Transcription factor PIF3 - Arabidopsis thaliana (Mouse-ear cress)

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O80536 (PIF3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 100. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Transcription factor PIF3

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

Gene names

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

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	524 AA.
Sequence status	Complete.
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.8 Ref.9
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. Ref.10 Ref.11 Ref.12
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 Reference proteome
Gene Ontology (GO)
Biological process	de-etiolation Inferred from mutant phenotype. Source: TAIR gibberellic acid mediated signaling pathway Inferred from mutant phenotype. Source: TAIR positive regulation of anthocyanin metabolic process Inferred from mutant phenotype. Source: TAIR red, far-red light phototransduction Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Traceable author statement Ref.11. Source: TAIR transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from direct assay Ref.1. Source: TAIR
Molecular function	DNA binding Inferred from direct assay. Source: TAIR protein binding Inferred from physical interaction Ref.11 Ref.1. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
HFR1	Q9FE22	6	EBI-625701,EBI-626001
PHYA	P14712	8	EBI-625701,EBI-624446
PHYB	P14713	17	EBI-625701,EBI-300727
PIF4	Q8W2F3-2	3	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

Helix-loop-helix motif

DNA binding

340 – 356

Basic motif

Compositional bias

353 – 358

Poly-Arg

Compositional bias

422 – 428

Poly-Ala

Natural variations

Natural variant

124

E → D in strain: cv. An-2 and cv. Su-0. Ref.7

Natural variant

141

K → N in strain: cv. An-2 and cv. Su-0. Ref.7

Natural variant

176

Q → H in strain: cv. An-2 and cv. Su-0. Ref.7

Natural variant

186

Q → K in strain: cv. An-2 and cv. Su-0. Ref.7

Natural variant

209

F → L in strain: cv. An-2 and cv. Su-0. Ref.7

Natural variant

220

T → I in strain: cv. An-2 and cv. Su-0. Ref.7

Natural variant

236

V → I in strain: cv. An-2 and cv. Su-0. Ref.7

Experimental info

Sequence conflict

E → D in AAC99771. Ref.3

Sequence conflict

344

S → L in AAC99771. Ref.3

Sequences

Sequence

Length

Mass (Da)

Tools

O80536 [UniParc].

Last modified November 1, 1998. Version 1.
Checksum: 1044AC01D598DE7C
Show »

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

« Hide

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. Davis R.W. Nature 408:816-820(2000) [PubMed: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[5]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[6]	"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.
[7]	"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.
[8]	"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.
[9]	"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.
[10]	"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.
[11]	"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.
[12]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF100166 mRNA. Translation: AAC95156.1. AF251693 mRNA. Translation: AAL55715.1. AF088280 mRNA. Translation: AAC99771.1. AC003970 Genomic DNA. Translation: AAC33213.1. CP002684 Genomic DNA. Translation: AEE28457.1. CP002684 Genomic DNA. Translation: AEE28458.1. 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. NM_100824.2. NP_849626.1. NM_179295.2.
UniGene	At.10926.
3D structure databases
ProteinModelPortal	O80536.
SMR	O80536. Positions 348-397.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-33892N.
IntAct	O80536. 12 interactions.
STRING	O80536.
Proteomic databases
PRIDE	O80536.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G09530.1; AT1G09530.1; AT1G09530. AT1G09530.2; AT1G09530.2; AT1G09530.
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
GeneTree	EPGT00050000008845.
InParanoid	O80536.
OMA	WENGQIS.
PhylomeDB	O80536.
ProtClustDB	CLSN2679266.
Gene expression databases
ArrayExpress	O80536.
Genevestigator	O80536.
GermOnline	AT1G09530. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR011598. HLH_DNA-bd. [Graphical view]
Gene3D	G3DSA:4.10.280.10. HLH_DNA_bd. 1 hit.
KO	K12126.
Pfam	PF00010. HLH. 1 hit. [Graphical view]
SMART	SM00353. HLH. 1 hit. [Graphical view]
SUPFAM	SSF47459. HLH_basic. 1 hit.
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

Q9SBC5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2002
Last sequence update:	November 1, 1998
Last modified:	December 14, 2011
This is version 100 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Natural variations

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents