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Protein

Phytochrome D

Gene

PHYD

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Binding sitei360Phytochromobilin chromophore (covalent; via 1 link)By similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionPhotoreceptor protein, Receptor
Biological processSensory transduction, Transcription, Transcription regulation
LigandChromophore

Names & Taxonomyi

Protein namesi
Recommended name:
Phytochrome D
Gene namesi
Name:PHYD
Ordered Locus Names:At4g16250
ORF Names:dl4165c
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

AraportiAT4G16250
TAIRilocus:2005535 AT4G16250

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001719651 – 1164Phytochrome DAdd BLAST1164

Post-translational modificationi

Contains one covalently linked phytochromobilin chromophore.By similarity

Proteomic databases

PaxDbiP42497
PRIDEiP42497

PTM databases

iPTMnetiP42497

Expressioni

Gene expression databases

ExpressionAtlasiP42497 baseline and differential
GenevisibleiP42497 AT

Interactioni

Subunit structurei

Homodimer.

Binary interactionsi

Show more details

GO - Molecular functioni

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

Protein-protein interaction databases

BioGridi126139 interactors.
IntActiP42497 4 interactors.
STRINGi3702.AT4G16250.1

Structurei

3D structure databases

ProteinModelPortaliP42497
SMRiP42497
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini255 – 437GAFAdd BLAST183
Domaini656 – 727PAS 1PROSITE-ProRule annotationAdd BLAST72
Domaini790 – 861PAS 2PROSITE-ProRule annotationAdd BLAST72
Domaini938 – 1157Histidine kinasePROSITE-ProRule annotationAdd BLAST220

Sequence similaritiesi

Belongs to the phytochrome family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410IJ3B Eukaryota
COG4251 LUCA
HOGENOMiHOG000272703
InParanoidiP42497
KOiK12122
OMAiERTEFFI
OrthoDBiEOG09360112
PhylomeDBiP42497

Family and domain databases

CDDicd00075 HATPase_c, 1 hit
cd00082 HisKA, 1 hit
cd00130 PAS, 2 hits
Gene3Di3.30.450.403 hits
3.30.565.101 hit
InterProiView protein in InterPro
IPR003018 GAF
IPR029016 GAF-like_dom_sf
IPR003594 HATPase_C
IPR036890 HATPase_C_sf
IPR005467 His_kinase_dom
IPR003661 HisK_dim/P
IPR000014 PAS
IPR035965 PAS-like_dom_sf
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
SUPFAMiSSF55785 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.

P42497-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVSGGGSKTS GGEAASSGHR RSRHTSAAEQ AQSSANKALR SQNQQPQNHG
60 70 80 90 100
GGTESTNKAI QQYTVDARLH AVFEQSGESG KSFDYSQSLK TAPYDSSVPE
110 120 130 140 150
QQITAYLSRI QRGGYTQPFG CLIAVEESTF TIIGYSENAR EMLGLMSQSV
160 170 180 190 200
PSIEDKSEVL TIGTDLRSLF KSSSYLLLER AFVAREITLL NPIWIHSNNT
210 220 230 240 250
GKPFYAILHR VDVGILIDLE PARTEDPALS IAGAVQSQKL AVRAISHLQS
260 270 280 290 300
LPSGDIKLLC DTVVESVRDL TGYDRVMVYK FHEDEHGEVV AESKRNDLEP
310 320 330 340 350
YIGLHYPATD IPQASRFLFK QNRVRMIVDC YASPVRVVQD DRLTQFICLV
360 370 380 390 400
GSTLRAPHGC HAQYMTNMGS IASLAMAVII NGNEEDGNGV NTGGRNSMRL
410 420 430 440 450
WGLVVCHHTS ARCIPFPLRY ACEFLMQAFG LQLNMELQLA LQVSEKRVLR
460 470 480 490 500
MQTLLCDMLL RDSPAGIVTQ RPSIMDLVKC NGAAFLYQGK YYPLGVTPTD
510 520 530 540 550
SQINDIVEWL VANHSDSTGL STDSLGDAGY PRAAALGDAV CGMAVACITK
560 570 580 590 600
RDFLFWFRSH TEKEIKWGGA KHHPEDKDDG QRMNPRSSFQ TFLEVVKSRC
610 620 630 640 650
QPWETAEMDA IHSLQLILRD SFKESEAMDS KAAAAGAVQP HGDDMVQQGM
660 670 680 690 700
QEIGAVAREM VRLIETATVP IFAVDIDGCI NGWNAKIAEL TGLSVEDAMG
710 720 730 740 750
KSLVRELIYK EYKETVDRLL SCALKGDEGK NVEVKLKTFG SELQGKAMFV
760 770 780 790 800
VVNACSSKDY LNNIVGVCFV GQDVTGHKIV MDKFINIQGD YKAIIHSPNP
810 820 830 840 850
LIPPIFAADE NTCCLEWNTA MEKLTGWPRS EVIGKLLVRE VFGSYCRLKG
860 870 880 890 900
PDALTKFMIV LHNAIGGQDT DKFPFPFFDR KGEFIQALLT LNKRVSIDGK
910 920 930 940 950
IIGAFCFLQI PSPELQQALE VQRRQESEYF SRRKELAYIF QVIKNPLSGL
960 970 980 990 1000
RFTNSLLEDM DLNEDQKQLL ETSVSCEKQI SKIVGDMDVK SIDDGSFLLE
1010 1020 1030 1040 1050
RTEFFIGNVT NAVVSQVMLV VRERNLQLIR NIPTEVKSMA VYGDQIRLQQ
1060 1070 1080 1090 1100
VLAEFLLSIV RYAPMEGSVE LHLCPTLNQM ADGFSAVRLE FRMACAGEGV
1110 1120 1130 1140 1150
PPEKVQDMFH SSRWTSPEGL GLSVCRKILK LMNGGVQYIR EFERSYFLIV
1160
IELPVPLMMM MPSS
Length:1,164
Mass (Da):129,268
Last modified:December 1, 2000 - v2
Checksum:iBB7CFE19C50ACBAB
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti425L → F in CAA54072 (PubMed:8049367).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76609 Genomic DNA Translation: CAA54072.1
Z97340 Genomic DNA Translation: CAB10404.1
AL161543 Genomic DNA Translation: CAB78667.1
CP002687 Genomic DNA Translation: AEE83721.1
PIRiB71429
RefSeqiNP_193360.1, NM_117721.2
UniGeneiAt.33095

Genome annotation databases

EnsemblPlantsiAT4G16250.1; AT4G16250.1; AT4G16250
GeneIDi827319
GrameneiAT4G16250.1; AT4G16250.1; AT4G16250
KEGGiath:AT4G16250

Similar proteinsi

Entry informationi

Entry nameiPHYD_ARATH
AccessioniPrimary (citable) accession number: P42497
Secondary accession number(s): O23472
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: December 1, 2000
Last modified: April 25, 2018
This is version 164 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome