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Protein

Phytochrome D

Gene

PHYD

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 sitei360 – 3601Phytochromobilin 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-1151-MONOMER.

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

TAIRiAT4G16250.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: TAIR
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11641164Phytochrome DPRO_0000171965Add
BLAST

Post-translational modificationi

Contains one covalently linked phytochromobilin chromophore.By similarity

Proteomic databases

PaxDbiP42497.
PRIDEiP42497.

PTM databases

iPTMnetiP42497.

Expressioni

Gene expression databases

GenevisibleiP42497. AT.

Interactioni

Subunit structurei

Homodimer.

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-624382,EBI-624382
PHYBP147136EBI-624382,EBI-300727
PHYCP147142EBI-624382,EBI-624366
PHYEP424984EBI-624382,EBI-624404

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi12613. 9 interactions.
IntActiP42497. 4 interactions.
STRINGi3702.AT4G16250.1.

Structurei

3D structure databases

ProteinModelPortaliP42497.
SMRiP42497. Positions 103-621.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini255 – 437183GAFAdd
BLAST
Domaini656 – 72772PAS 1PROSITE-ProRule annotationAdd
BLAST
Domaini790 – 86172PAS 2PROSITE-ProRule annotationAdd
BLAST
Domaini938 – 1157220Histidine 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

eggNOGiENOG410IJ3B. Eukaryota.
COG4251. LUCA.
HOGENOMiHOG000272703.
InParanoidiP42497.
KOiK12122.
OMAiINDIVEW.
OrthoDBiEOG09360112.
PhylomeDBiP42497.

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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti425 – 4251L → F in CAA54072 (PubMed:8049367).Curated

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_117721.1.
UniGeneiAt.33095.

Genome annotation databases

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

Cross-referencesi

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_117721.1.
UniGeneiAt.33095.

3D structure databases

ProteinModelPortaliP42497.
SMRiP42497. Positions 103-621.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi12613. 9 interactions.
IntActiP42497. 4 interactions.
STRINGi3702.AT4G16250.1.

PTM databases

iPTMnetiP42497.

Proteomic databases

PaxDbiP42497.
PRIDEiP42497.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

TAIRiAT4G16250.

Phylogenomic databases

eggNOGiENOG410IJ3B. Eukaryota.
COG4251. LUCA.
HOGENOMiHOG000272703.
InParanoidiP42497.
KOiK12122.
OMAiINDIVEW.
OrthoDBiEOG09360112.
PhylomeDBiP42497.

Enzyme and pathway databases

BioCyciARA:GQT-1151-MONOMER.

Miscellaneous databases

PROiP42497.

Gene expression databases

GenevisibleiP42497. 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...

Entry informationi

Entry nameiPHYD_ARATH
AccessioniPrimary (citable) accession number: P42497
Secondary accession number(s): O23472
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: December 1, 2000
Last modified: September 7, 2016
This is version 148 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.