P14712 (PHYA_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Phytochrome A

Alternative name(s):
Protein ELONGATED HYPOCOTYL 8
Protein FAR RED ELONGATED 1
Protein FAR RED ELONGATED HYPOCOTYL 2

Gene names

Name:	PHYA
Synonyms:	FHY2, FRE1, HY8
Ordered Locus Names:	At1g09570
ORF Names:	F14J9.23

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	1122 AA.
Sequence status	Complete.
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 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. Ref.6 Ref.8
Subunit structure	Homodimer. Interacts with NDPK2 and PKS4. Stabilized by interactions with PAPP5 and FYPP3 which are enhanced in the phosphorylated Pfr form. Interacts with FHY1 and FHY3; when underphosphorylated. Interacts with COP1/SPA1 complex. Ref.6 Ref.7 Ref.8 Ref.9 Ref.10
Subcellular location	Cytoplasm. Nucleus › nucleoplasm. Nucleus speckle. Note: Cytoplasmic in darkness, but translocated to the nucleus upon illumination, when associated with PAPP5 into speckles. Ref.8
Post-translational modification	Phosphorylated. Contains one covalently linked phytochromobilin chromophore By similarity.
Miscellaneous	PHYA association with FHY1 and FHY3 protect underphosphorylated PHYA from being recognized by the COP1/SPA complex.
Sequence similarities	Belongs to the phytochrome family. Contains 1 GAF domain. Contains 1 histidine kinase domain. Contains 1 PAC (PAS-associated C-terminal) domain. Contains 2 PAS (PER-ARNT-SIM) domains.

Ontologies

Keywords
Biological process	Sensory transduction Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat
Ligand	Chromophore
Molecular function	Photoreceptor protein Receptor
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	gravitropism Inferred from mutant phenotype. Source: TAIR peptidyl-histidine phosphorylation Inferred from electronic annotation. Source: InterPro photomorphogenesis Inferred from mutant phenotype. Source: TAIR phototropism Inferred from mutant phenotype. Source: TAIR protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW protein-tetrapyrrole linkage Inferred from electronic annotation. Source: InterPro red light signaling pathway Inferred from mutant phenotype. Source: TAIR regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW response to arsenic-containing substance Inferred from mutant phenotype. Source: TAIR response to continuous far red light stimulus by the high-irradiance response system Inferred from mutant phenotype. Source: TAIR response to very low fluence red light stimulus Inferred from mutant phenotype. Source: TAIR transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	membrane Inferred from electronic annotation. Source: InterPro nuclear speck Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro G-protein coupled photoreceptor activity Inferred from electronic annotation. Source: InterPro far-red light photoreceptor activity Inferred from mutant phenotype. Source: TAIR 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
itself		3	EBI-624446,EBI-624446
E1	Q80936	2	EBI-624446,EBI-1163369	From a different organism.
NDPK2	O64903	3	EBI-624446,EBI-349517
PIF3	O80536	8	EBI-624446,EBI-625701
PIF4	Q8W2F3-2	2	EBI-624446,EBI-625732
PKS1	Q9SWI1	3	EBI-624446,EBI-626200
T7H20_250	Q9LZL2	3	EBI-624446,EBI-1163353

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: P14712-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: P14712-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-108: Missing.

Note: Derived from EST data. No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1122	1122	Phytochrome A		PRO_0000171962
Regions
	Domain	218 – 402	185	GAF
	Domain	618 – 688	71	PAS 1
	Domain	748 – 822	75	PAS 2
	Domain	902 – 1119	218	Histidine kinase
Sites
	Binding site	323	1	Phytochromobilin chromophore (covalent; via 1 link) By similarity
Natural variations
	Alternative sequence	1 – 108	108	Missing in isoform 2.		VSP_036311
Experimental info
	Mutagenesis	727	1	G → E in HY8-3; no regulatory activity. Ref.2
	Sequence conflict	835	1	E → D in CAA35221. Ref.1
	Sequence conflict	862	1	E → K in CAA35221. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified December 15, 1998. Version 2. Checksum: D8B359713430744B	FASTA	1,122	124,501
	10 20 30 40 50 60 MSGSRPTQSS EGSRRSRHSA RIIAQTTVDA KLHADFEESG SSFDYSTSVR VTGPVVENQP 70 80 90 100 110 120 PRSDKVTTTY LHHIQKGKLI QPFGCLLALD EKTFKVIAYS ENASELLTMA SHAVPSVGEH 130 140 150 160 170 180 PVLGIGTDIR SLFTAPSASA LQKALGFGDV SLLNPILVHC RTSAKPFYAI IHRVTGSIII 190 200 210 220 230 240 DFEPVKPYEV PMTAAGALQS YKLAAKAITR LQSLPSGSME RLCDTMVQEV FELTGYDRVM 250 260 270 280 290 300 AYKFHEDDHG EVVSEVTKPG LEPYLGLHYP ATDIPQAARF LFMKNKVRMI VDCNAKHARV 310 320 330 340 350 360 LQDEKLSFDL TLCGSTLRAP HSCHLQYMAN MDSIASLVMA VVVNEEDGEG DAPDATTQPQ 370 380 390 400 410 420 KRKRLWGLVV CHNTTPRFVP FPLRYACEFL AQVFAIHVNK EVELDNQMVE KNILRTQTLL 430 440 450 460 470 480 CDMLMRDAPL GIVSQSPNIM DLVKCDGAAL LYKDKIWKLG TTPSEFHLQE IASWLCEYHM 490 500 510 520 530 540 DSTGLSTDSL HDAGFPRALS LGDSVCGMAA VRISSKDMIF WFRSHTAGEV RWGGAKHDPD 550 560 570 580 590 600 DRDDARRMHP RSSFKAFLEV VKTRSLPWKD YEMDAIHSLQ LILRNAFKDS ETTDVNTKVI 610 620 630 640 650 660 YSKLNDLKID GIQELEAVTS EMVRLIETAT VPILAVDSDG LVNGWNTKIA ELTGLSVDEA 670 680 690 700 710 720 IGKHFLTLVE DSSVEIVKRM LENALEGTEE QNVQFEIKTH LSRADAGPIS LVVNACASRD 730 740 750 760 770 780 LHENVVGVCF VAHDLTGQKT VMDKFTRIEG DYKAIIQNPN PLIPPIFGTD EFGWCTEWNP 790 800 810 820 830 840 AMSKLTGLKR EEVIDKMLLG EVFGTQKSCC RLKNQEAFVN LGIVLNNAVT SQDPEKVSFA 850 860 870 880 890 900 FFTRGGKYVE CLLCVSKKLD REGVVTGVFC FLQLASHELQ QALHVQRLAE RTAVKRLKAL 910 920 930 940 950 960 AYIKRQIRNP LSGIMFTRKM IEGTELGPEQ RRILQTSALC QKQLSKILDD SDLESIIEGC 970 980 990 1000 1010 1020 LDLEMKEFTL NEVLTASTSQ VMMKSNGKSV RITNETGEEV MSDTLYGDSI RLQQVLADFM 1030 1040 1050 1060 1070 1080 LMAVNFTPSG GQLTVSASLR KDQLGRSVHL ANLEIRLTHT GAGIPEFLLN QMFGTEEDVS 1090 1100 1110 1120 EEGLSLMVSR KLVKLMNGDV QYLRQAGKSS FIITAELAAA NK
	Isoform 2 [UniParc]. Checksum: 173404F60475F586	FASTA	1,014	112,622
	10 20 30 40 50 60 MASHAVPSVG EHPVLGIGTD IRSLFTAPSA SALQKALGFG DVSLLNPILV HCRTSAKPFY 70 80 90 100 110 120 AIIHRVTGSI IIDFEPVKPY EVPMTAAGAL QSYKLAAKAI TRLQSLPSGS MERLCDTMVQ 130 140 150 160 170 180 EVFELTGYDR VMAYKFHEDD HGEVVSEVTK PGLEPYLGLH YPATDIPQAA RFLFMKNKVR 190 200 210 220 230 240 MIVDCNAKHA RVLQDEKLSF DLTLCGSTLR APHSCHLQYM ANMDSIASLV MAVVVNEEDG 250 260 270 280 290 300 EGDAPDATTQ PQKRKRLWGL VVCHNTTPRF VPFPLRYACE FLAQVFAIHV NKEVELDNQM 310 320 330 340 350 360 VEKNILRTQT LLCDMLMRDA PLGIVSQSPN IMDLVKCDGA ALLYKDKIWK LGTTPSEFHL 370 380 390 400 410 420 QEIASWLCEY HMDSTGLSTD SLHDAGFPRA LSLGDSVCGM AAVRISSKDM IFWFRSHTAG 430 440 450 460 470 480 EVRWGGAKHD PDDRDDARRM HPRSSFKAFL EVVKTRSLPW KDYEMDAIHS LQLILRNAFK 490 500 510 520 530 540 DSETTDVNTK VIYSKLNDLK IDGIQELEAV TSEMVRLIET ATVPILAVDS DGLVNGWNTK 550 560 570 580 590 600 IAELTGLSVD EAIGKHFLTL VEDSSVEIVK RMLENALEGT EEQNVQFEIK THLSRADAGP 610 620 630 640 650 660 ISLVVNACAS RDLHENVVGV CFVAHDLTGQ KTVMDKFTRI EGDYKAIIQN PNPLIPPIFG 670 680 690 700 710 720 TDEFGWCTEW NPAMSKLTGL KREEVIDKML LGEVFGTQKS CCRLKNQEAF VNLGIVLNNA 730 740 750 760 770 780 VTSQDPEKVS FAFFTRGGKY VECLLCVSKK LDREGVVTGV FCFLQLASHE LQQALHVQRL 790 800 810 820 830 840 AERTAVKRLK ALAYIKRQIR NPLSGIMFTR KMIEGTELGP EQRRILQTSA LCQKQLSKIL 850 860 870 880 890 900 DDSDLESIIE GCLDLEMKEF TLNEVLTAST SQVMMKSNGK SVRITNETGE EVMSDTLYGD 910 920 930 940 950 960 SIRLQQVLAD FMLMAVNFTP SGGQLTVSAS LRKDQLGRSV HLANLEIRLT HTGAGIPEFL 970 980 990 1000 1010 LNQMFGTEED VSEEGLSLMV SRKLVKLMNG DVQYLRQAGK SSFIITAELA AANK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family." Sharrock R.A., Quail P.H. Genes Dev. 3:1745-1757(1989) [PubMed: 2606345] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1). Strain: cv. Columbia.
[2]	"Arabidopsis HY8 locus encodes phytochrome A." Dehesh K., Franci C., Parks B.M., Seeley K.A., Short T.W., Tepperman J.M., Quail P.H. Plant Cell 5:1081-1088(1993) [PubMed: 8400877] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF GLY-727. Strain: cv. RLD.
[3]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[5]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Strain: cv. Columbia.
[6]	"A phytochrome-associated protein phosphatase 2A modulates light signals in flowering time control in Arabidopsis." Kim D.-H., Kang J.-G., Yang S.-S., Chung K.-S., Song P.-S., Park C.-M. Plant Cell 14:3043-3056(2002) [PubMed: 12468726] [Abstract] Cited for: FUNCTION, INTERACTION WITH FYPP3.
[7]	"Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling." Im Y.J., Kim J.I., Shen Y., Na Y., Han Y.J., Kim S.H., Song P.S., Eom S.H. J. Mol. Biol. 343:659-670(2004) [PubMed: 15465053] [Abstract] Cited for: INTERACTION WITH NDPK2.
[8]	"Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer." Ryu J.S., Kim J.-I., Kunkel T., Kim B.C., Cho D.S., Hong S.H., Kim S.-H., Fernandez A.P., Kim Y., Alonso J.M., Ecker J.R., Nagy F., Lim P.O., Song P.-S., Schaefer E., Nam H.G. Cell 120:395-406(2005) [PubMed: 15707897] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH PAPP5 AND NDPK2.
[9]	"Arabidopsis COP1/SPA1 complex and FHY1/FHY3 associate with distinct phosphorylated forms of phytochrome A in balancing light signaling." Saijo Y., Zhu D., Li J., Rubio V., Zhou Z., Shen Y., Hoecker U., Wang H., Deng X.W. Mol. Cell 31:607-613(2008) [PubMed: 18722184] [Abstract] Cited for: INTERACTION WITH COP1; SPA1; FHY1 AND FHY3.
[10]	"PHYTOCHROME KINASE SUBSTRATE4 modulates phytochrome-mediated control of hypocotyl growth orientation." Schepens I., Boccalandro H.E., Kami C., Casal J.J., Fankhauser C. Plant Physiol. 147:661-671(2008) [PubMed: 18390804] [Abstract] Cited for: INTERACTION WITH PKS4.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X17341 mRNA. Translation: CAA35221.1. L21154 Genomic DNA. Translation: AAA21351.1. AC003970 Genomic DNA. Translation: AAC33219.1. CP002684 Genomic DNA. Translation: AEE28462.1. CP002684 Genomic DNA. Translation: AEE28463.1. AY039520 mRNA. Translation: AAK62577.1.
IPI	IPI00535033. IPI00891850.
PIR	FKMUA. A33473. D86229.
RefSeq	NP_001117256.1. NM_001123784.1. NP_172428.1. NM_100828.3.
UniGene	At.22828.
3D structure databases
ProteinModelPortal	P14712.
SMR	P14712. Positions 74-585.
ModBase	Search...
Protein-protein interaction databases
IntAct	P14712. 14 interactions.
MINT	MINT-1174780.
STRING	P14712.
Proteomic databases
PRIDE	P14712.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G09570.1; AT1G09570.1; AT1G09570.
GeneID	837483.
GenomeReviews	Gene locus AT1G09570 in contig CT485782_GR.
KEGG	ath:AT1G09570.
NMPDR	fig|3702.1.peg.1183.
Organism-specific databases
TAIR	At1g09570.
Phylogenomic databases
eggNOG	KOG0519.
GeneTree	EPGT00050000008838.
HOGENOM	HBG318405.
InParanoid	P14712.
OMA	RWGGAKH.
PhylomeDB	P14712.
ProtClustDB	CLSN2679275.
Gene expression databases
ArrayExpress	P14712.
Genevestigator	P14712.
GermOnline	AT1G09570. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR003594. ATPase-like_ATP-bd. IPR003018. GAF. IPR001610. PAC. 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. 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.
KO	K12120.
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. [Graphical view]
PIRSF	PIRSF000084. Phytochrome. 1 hit.
PRINTS	PR01033. PHYTOCHROME.
SMART	SM00065. GAF. 1 hit. SM00387. HATPase_c. 1 hit. SM00388. HisKA. 1 hit. SM00086. PAC. 1 hit. SM00091. PAS. 2 hits. [Graphical view]
SUPFAM	SSF55874. ATP_bd_ATPase. 1 hit.
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

PHYA_ARATH

Accession

Primary (citable) accession number: P14712
Secondary accession number(s): B3H6K9

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	December 15, 1998
Last modified:	January 25, 2012
This is version 124 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program