinasePROSITE-ProRule annotationAdd
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

eggNOGiENOG410IPET. Eukaryota.
COG0642. LUCA.
COG4251. LUCA.
HOGENOMiHOG000272703.
InParanoidiP42498.
KOiK12123.
OMAiARFLFKQ.

Family and domain databases

Gene3Di3.30.450.40. 1 hit.
3.30.565.10. 1 hit.
InterProiIPR003018. 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.
[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.

P42498-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGFESSSSAA SNMKPQPQKS NTAQYSVDAA LFADFAQSIY TGKSFNYSKS
60 70 80 90 100
VISPPNHVPD EHITAYLSNI QRGGLVQPFG CLIAVEEPSF RILGLSDNSS
110 120 130 140 150
DFLGLLSLPS TSHSGEFDKV KGLIGIDART LFTPSSGASL SKAASFTEIS
160 170 180 190 200
LLNPVLVHSR TTQKPFYAIL HRIDAGIVMD LEPAKSGDPA LTLAGAVQSQ
210 220 230 240 250
KLAVRAISRL QSLPGGDIGA LCDTVVEDVQ RLTGYDRVMV YQFHEDDHGE
260 270 280 290 300
VVSEIRRSDL EPYLGLHYPA TDIPQAARFL FKQNRVRMIC DCNATPVKVV
310 320 330 340 350
QSEELKRPLC LVNSTLRAPH GCHTQYMANM GSVASLALAI VVKGKDSSKL
360 370 380 390 400
WGLVVGHHCS PRYVPFPLRY ACEFLMQAFG LQLQMELQLA SQLAEKKAMR
410 420 430 440 450
TQTLLCDMLL RDTVSAIVTQ SPGIMDLVKC DGAALYYKGK CWLVGVTPNE
460 470 480 490 500
SQVKDLVNWL VENHGDDSTG LTTDSLVDAG YPGAISLGDA VCGVAAAGFS
510 520 530 540 550
SKDYLLWFRS NTASAIKWGG AKHHPKDKDD AGRMHPRSSF TAFLEVAKSR
560 570 580 590 600
SLPWEISEID AIHSLRLIMR ESFTSSRPVL SGNGVARDAN ELTSFVCEMV
610 620 630 640 650
RVIETATAPI FGVDSSGCIN GWNKKTAEMT GLLASEAMGK SLADEIVQEE
660 670 680 690 700
SRAALESLLC KALQGEEEKS VMLKLRKFGQ NNHPDYSSDV CVLVNSCTSR
710 720 730 740 750
DYTENIIGVC FVGQDITSEK AITDRFIRLQ GDYKTIVQSL NPLIPPIFAS
760 770 780 790 800
DENACCSEWN AAMEKLTGWS KHEVIGKMLP GEVFGVFCKV KCQDSLTKFL
810 820 830 840 850
ISLYQGIAGD NVPESSLVEF FNKEGKYIEA SLTANKSTNI EGKVIRCFFF
860 870 880 890 900
LQIINKESGL SCPELKESAQ SLNELTYVRQ EIKNPLNGIR FAHKLLESSE
910 920 930 940 950
ISASQRQFLE TSDACEKQIT TIIESTDLKS IEEGKLQLET EEFRLENILD
960 970 980 990 1000
TIISQVMIIL RERNSQLRVE VAEEIKTLPL NGDRVKLQLI LADLLRNIVN
1010 1020 1030 1040 1050
HAPFPNSWVG ISISPGQELS RDNGRYIHLQ FRMIHPGKGL PSEMLSDMFE
1060 1070 1080 1090 1100
TRDGWVTPDG LGLKLSRKLL EQMNGRVSYV REDERCFFQV DLQVKTMLGV
1110
ESRGTEGSSS IK
Length:1,112
Mass (Da):122,516
Last modified:May 3, 2011 - v2
Checksum:i2E06677039213B57
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti498 – 4981G → E in CAA54075 (PubMed:8049367).Curated
Sequence conflicti498 – 4981G → E in CAB53654 (PubMed:10617198).Curated
Sequence conflicti498 – 4981G → E in CAB78815 (PubMed:10617198).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76610 Genomic DNA. Translation: CAA54075.1.
AL110123 Genomic DNA. Translation: CAB53654.1.
AL161548 Genomic DNA. Translation: CAB78815.1.
CP002687 Genomic DNA. Translation: AEE84000.1.
AK221424 mRNA. Translation: BAD94419.1.
PIRiS46313.
RefSeqiNP_193547.4. NM_117923.7.
UniGeneiAt.32943.
At.70995.

Genome annotation databases

EnsemblPlantsiAT4G18130.1; AT4G18130.1; AT4G18130.
GeneIDi827538.
GrameneiAT4G18130.1; AT4G18130.1; AT4G18130.
KEGGiath:AT4G18130.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76610 Genomic DNA. Translation: CAA54075.1.
AL110123 Genomic DNA. Translation: CAB53654.1.
AL161548 Genomic DNA. Translation: CAB78815.1.
CP002687 Genomic DNA. Translation: AEE84000.1.
AK221424 mRNA. Translation: BAD94419.1.
PIRiS46313.
RefSeqiNP_193547.4. NM_117923.7.
UniGeneiAt.32943.
At.70995.

3D structure databases

ProteinModelPortaliP42498.
SMRiP42498. Positions 63-572.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi12831. 3 interactions.
IntActiP42498. 2 interactions.
STRINGi3702.AT4G18130.1.

Proteomic databases

PaxDbiP42498.
PRIDEiP42498.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G18130.1; AT4G18130.1; AT4G18130.
GeneIDi827538.
GrameneiAT4G18130.1; AT4G18130.1; AT4G18130.
KEGGiath:AT4G18130.

Organism-specific databases

TAIRiAT4G18130.

Phylogenomic databases

eggNOGiENOG410IPET. Eukaryota.
COG0642. LUCA.
COG4251. LUCA.
HOGENOMiHOG000272703.
InParanoidiP42498.
KOiK12123.
OMAiARFLFKQ.

Enzyme and pathway databases

BioCyciARA:GQT-1963-MONOMER.

Miscellaneous databases

PROiP42498.

Gene expression databases

GenevisibleiP42498. AT.

Family and domain databases

Gene3Di3.30.450.40. 1 hit.
3.30.565.10. 1 hit.
InterProiIPR003018. 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.
[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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE."
    Clack T., Mathews S., Sharrock R.A.
    Plant Mol. Biol. 25:413-427(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: cv. Landsberg erecta.
  2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-316.
    Strain: cv. Columbia.

Entry informationi

Entry nameiPHYE_ARATH
AccessioniPrimary (citable) accession number: P42498
Secondary accession number(s): Q56Y99
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: May 3, 2011
Last modified: February 17, 2016
This is version 145 of the entry and version 2 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

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.