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O80536 (PIF3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 121. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length524 AA.
Sequence statusComplete.
Protein existenceEvidence 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 bHLH (basic helix-loop-helix) domain.

Ontologies

Keywords
   Biological processPhytochrome signaling pathway
Transcription
Transcription regulation
   Cellular componentNucleus
   LigandDNA-binding
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processde-etiolation

Inferred from mutant phenotype PubMed 18252845. Source: TAIR

gibberellic acid mediated signaling pathway

Inferred from mutant phenotype PubMed 18053005. Source: TAIR

positive regulation of anthocyanin metabolic process

Inferred from mutant phenotype PubMed 17319847. Source: TAIR

red or far-red light signaling pathway

Inferred from mutant phenotype PubMed 10318970. Source: TAIR

red, far-red light phototransduction

Inferred from electronic annotation. Source: UniProtKB-KW

regulation of transcription, DNA-templated

Traceable author statement Ref.11. Source: TAIR

response to red or far red light

Inferred from mutant phenotype PubMed 10318970. Source: TAIR

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from direct assay Ref.1. Source: TAIR

   Molecular_functionDNA binding

Inferred from direct assay PubMed 17319847. Source: TAIR

identical protein binding

Inferred from physical interaction PubMed 10995393Ref.11PubMed 21928113. Source: IntAct

protein binding

Inferred from physical interaction Ref.8PubMed 10995393PubMed 11069292PubMed 12006496Ref.11PubMed 15155879PubMed 15448264PubMed 15486100PubMed 15486102PubMed 19286967PubMed 21928113PubMed 22904146Ref.1. Source: IntAct

sequence-specific DNA binding transcription factor activity

Inferred from sequence or structural similarity PubMed 11118137Ref.2. Source: TAIR

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 524524Transcription factor PIF3
PRO_0000127428

Regions

Domain343 – 39250bHLH
Compositional bias353 – 3586Poly-Arg
Compositional bias422 – 4287Poly-Ala

Natural variations

Natural variant1241E → D in strain: cv. An-2 and cv. Su-0. Ref.7
Natural variant1411K → N in strain: cv. An-2 and cv. Su-0. Ref.7
Natural variant1761Q → H in strain: cv. An-2 and cv. Su-0. Ref.7
Natural variant1861Q → K in strain: cv. An-2 and cv. Su-0. Ref.7
Natural variant2091F → L in strain: cv. An-2 and cv. Su-0. Ref.7
Natural variant2201T → I in strain: cv. An-2 and cv. Su-0. Ref.7
Natural variant2361V → I in strain: cv. An-2 and cv. Su-0. Ref.7

Experimental info

Sequence conflict151E → D in AAC99771. Ref.3
Sequence conflict3441S → L in AAC99771. Ref.3

Sequences

Sequence LengthMass (Da)Tools
O80536 [UniParc].

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

FASTA52456,990
        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' 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] [Europe PMC] [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] [Europe PMC] [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. expand/collapse author list , 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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.
PIRH86228.
RefSeqNP_172424.1. NM_100824.2.
NP_849626.1. NM_179295.2.
UniGeneAt.10926.

3D structure databases

ProteinModelPortalO80536.
SMRO80536. Positions 346-395.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid22720. 21 interactions.
DIPDIP-33892N.
IntActO80536. 12 interactions.
MINTMINT-8058904.

Proteomic databases

PRIDEO80536.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT1G09530.1; AT1G09530.1; AT1G09530.
AT1G09530.2; AT1G09530.2; AT1G09530.
GeneID837479.
KEGGath:AT1G09530.

Organism-specific databases

TAIRAT1G09530.

Phylogenomic databases

eggNOGNOG285764.
InParanoidO80536.
KOK12126.
OMAQIMSMAS.
PhylomeDBO80536.

Gene expression databases

GenevestigatorO80536.

Family and domain databases

Gene3D4.10.280.10. 1 hit.
InterProIPR011598. bHLH_dom.
[Graphical view]
PfamPF00010. HLH. 1 hit.
[Graphical view]
SMARTSM00353. HLH. 1 hit.
[Graphical view]
SUPFAMSSF47459. SSF47459. 1 hit.
PROSITEPS50888. BHLH. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePIF3_ARATH
AccessionPrimary (citable) accession number: O80536
Secondary accession number(s): A5Y7A2 expand/collapse secondary AC list , 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 11, 2014
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names