Reviewed, UniProtKB/Swiss-Prot O80536 (PIF3_ARATH)

Names and origin

Protein names

Recommended name:
    Transcription factor PIF3
Alternative name(s):
    Phytochrome-interacting factor 3
    Phytochrome-associated protein 3
    Transcription factor EN 100
    bHLH transcription factor bHLH008
    Basic helix-loop-helix protein 8
      Short name=bHLH 8
      Short name=AtbHLH8

Gene names

Name:	PIF3
Synonyms:	BHLH8, EN100, PAP3
Ordered Locus Names:	At1g09530
ORF Names:	F14J9.19

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	524 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Transcription factor acting positively in the phytochrome signaling pathway. Activates transcription by binding to the G box (5'-CACGTG-3'). Ref.7 Ref.8
Subunit structure	Homodimer Probable. Can form a heterodimer with REP1 and PIF4. Phytochrome B binds specifically to DNA-bound PIF3, but only upon red light induced conversion to the Pfr form (PfrB). Reconversion to Pr form causes rapid dissociation. Interacts with APRR1/TOC1.
Subcellular location	Nucleus.
Induction	By UV treatment. Ref.2
Sequence similarities	Contains 1 basic helix-loop-helix (bHLH) domain.

Ontologies

Keywords
Biological process	Phytochrome signaling pathway Transcription Transcription regulation
Cellular component	Nucleus
Ligand	DNA-binding
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	de-etiolation Inferred from mutant phenotype. Source: TAIR gibberellic acid mediated signaling Inferred from mutant phenotype. Source: TAIR positive regulation of anthocyanin metabolic process Inferred from mutant phenotype. Source: TAIR red or far red light signaling pathway Inferred from mutant phenotype. Source: TAIR red, far-red light phototransduction Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Ref.1 Inferred from direct assay. Source: TAIR
Molecular function	DNA binding Inferred from direct assay. Source: TAIR identical protein binding Inferred from physical interaction. Source: IntAct transcription regulator activity Ref.10 Traceable author statement. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-625701,EBI-625701
HFR1	Q9FE22	1	EBI-625701,EBI-626001
PHYA	P14712	6	EBI-625701,EBI-624446
PHYB	P14713	13	EBI-625701,EBI-300727
PIF4	Q8W2F3-2	1	EBI-625701,EBI-625732

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 524	524	Transcription factor PIF3		PRO_0000127428
Regions
	Domain	357 – 397	41	Helix-loop-helix motif
	DNA binding	340 – 356	17	Basic motif
	Compositional bias	353 – 358	6	Poly-Arg
	Compositional bias	422 – 428	7	Poly-Ala
Natural variations
	Natural variant	124	1	E → D in strain: cv. An-2 and cv. Su-0. Ref.6
	Natural variant	141	1	K → N in strain: cv. An-2 and cv. Su-0. Ref.6
	Natural variant	176	1	Q → H in strain: cv. An-2 and cv. Su-0. Ref.6
	Natural variant	186	1	Q → K in strain: cv. An-2 and cv. Su-0. Ref.6
	Natural variant	209	1	F → L in strain: cv. An-2 and cv. Su-0. Ref.6
	Natural variant	220	1	T → I in strain: cv. An-2 and cv. Su-0. Ref.6
	Natural variant	236	1	V → I in strain: cv. An-2 and cv. Su-0. Ref.6
Experimental info
	Sequence conflict	15	1	E → D in AAC99771. Ref.3
	Sequence conflict	344	1	S → L in AAC99771. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	O80536-1 [UniParc]. Last modified November 1, 1998. Version 1. Checksum: 1044AC01D598DE7C	FASTA	524	56,990
	10 20 30 40 50 60 MPLFELFRLT KAKLESAQDR NPSPPVDEVV ELVWENGQIS TQSQSSRSRN IPPPQANSSR 70 80 90 100 110 120 AREIGNGSKT TMVDEIPMSV PSLMTGLSQD DDFVPWLNHH PSLDGYCSDF LRDVSSPVTV 130 140 150 160 170 180 NEQESDMAVN QTAFPLFQRR KDGNESAPAA SSSQYNGFQS HSLYGSDRAR DLPSQQTNPD 190 200 210 220 230 240 RFTQTQEPLI TSNKPSLVNF SHFLRPATFA KTTNNNLHDT KEKSPQSPPN VFQTRVLGAK 250 260 270 280 290 300 DSEDKVLNES VASATPKDNQ KACLISEDSC RKDQESEKAV VCSSVGSGNS LDGPSESPSL 310 320 330 340 350 360 SLKRKHSNIQ DIDCHSEDVE EESGDGRKEA GPSRTGLGSK RSRSAEVHNL SERRRRDRIN 370 380 390 400 410 420 EKMRALQELI PNCNKVDKAS MLDEAIEYLK SLQLQVQIMS MASGYYLPPA VMFPPGMGHY 430 440 450 460 470 480 PAAAAAMAMG MGMPYAMGLP DLSRGGSSVN HGPQFQVSGM QQQPVAMGIP RVSGGGIFAG 490 500 510 520 SSTIGNGSTR DLSGSKDQTT TNNNSNLKPI KRKQGSSDQF CGSS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein." Ni M., Tepperman J.M., Quail P.H. Cell 95:657-667(1998) [PubMed: 9845368] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA]. Strain: cv. Columbia.
[2]	"The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity." Heim M.A., Jakoby M., Werber M., Martin C., Weisshaar B., Bailey P.C. Mol. Biol. Evol. 20:735-747(2003) [PubMed: 12679534] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], INDUCTION BY UV LIGHT, GENE FAMILY, NOMENCLATURE. Strain: cv. Columbia.
[3]	"Identification and characterization of three phytochrome-associated proteins." Lee J., Yi H., Shin B., Song P.-S., Choi G. Submitted (AUG-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Columbia.
[4]	"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.
[5]	"Functional annotation of a full-length Arabidopsis cDNA collection." Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A., Shinozaki K. Science 296:141-145(2002) [PubMed: 11910074] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[6]	"Sequence diversity and haplotype associations with phenotypic responses to crowding: GIGANTEA affects fruit set in Arabidopsis thaliana." Brock M.T., Tiffin P., Weinig C. Mol. Ecol. 16:3050-3062(2007) [PubMed: 17614917] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 12-272, VARIANTS ASP-124; ASN-141; HIS-176; LYS-186; LEU-209; ILE-220 AND ILE-236. Strain: cv. An-2, cv. Bla-6, cv. Br-0, cv. Bu-2, cv. Columbia, cv. Di-1, cv. Et-0, cv. Kl-1, cv. Li-5:3, cv. Ma-2, cv. Mt-0, cv. Pa-2, cv. Pi-0, cv. Su-0 and cv. Tsu-1.
[7]	"Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light." Ni M., Tepperman J.M., Quail P.H. Nature 400:781-784(1999) [PubMed: 10466729] [Abstract] Cited for: FUNCTION.
[8]	"Direct targeting of light signals to a promoter element-bound transcription factor." Martinez-Garcia J.F., Huq E., Quail P.H. Science 288:859-863(2000) [PubMed: 10797009] [Abstract] Cited for: FUNCTION.
[9]	"The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants." Makino S., Matsushika A., Kojima M., Yamashino T., Mizuno T. Plant Cell Physiol. 43:58-69(2002) [PubMed: 11828023] [Abstract] Cited for: INTERACTION WITH APRR1.
[10]	"The Arabidopsis basic/helix-loop-helix transcription factor family." Toledo-Ortiz G., Huq E., Quail P.H. Plant Cell 15:1749-1770(2003) [PubMed: 12897250] [Abstract] Cited for: GENE FAMILY, INTERACTION WITH PIF4.
[11]	"A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana." Yamashino T., Matsushika A., Fujimori T., Sato S., Kato T., Tabata S., Mizuno T. Plant Cell Physiol. 44:619-629(2003) [PubMed: 12826627] [Abstract] Cited for: INTERACTION WITH APRR1.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF100166 mRNA. Translation: AAC95156.1. AF251693 mRNA. Translation: AAL55715.1. AF088280 mRNA. Translation: AAC99771.1. AC003970 Genomic DNA. Translation: AAC33213.1. AK117255 mRNA. Translation: BAC41930.1. EF193482 Genomic DNA. Translation: ABP96435.1. EF193483 Genomic DNA. Translation: ABP96436.1. EF193484 Genomic DNA. Translation: ABP96437.1. EF193485 Genomic DNA. Translation: ABP96438.1. EF193486 Genomic DNA. Translation: ABP96439.1. EF193487 Genomic DNA. Translation: ABP96440.1. EF193488 Genomic DNA. Translation: ABP96441.1. EF193489 Genomic DNA. Translation: ABP96442.1. EF193490 Genomic DNA. Translation: ABP96443.1. EF193491 Genomic DNA. Translation: ABP96444.1. EF193492 Genomic DNA. Translation: ABP96445.1. EF193493 Genomic DNA. Translation: ABP96446.1. EF193494 Genomic DNA. Translation: ABP96447.1. EF193495 Genomic DNA. Translation: ABP96448.1. EF193496 Genomic DNA. Translation: ABP96449.1.
IPI	IPI00530297.
PIR	H86228.
RefSeq	NP_172424.1. NP_849626.1.
UniGene	At.10926
3D structure databases
HSSP	HSSP built from PDB template 1HLO based on UniProtKB P25912.
ModBase	Search...
Protein-protein interaction databases
IntAct	O80536. 10 interactions.
Genome annotation databases
GeneID	837479.
GenomeReviews	Gene locus AT1G09530 in contig CT485782_GR.
KEGG	ath:AT1G09530.
NMPDR	fig|3702.1.peg.1178.
Organism-specific databases
TAIR	At1g09530.
Phylogenomic databases
OMA	O80536. SSHEAIQ.
Gene expression databases
ArrayExpress	O80536.
GermOnline	AT1G09530. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR001092. HLH_basic. IPR011598. HLH_DNA_bd. [Graphical view]
Gene3D	G3DSA:4.10.280.10. HLH_DNA_bd. 1 hit.
Pfam	PF00010. HLH. 1 hit. [Graphical view]
SMART	SM00353. HLH. 1 hit. [Graphical view]
PROSITE	PS50888. HLH. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PIF3_ARATH

Accession

Primary (citable) accession number: O80536
Secondary accession number(s): A5Y7A2 , A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, Q9SBC5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2002
Last sequence update:	November 1, 1998
Last modified:	June 16, 2009
This is version 74 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)