Reviewed, UniProtKB/Swiss-Prot P06593 (PHYA3_AVESA)

Names and origin

Protein names

Recommended name:
    Phytochrome A type 3
      Short name=AP3

Gene names

Name:	PHYA3
Synonyms:	PHY3

Organism

Avena sativa (Oat)

Taxonomic identifier

4498 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Pooideae › Poeae › Aveninae › Avena

Protein attributes

Sequence length	1129 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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.
Subunit structure	Homodimer.
Post-translational modification	Contains one covalently linked phytochromobilin chromophore.
Sequence similarities	Belongs to the phytochrome family. Contains 1 GAF domain. Contains 1 histidine kinase domain. Contains 2 PAS (PER-ARNT-SIM) domains.

Ontologies

Keywords
Biological process	Sensory transduction Transcription Transcription regulation
Domain	Repeat
Ligand	Chromophore
Molecular function	Photoreceptor protein Receptor
Technical term	Direct protein sequencing
Gene Ontology (GO)
Biological process	peptidyl-histidine phosphorylation Inferred from electronic annotation. Source: InterPro protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW protein-tetrapyrrole linkage Inferred from electronic annotation. Source: InterPro red, far-red light phototransduction Inferred from electronic annotation. Source: InterPro regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW signal transduction Inferred from electronic annotation. Source: InterPro transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	membrane Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro G-protein coupled photoreceptor activity Inferred from electronic annotation. Source: InterPro protein homodimerization activity Inferred from electronic annotation. Source: InterPro two-component sensor activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PIF1	Q8GZM7	1	EBI-630413,EBI-630400	From a different organism.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed Ref.3
	Chain	2 – 1129	1128	Phytochrome A type 3		PRO_0000171967
Regions
	Domain	217 – 402	186	GAF
	Domain	618 – 688	71	PAS 1
	Domain	748 – 822	75	PAS 2
	Domain	902 – 1122	221	Histidine kinase
Sites
	Binding site	322	1	Phytochromobilin chromophore (covalent; via 1 link)
Experimental info
	Sequence conflict	279	1	L → F in AAA76820. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P06593-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 8AC1083533567ACF	FASTA	1,129	124,993
	10 20 30 40 50 60 MSSSRPASSS SSRNRQSSQA RVLAQTTLDA ELNAEYEESG DSFDYSKLVE AQRDGPPVQQ 70 80 90 100 110 120 GRSEKVIAYL QHIQKGKLIQ TFGCLLALDE KSFNVIAFSE NAPEMLTTVS HAVPSVDDPP 130 140 150 160 170 180 RLGIGTNVRS LFSDQGATAL HKALGFADVS LLNPILVQCK TSGKPFYAIV HRATGCLVVD 190 200 210 220 230 240 FEPVKPTEFP ATAAGALQSY KLAAKAISKI QSLPGGSMEV LCNTVVKEVF DLTGYDRVMA 250 260 270 280 290 300 YKFHEDDHGE VFSEITKPGL EPYLGLHYPA TDIPQAARLL FMKNKVRMIC DCRARSIKVI 310 320 330 340 350 360 EAEALPFDIS LCGSALRAPH SCHLQYMENM NSIASLVMAV VVNENEEDDE AESEQPAQQQ 370 380 390 400 410 420 KKKKLWGLLV CHHESPRYVP FPLRYACEFL AQVFAVHVNR EFELEKQLRE KNILKMQTML 430 440 450 460 470 480 SDMLFREASP LTIVSGTPNI MDLVKCDGAA LLYGGKVWRL RNAPTESQIH DIAFWLSDVH 490 500 510 520 530 540 RDSTGLSTDS LHDAGYPGAA ALGDMICGMA VAKINSKDIL FWFRSHTAAE IRWGGAKNDP 550 560 570 580 590 600 SDMDDSRRMH PRLSFKAFLE VVKMKSLPWS DYEMDAIHSL QLILRGTLND ASKPKREASL 610 620 630 640 650 660 DNQIGDLKLD GLAELQAVTS EMVRLMETAT VPILAVDGNG LVNGWNQKAA ELTGLRVDDA 670 680 690 700 710 720 IGRHILTLVE DSSVPVVQRM LYLALQGKEE KEVRFEVKTH GPKRDDGPVI LVVNACASRD 730 740 750 760 770 780 LHDHVVGVCF VAQDMTVHKL VMDKFTRVEG DYKAIIHNPN PLIPPIFGAD EFGWCSEWNA 790 800 810 820 830 840 AMTKLTGWNR DEVLDKMLLG EVFDSSNASC PLKNRDAFVS LCVLINSALA GEETEKAPFG 850 860 870 880 890 900 FFDRSGKYIE CLLSANRKEN EGGLITGVFC FIHVASHELQ HALQVQQASE QTSLKRLKAF 910 920 930 940 950 960 SYMRHAINNP LSGMLYSRKA LKNTDLNEEQ MKQIHVGDNC HHQINKILAD LDQDSITEKS 970 980 990 1000 1010 1020 SCLDLEMAEF LLQDVVVAAV SQVLITCQGK GIRISCNLPE RFMKQSVYGD GVRLQQILSD 1030 1040 1050 1060 1070 1080 FLFISVKFSP VGGSVEISSK LTKNSIGENL HLIDLELRIK HQGLGVPAEL MAQMFEEDNK 1090 1100 1110 1120 EQSEEGLSLL VSRNLLRLMN GDVRHLREAG VSTFIITAEL ASAPTAMGQ

References

[1]	"Analysis of cloned cDNA and genomic sequences for phytochrome: complete amino acid sequences for two gene products expressed in etiolated Avena." Hershey H.P., Barker R.F., Idler K.B., Lissemore J.L., Quail P.H. Nucleic Acids Res. 13:8543-8559(1985) [PubMed: 3001642] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"Nucleotide sequence and characterization of a gene encoding the phytochrome polypeptide from Avena." Hershey H.P., Barker R.F., Idler K.B., Murray M.G., Quail P.H. Gene 61:339-348(1987) [PubMed: 2965664] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The amino-terminal structure of oat phytochrome." Grimm R., Kellermann J., Schaefer W., Ruediger W. FEBS Lett. 234:497-499(1988) Cited for: PROTEIN SEQUENCE OF 2-13.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X03242 mRNA. Translation: CAA26999.1. M18822 Genomic DNA. Translation: AAA76820.1.
PIR	A29631.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	P06593. 1 interaction.
Organism-specific databases
Gramene	P06593.
Family and domain databases
InterPro	IPR003594. ATP_bd_ATPase. IPR003018. GAF. IPR000014. PAS. IPR013654. PAS_2. IPR013767. PAS_fold. IPR016132. Phyto_chromo_attachment. IPR013516. Phyto_chromo_BS. IPR001294. Phytochrome. IPR012129. Phytochrome_A-E. IPR013515. Phytochrome_Cr. IPR003661. Sig_transdc_His_kin_sub1_dim/P. IPR005467. Sig_transdc_His_kinase_core. [Graphical view]
Gene3D	G3DSA:3.30.565.10. ATP_bd_ATPase. 1 hit.
Pfam	PF01590. GAF. 1 hit. PF02518. HATPase_c. 1 hit. PF00512. HisKA. 1 hit. PF00989. PAS. 2 hits. PF08446. PAS_2. 1 hit. PF00360. Phytochrome. 1 hit. [Graphical view]
PIRSF	PIRSF000084. Phytochrome. 1 hit.
PRINTS	PR01033. PHYTOCHROME.
SMART	SM00065. GAF. 1 hit. SM00387. HATPase_c. 1 hit. SM00388. HisKA. 1 hit. SM00091. PAS. 2 hits. [Graphical view]
TIGRFAMs	TIGR00229. sensory_box. 1 hit.
PROSITE	PS50109. HIS_KIN. 1 hit. PS50112. PAS. 2 hits. PS00245. PHYTOCHROME_1. 1 hit. PS50046. PHYTOCHROME_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PHYA3_AVESA

Accession

Primary (citable) accession number: P06593

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 83 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)