Entry euk:PIF3_ARATH

ID   PIF3_ARATH              Reviewed;         524 AA.
AC   O80536; A5Y7A2; A5Y7A3; A5Y7A4; A5Y7A5; A5Y7A6; A5Y7A7; A5Y7A8;
AC   A5Y7A9; A5Y7B0; A5Y7B1; A5Y7B2; A5Y7B3; A5Y7B4; A5Y7B5; A5Y7B6;
AC   Q9SBC5;
DT   10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1998, sequence version 1.
DT   10-MAY-2017, entry version 143.
DE   RecName: Full=Transcription factor PIF3;
DE   AltName: Full=Basic helix-loop-helix protein 8;
DE            Short=AtbHLH8;
DE            Short=bHLH 8;
DE   AltName: Full=Phytochrome-associated protein 3;
DE   AltName: Full=Phytochrome-interacting factor 3;
DE   AltName: Full=Transcription factor EN 100;
DE   AltName: Full=bHLH transcription factor bHLH008;
GN   Name=PIF3; Synonyms=BHLH8, EN100, PAP3; OrderedLocusNames=At1g09530;
GN   ORFNames=F14J9.19;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=9845368; DOI=10.1016/S0092-8674(00)81636-0;
RA   Ni M., Tepperman J.M., Quail P.H.;
RT   "PIF3, a phytochrome-interacting factor necessary for normal
RT   photoinduced signal transduction, is a novel basic helix-loop-helix
RT   protein.";
RL   Cell 95:657-667(1998).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA], INDUCTION BY UV LIGHT, GENE FAMILY, AND
RP   NOMENCLATURE.
RC   STRAIN=cv. Columbia;
RX   PubMed=12679534; DOI=10.1093/molbev/msg088;
RA   Heim M.A., Jakoby M., Werber M., Martin C., Weisshaar B., Bailey P.C.;
RT   "The basic helix-loop-helix transcription factor family in plants: a
RT   genome-wide study of protein structure and functional diversity.";
RL   Mol. Biol. Evol. 20:735-747(2003).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   STRAIN=cv. Columbia;
RA   Lee J., Yi H., Shin B., Song P.-S., Choi G.;
RT   "Identification and characterization of three phytochrome-associated
RT   proteins.";
RL   Submitted (AUG-1998) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130712; DOI=10.1038/35048500;
RA   Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S.,
RA   White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
RA   Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
RA   Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
RA   Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
RA   Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
RA   Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
RA   Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
RA   Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
RA   Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
RA   Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
RA   Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
RA   Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
RA   Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA   Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M.,
RA   Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis
RT   thaliana.";
RL   Nature 408:816-820(2000).
RN   [5]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Portal (Araport);
RL   Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11910074; DOI=10.1126/science.1071006;
RA   Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA   Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M.,
RA   Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T.,
RA   Shibata K., Shinagawa A., Shinozaki K.;
RT   "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL   Science 296:141-145(2002).
RN   [7]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 12-272, AND VARIANTS ASP-124;
RP   ASN-141; HIS-176; LYS-186; LEU-209; ILE-220 AND ILE-236.
RC   STRAIN=cv. An-2, cv. Bla-6, cv. Br-0, cv. Bu-2, cv. Columbia,
RC   cv. Di-1, cv. Et-0, cv. Kl-1, cv. Li-5:3, cv. Ma-2, cv. Mt-0,
RC   cv. Pa-2, cv. Pi-0, cv. Su-0, and cv. Tsu-1;
RX   PubMed=17614917; DOI=10.1111/j.1365-294X.2007.03298.x;
RA   Brock M.T., Tiffin P., Weinig C.;
RT   "Sequence diversity and haplotype associations with phenotypic
RT   responses to crowding: GIGANTEA affects fruit set in Arabidopsis
RT   thaliana.";
RL   Mol. Ecol. 16:3050-3062(2007).
RN   [8]
RP   FUNCTION.
RX   PubMed=10466729; DOI=10.1038/23500;
RA   Ni M., Tepperman J.M., Quail P.H.;
RT   "Binding of phytochrome B to its nuclear signalling partner PIF3 is
RT   reversibly induced by light.";
RL   Nature 400:781-784(1999).
RN   [9]
RP   FUNCTION.
RX   PubMed=10797009; DOI=10.1126/science.288.5467.859;
RA   Martinez-Garcia J.F., Huq E., Quail P.H.;
RT   "Direct targeting of light signals to a promoter element-bound
RT   transcription factor.";
RL   Science 288:859-863(2000).
RN   [10]
RP   INTERACTION WITH APRR1.
RX   PubMed=11828023; DOI=10.1093/pcp/pcf005;
RA   Makino S., Matsushika A., Kojima M., Yamashino T., Mizuno T.;
RT   "The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis
RT   thaliana: I. Characterization with APRR1-overexpressing plants.";
RL   Plant Cell Physiol. 43:58-69(2002).
RN   [11]
RP   GENE FAMILY, AND INTERACTION WITH PIF4.
RX   PubMed=12897250; DOI=10.1105/tpc.013839;
RA   Toledo-Ortiz G., Huq E., Quail P.H.;
RT   "The Arabidopsis basic/helix-loop-helix transcription factor family.";
RL   Plant Cell 15:1749-1770(2003).
RN   [12]
RP   GENE FAMILY, AND NOMENCLATURE.
RX   PubMed=14600211; DOI=10.1105/tpc.151140;
RA   Bailey P.C., Martin C., Toledo-Ortiz G., Quail P.H., Huq E.,
RA   Heim M.A., Jakoby M., Werber M., Weisshaar B.;
RT   "Update on the basic helix-loop-helix transcription factor gene family
RT   in Arabidopsis thaliana.";
RL   Plant Cell 15:2497-2502(2003).
RN   [13]
RP   INTERACTION WITH APRR1.
RX   PubMed=12826627; DOI=10.1093/pcp/pcg078;
RA   Yamashino T., Matsushika A., Fujimori T., Sato S., Kato T., Tabata S.,
RA   Mizuno T.;
RT   "A link between circadian-controlled bHLH factors and the APRR1/TOC1
RT   quintet in Arabidopsis thaliana.";
RL   Plant Cell Physiol. 44:619-629(2003).
RN   [14]
RP   INTERACTION WITH PIA2, AND PHOSPHORYLATION BY PHYA.
RC   STRAIN=cv. Columbia;
RX   PubMed=27143545; DOI=10.1093/jb/mvw031;
RA   Yoo J., Cho M.-H., Lee S.-W., Bhoo S.H.;
RT   "Phytochrome-interacting ankyrin repeat protein 2 modulates
RT   phytochrome A-mediated PIF3 phosphorylation in light signal
RT   transduction.";
RL   J. Biochem. 160:243-249(2016).
CC   -!- FUNCTION: Transcription factor acting positively in the
CC       phytochrome signaling pathway. Activates transcription by binding
CC       to the G box (5'-CACGTG-3'). {ECO:0000269|PubMed:10466729,
CC       ECO:0000269|PubMed:10797009}.
CC   -!- SUBUNIT: Homodimer (Probable). Can form a heterodimer with REP1
CC       and PIF4. Phytochrome B binds specifically to DNA-bound PIF3, but
CC       only upon red light induced conversion to the Pfr form (PfrB).
CC       Reconversion to Pr form causes rapid dissociation. Interacts with
CC       APRR1/TOC1. Binds to PIA2; this interaction may trigger the
CC       repression of PHYA-mediated phosphorylation (PubMed:27143545).
CC       {ECO:0000269|PubMed:11828023, ECO:0000269|PubMed:12826627,
CC       ECO:0000269|PubMed:12897250, ECO:0000269|PubMed:27143545,
CC       ECO:0000305}.
CC   -!- INTERACTION:
CC       Self; NbExp=3; IntAct=EBI-625701, EBI-625701;
CC       Q9FE22:HFR1; NbExp=6; IntAct=EBI-625701, EBI-626001;
CC       P14712:PHYA; NbExp=8; IntAct=EBI-625701, EBI-624446;
CC       P14713:PHYB; NbExp=19; IntAct=EBI-625701, EBI-300727;
CC       Q8GZM7:PIF1; NbExp=6; IntAct=EBI-625701, EBI-630400;
CC       Q8W2F3-2:PIF4; NbExp=3; IntAct=EBI-625701, EBI-625732;
CC   -!- SUBCELLULAR LOCATION: Nucleus.
CC   -!- INDUCTION: By UV treatment. {ECO:0000269|PubMed:12679534}.
CC   -!- PTM: Phosphorylated by PHYA; this phosphorylation is repressed by
CC       PIA2. {ECO:0000269|PubMed:27143545}.
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DR   EMBL; AF100166; AAC95156.1; -; mRNA.
DR   EMBL; AF251693; AAL55715.1; -; mRNA.
DR   EMBL; AF088280; AAC99771.1; -; mRNA.
DR   EMBL; AC003970; AAC33213.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE28457.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE28458.1; -; Genomic_DNA.
DR   EMBL; CP002684; ANM60410.1; -; Genomic_DNA.
DR   EMBL; CP002684; ANM60411.1; -; Genomic_DNA.
DR   EMBL; CP002684; ANM60412.1; -; Genomic_DNA.
DR   EMBL; CP002684; ANM60413.1; -; Genomic_DNA.
DR   EMBL; AK117255; BAC41930.1; -; mRNA.
DR   EMBL; EF193482; ABP96435.1; -; Genomic_DNA.
DR   EMBL; EF193483; ABP96436.1; -; Genomic_DNA.
DR   EMBL; EF193484; ABP96437.1; -; Genomic_DNA.
DR   EMBL; EF193485; ABP96438.1; -; Genomic_DNA.
DR   EMBL; EF193486; ABP96439.1; -; Genomic_DNA.
DR   EMBL; EF193487; ABP96440.1; -; Genomic_DNA.
DR   EMBL; EF193488; ABP96441.1; -; Genomic_DNA.
DR   EMBL; EF193489; ABP96442.1; -; Genomic_DNA.
DR   EMBL; EF193490; ABP96443.1; -; Genomic_DNA.
DR   EMBL; EF193491; ABP96444.1; -; Genomic_DNA.
DR   EMBL; EF193492; ABP96445.1; -; Genomic_DNA.
DR   EMBL; EF193493; ABP96446.1; -; Genomic_DNA.
DR   EMBL; EF193494; ABP96447.1; -; Genomic_DNA.
DR   EMBL; EF193495; ABP96448.1; -; Genomic_DNA.
DR   EMBL; EF193496; ABP96449.1; -; Genomic_DNA.
DR   PIR; H86228; H86228.
DR   RefSeq; NP_001318964.1; NM_001331836.1.
DR   RefSeq; NP_001318965.1; NM_001331837.1.
DR   RefSeq; NP_001322700.1; NM_001331838.1.
DR   RefSeq; NP_001322701.1; NM_001331839.1.
DR   RefSeq; NP_172424.1; NM_100824.3.
DR   RefSeq; NP_849626.1; NM_179295.3.
DR   UniGene; At.10926; -.
DR   ProteinModelPortal; O80536; -.
DR   SMR; O80536; -.
DR   BioGrid; 22720; 33.
DR   DIP; DIP-33892N; -.
DR   IntAct; O80536; 12.
DR   MINT; MINT-8058904; -.
DR   STRING; 3702.AT1G09530.1; -.
DR   PaxDb; O80536; -.
DR   EnsemblPlants; AT1G09530.1; AT1G09530.1; AT1G09530.
DR   EnsemblPlants; AT1G09530.2; AT1G09530.2; AT1G09530.
DR   EnsemblPlants; AT1G09530.3; AT1G09530.3; AT1G09530.
DR   EnsemblPlants; AT1G09530.4; AT1G09530.4; AT1G09530.
DR   EnsemblPlants; AT1G09530.5; AT1G09530.5; AT1G09530.
DR   EnsemblPlants; AT1G09530.6; AT1G09530.6; AT1G09530.
DR   GeneID; 837479; -.
DR   Gramene; AT1G09530.1; AT1G09530.1; AT1G09530.
DR   Gramene; AT1G09530.2; AT1G09530.2; AT1G09530.
DR   Gramene; AT1G09530.3; AT1G09530.3; AT1G09530.
DR   Gramene; AT1G09530.4; AT1G09530.4; AT1G09530.
DR   Gramene; AT1G09530.5; AT1G09530.5; AT1G09530.
DR   Gramene; AT1G09530.6; AT1G09530.6; AT1G09530.
DR   KEGG; ath:AT1G09530; -.
DR   Araport; AT1G09530; -.
DR   TAIR; locus:2012345; AT1G09530.
DR   eggNOG; ENOG410IV8V; Eukaryota.
DR   eggNOG; ENOG4111SYS; LUCA.
DR   InParanoid; O80536; -.
DR   KO; K12126; -.
DR   OMA; HFLRPAT; -.
DR   OrthoDB; EOG093605W3; -.
DR   PhylomeDB; O80536; -.
DR   PRO; PR:O80536; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   Genevisible; O80536; AT.
DR   GO; GO:0005634; C:nucleus; IDA:TAIR.
DR   GO; GO:0003677; F:DNA binding; IDA:TAIR.
DR   GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR   GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR   GO; GO:0003700; F:transcription factor activity, sequence-specific DNA binding; ISS:TAIR.
DR   GO; GO:0009704; P:de-etiolation; IMP:TAIR.
DR   GO; GO:0009740; P:gibberellic acid mediated signaling pathway; IMP:TAIR.
DR   GO; GO:0031539; P:positive regulation of anthocyanin metabolic process; IMP:TAIR.
DR   GO; GO:0010017; P:red or far-red light signaling pathway; IMP:TAIR.
DR   GO; GO:0009585; P:red, far-red light phototransduction; IEA:UniProtKB-KW.
DR   GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
DR   GO; GO:0009639; P:response to red or far red light; IMP:TAIR.
DR   GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
DR   CDD; cd00083; HLH; 1.
DR   Gene3D; 4.10.280.10; -; 1.
DR   InterPro; IPR011598; bHLH_dom.
DR   Pfam; PF00010; HLH; 1.
DR   SMART; SM00353; HLH; 1.
DR   SUPFAM; SSF47459; SSF47459; 1.
DR   PROSITE; PS50888; BHLH; 1.
PE   1: Evidence at protein level;
KW   Complete proteome; DNA-binding; Nucleus; Phosphoprotein;
KW   Phytochrome signaling pathway; Reference proteome; Transcription;
KW   Transcription regulation.
FT   CHAIN         1    524       Transcription factor PIF3.
FT                                /FTId=PRO_0000127428.
FT   DOMAIN      343    392       bHLH. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00981}.
FT   COMPBIAS    353    358       Poly-Arg.
FT   COMPBIAS    422    428       Poly-Ala.
FT   VARIANT     124    124       E -> D (in strain: cv. An-2 and cv. Su-
FT                                0). {ECO:0000269|PubMed:17614917}.
FT   VARIANT     141    141       K -> N (in strain: cv. An-2 and cv. Su-
FT                                0). {ECO:0000269|PubMed:17614917}.
FT   VARIANT     176    176       Q -> H (in strain: cv. An-2 and cv. Su-
FT                                0). {ECO:0000269|PubMed:17614917}.
FT   VARIANT     186    186       Q -> K (in strain: cv. An-2 and cv. Su-
FT                                0). {ECO:0000269|PubMed:17614917}.
FT   VARIANT     209    209       F -> L (in strain: cv. An-2 and cv. Su-
FT                                0). {ECO:0000269|PubMed:17614917}.
FT   VARIANT     220    220       T -> I (in strain: cv. An-2 and cv. Su-
FT                                0). {ECO:0000269|PubMed:17614917}.
FT   VARIANT     236    236       V -> I (in strain: cv. An-2 and cv. Su-
FT                                0). {ECO:0000269|PubMed:17614917}.
FT   CONFLICT     15     15       E -> D (in Ref. 3; AAC99771).
FT                                {ECO:0000305}.
FT   CONFLICT    344    344       S -> L (in Ref. 3; AAC99771).
FT                                {ECO:0000305}.
CC   --------------------------------------------------------------------------
CC   The following FT lines are automated annotations from the MyHits database.
CC   --------------------------------------------------------------------------
FT   MYHIT       347    393       ipfam:HLH [T]
FT   MYHIT       349    398       ismart:HLH [T]
FT   MYHIT       343    392       iprf:BHLH [T]
SQ   SEQUENCE   524 AA;  56990 MW;  1044AC01D598DE7C CRC64;
     MPLFELFRLT KAKLESAQDR NPSPPVDEVV ELVWENGQIS TQSQSSRSRN IPPPQANSSR
     AREIGNGSKT TMVDEIPMSV PSLMTGLSQD DDFVPWLNHH PSLDGYCSDF LRDVSSPVTV
     NEQESDMAVN QTAFPLFQRR KDGNESAPAA SSSQYNGFQS HSLYGSDRAR DLPSQQTNPD
     RFTQTQEPLI TSNKPSLVNF SHFLRPATFA KTTNNNLHDT KEKSPQSPPN VFQTRVLGAK
     DSEDKVLNES VASATPKDNQ KACLISEDSC RKDQESEKAV VCSSVGSGNS LDGPSESPSL
     SLKRKHSNIQ DIDCHSEDVE EESGDGRKEA GPSRTGLGSK RSRSAEVHNL SERRRRDRIN
     EKMRALQELI PNCNKVDKAS MLDEAIEYLK SLQLQVQIMS MASGYYLPPA VMFPPGMGHY
     PAAAAAMAMG MGMPYAMGLP DLSRGGSSVN HGPQFQVSGM QQQPVAMGIP RVSGGGIFAG
     SSTIGNGSTR DLSGSKDQTT TNNNSNLKPI KRKQGSSDQF CGSS
//