ID   RPT3_ARATH              Reviewed;         746 AA.
AC   Q9FMF5; F4KDL6; F4KDL7; Q0WSP1; Q9SPB4;
DT   22-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT   28-JUN-2011, sequence version 2.
DT   02-SEP-2026, entry version 154.
DE   RecName: Full=Root phototropism protein 3;
DE   AltName: Full=BTB/POZ domain-containing protein RPT3;
DE   AltName: Full=Non-phototropic hypocotyl protein 3;
GN   Name=RPT3; Synonyms=JK218, NPH3; OrderedLocusNames=At5g64330;
GN   ORFNames=MSJ1.17;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION,
RP   INTERACTION WITH PHOT1, PHOSPHORYLATION AT TYR-546, AND MUTAGENESIS OF
RP   TYR-546.
RC   STRAIN=cv. Columbia;
RX   PubMed=10542152; DOI=10.1126/science.286.5441.961;
RA   Motchoulski A., Liscum E.;
RT   "Arabidopsis NPH3: a NPH1 photoreceptor-interacting protein essential for
RT   phototropism.";
RL   Science 286:961-964(1999).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=9501997; DOI=10.1093/dnares/4.6.401;
RA   Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA   Tabata S.;
RT   "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT   features of the regions of 1,191,918 bp covered by seventeen physically
RT   assigned P1 clones.";
RL   DNA Res. 4:401-414(1997).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Resource (TAIR);
RT   "Community-consensus reference genome of Arabidopsis thaliana Col-0.";
RL   Submitted (FEB-2026) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC   STRAIN=cv. Columbia;
RA   Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA   Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA   Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA   Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA   Shinozaki K.;
RT   "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL   Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   PHOSPHORYLATION.
RX   PubMed=11537679; DOI=10.1073/pnas.89.10.4718;
RA   Reymond P., Short T.W., Briggs W.R., Poff K.L.;
RT   "Light-induced phosphorylation of a membrane protein plays an early role in
RT   signal transduction for phototropism in Arabidopsis thaliana.";
RL   Proc. Natl. Acad. Sci. U.S.A. 89:4718-4721(1992).
RN   [7]
RP   FUNCTION.
RX   PubMed=10662859; DOI=10.1105/tpc.12.2.225;
RA   Sakai T., Wada T., Ishiguro S., Okada K.;
RT   "RPT2: a signal transducer of the phototropic response in Arabidopsis.";
RL   Plant Cell 12:225-236(2000).
RN   [8]
RP   FUNCTION, TISSUE SPECIFICITY, AND INTERACTION WITH RPT2.
RX   PubMed=15031408; DOI=10.1105/tpc.019901;
RA   Inada S., Ohgishi M., Mayama T., Okada K., Sakai T.;
RT   "RPT2 is a signal transducer involved in phototropic response and stomatal
RT   opening by association with phototropin 1 in Arabidopsis thaliana.";
RL   Plant Cell 16:887-896(2004).
RN   [9]
RP   DOMAIN BTB.
RX   PubMed=15749712; DOI=10.1074/jbc.m413247200;
RA   Gingerich D.J., Gagne J.M., Salter D.W., Hellmann H., Estelle M., Ma L.,
RA   Vierstra R.D.;
RT   "Cullins 3a and 3b assemble with members of the broad
RT   complex/tramtrack/bric-a-brac (BTB) protein family to form essential
RT   ubiquitin-protein ligases (E3s) in Arabidopsis.";
RL   J. Biol. Chem. 280:18810-18821(2005).
RN   [10]
RP   INDUCTION.
RX   PubMed=16908503; DOI=10.1093/jxb/erl086;
RA   Molas M.L., Kiss J.Z., Correll M.J.;
RT   "Gene profiling of the red light signalling pathways in roots.";
RL   J. Exp. Bot. 57:3217-3229(2006).
RN   [11]
RP   FUNCTION, INTERACTION WITH PKS1 AND PHOT1, AND SUBCELLULAR LOCATION.
RX   PubMed=16777956; DOI=10.1073/pnas.0603799103;
RA   Lariguet P., Schepens I., Hodgson D., Pedmale U.V., Trevisan M., Kami C.,
RA   de Carbonnel M., Alonso J.M., Ecker J.R., Liscum E., Fankhauser C.;
RT   "PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required
RT   for phototropism.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:10134-10139(2006).
RN   [12]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=cv. Columbia;
RX   PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA   Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA   Rathjen J.P., Peck S.C.;
RT   "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT   thaliana.";
RL   J. Proteomics 72:439-451(2009).
RN   [13]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19376835; DOI=10.1104/pp.109.138677;
RA   Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA   Grossmann J., Gruissem W., Baginsky S.;
RT   "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT   chloroplast kinase substrates and phosphorylation networks.";
RL   Plant Physiol. 150:889-903(2009).
RN   [14]
RP   FUNCTION, INTERACTION WITH PKS1; PKS2; PHOT1 AND PHOT2, AND DISRUPTION
RP   PHENOTYPE.
RX   PubMed=20071603; DOI=10.1104/pp.109.150441;
RA   de Carbonnel M., Davis P., Roelfsema M.R., Inoue S., Schepens I.,
RA   Lariguet P., Geisler M., Shimazaki K., Hangarter R., Fankhauser C.;
RT   "The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 protein is a phototropin
RT   signaling element that regulates leaf flattening and leaf positioning.";
RL   Plant Physiol. 152:1391-1405(2010).
RN   [15]
RP   FUNCTION, AND INTERACTION WITH CAR6 AND PHOT1.
RX   PubMed=21367967; DOI=10.1104/pp.110.167411;
RA   Knauer T., Duemmer M., Landgraf F., Forreiter C.;
RT   "A negative effector of blue light-induced and gravitropic bending in
RT   Arabidopsis.";
RL   Plant Physiol. 156:439-447(2011).
CC   -!- FUNCTION: May act as a substrate-specific adapter of an E3 ubiquitin-
CC       protein ligase complex (CUL3-RBX1-BTB) which mediates the
CC       ubiquitination and subsequent proteasomal degradation of target
CC       proteins (By similarity). Signal transducer of the phototropic response
CC       and photo-induced movements. Involved in the phot1 pathway under low
CC       blue light (LBL) fluence rate and in the phot2 pathway under higher
CC       fluence rate of blue light (HBL). Necessary for root and hypocotyl
CC       phototropisms, but not for the regulation of stomata opening. Not
CC       involved in chloroplast accumulation and translocation. {ECO:0000250,
CC       ECO:0000269|PubMed:10542152, ECO:0000269|PubMed:10662859,
CC       ECO:0000269|PubMed:15031408, ECO:0000269|PubMed:16777956,
CC       ECO:0000269|PubMed:20071603}.
CC   -!- PATHWAY: Protein modification; protein ubiquitination.
CC   -!- SUBUNIT: Interacts with PKS1, PKS2, RPT2, PHOT1 and PHOT2
CC       (PubMed:10542152, PubMed:15031408, PubMed:16777956, PubMed:20071603).
CC       Subunit of a complex made of CAR6, PHOT1 and RPT3/NPH3
CC       (PubMed:21367967). {ECO:0000269|PubMed:10542152,
CC       ECO:0000269|PubMed:15031408, ECO:0000269|PubMed:16777956,
CC       ECO:0000269|PubMed:20071603}.
CC   -!- INTERACTION:
CC       Q9FMF5; O48963: PHOT1; NbExp=3; IntAct=EBI-1553842, EBI-1553849;
CC       Q9FMF5; Q9SWI1: PKS1; NbExp=2; IntAct=EBI-1553842, EBI-626200;
CC   -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:10542152,
CC       ECO:0000269|PubMed:16777956}; Peripheral membrane protein
CC       {ECO:0000269|PubMed:10542152, ECO:0000269|PubMed:16777956}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q9FMF5-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q9FMF5-2; Sequence=VSP_041384, VSP_041385;
CC   -!- TISSUE SPECIFICITY: Expressed in hypocotyls, guard cells and mesophyll
CC       cells. {ECO:0000269|PubMed:15031408}.
CC   -!- INDUCTION: In the root, up-regulated by red light.
CC       {ECO:0000269|PubMed:16908503}.
CC   -!- DOMAIN: The BTB/POZ domain mediates the interaction with some component
CC       of ubiquitin ligase complexes. {ECO:0000269|PubMed:15749712}.
CC   -!- PTM: Phosphorylated in the dark. {ECO:0000305|PubMed:10542152,
CC       ECO:0000305|PubMed:11537679}.
CC   -!- DISRUPTION PHENOTYPE: Impaired leaf flattening and slight epinasty when
CC       grown under blue light. {ECO:0000269|PubMed:20071603}.
CC   -!- MISCELLANEOUS: [Isoform 2]: May be due to an intron retention.
CC       {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the NPH3 family. {ECO:0000255|PROSITE-
CC       ProRule:PRU00982}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAB09864.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AF180390; AAF05914.1; -; mRNA.
DR   EMBL; AB008268; BAB09864.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002688; AED97870.1; -; Genomic_DNA.
DR   EMBL; OZ408687; CAO7057720.1; -; Genomic_DNA.
DR   EMBL; AK227884; BAE99857.1; -; mRNA.
DR   RefSeq; NP_568989.1; NM_125829.4. [Q9FMF5-1]
DR   AlphaFoldDB; Q9FMF5; -.
DR   SMR; Q9FMF5; -.
DR   BioGRID; 21796; 6.
DR   DIP; DIP-61198N; -.
DR   FunCoup; Q9FMF5; 273.
DR   IntAct; Q9FMF5; 2.
DR   STRING; 3702.Q9FMF5; -.
DR   iPTMnet; Q9FMF5; -.
DR   PaxDb; 3702-Q9FMF5; -.
DR   ProteomicsDB; 228224; -. [Q9FMF5-1]
DR   GeneID; 836554; -.
DR   KEGG; ath:AT5G64330; -.
DR   Araport; AT5G64330; -.
DR   TAIR; AT5G64330; NPH3.
DR   eggNOG; ENOG502QR3H; Eukaryota.
DR   HOGENOM; CLU_005994_6_2_1; -.
DR   InParanoid; Q9FMF5; -.
DR   UniPathway; UPA00143; -.
DR   PRO; PR:Q9FMF5; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q9FMF5; baseline and differential.
DR   GO; GO:0005634; C:nucleus; ISM:TAIR.
DR   GO; GO:0005886; C:plasma membrane; EXP:UniProtKB.
DR   GO; GO:0009785; P:blue light signaling pathway; IPI:TAIR.
DR   GO; GO:0009638; P:phototropism; IMP:TAIR.
DR   GO; GO:0016567; P:protein ubiquitination; IMP:TAIR.
DR   CDD; cd18312; BTB_POZ_NPY3-like; 1.
DR   Gene3D; 3.30.710.10; Potassium Channel Kv1.1, Chain A; 1.
DR   InterPro; IPR000210; BTB/POZ_dom.
DR   InterPro; IPR043454; NPH3/RPT2-like.
DR   InterPro; IPR027356; NPH3_dom.
DR   InterPro; IPR011333; SKP1/BTB/POZ_sf.
DR   PANTHER; PTHR32370; OS12G0117600 PROTEIN; 1.
DR   Pfam; PF03000; NPH3; 1.
DR   SUPFAM; SSF54695; POZ domain; 1.
DR   PROSITE; PS50097; BTB; 1.
DR   PROSITE; PS51649; NPH3; 1.
PE   1: Evidence at protein level;
KW   Alternative splicing; Cell membrane; Membrane; Phosphoprotein;
KW   Reference proteome; Transducer; Ubl conjugation pathway.
FT   CHAIN           1..746
FT                   /note="Root phototropism protein 3"
FT                   /id="PRO_0000097439"
FT   DOMAIN          54..122
FT                   /note="BTB"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00037"
FT   DOMAIN          250..605
FT                   /note="NPH3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00982"
FT   REGION          1..24
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          461..500
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          708..746
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        9..19
FT                   /note="Gly residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        466..478
FT                   /note="Low complexity"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        735..746
FT                   /note="Basic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         546
FT                   /note="Phosphotyrosine"
FT                   /evidence="ECO:0000269|PubMed:10542152"
FT   VAR_SEQ         555..558
FT                   /note="AHPT -> VYIY (in isoform 2)"
FT                   /evidence="ECO:0000303|Ref.5"
FT                   /id="VSP_041384"
FT   VAR_SEQ         559..746
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000303|Ref.5"
FT                   /id="VSP_041385"
FT   MUTAGEN         546
FT                   /note="Missing: In nph3-2; loss of hypocotyl phototropism."
FT                   /evidence="ECO:0000269|PubMed:10542152"
FT   CONFLICT        519
FT                   /note="D -> V (in Ref. 5; BAE99857)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   746 AA;  81873 MW;  7D91D4224A5F3549 CRC64;
     MMWESESDGG VGVGGGGGRE YGDGVLSSNK HGGVKTDGFE LRGQSWFVAT DIPSDLLVKI
     GDMNFHLHKY PLLSRSGKMN RLIYESRDPD PTILILDDLP GGPEAFELAS KFCYGVPVDL
     TATNISGLRC AAEYLEMTED LEEGNLIFKT EAFLSYVVLS SWRDSILVLK SCEKLSPWAE
     NLQIVRRCSE SIAWKACSNP KGIRWAYTGK APSPSTTNFA GSSPRWNESK DSSFYCSPSR
     NTNSQPVPPD WWFEDVSILR IDHFVRVITA IKVKGMRFEL LGAVIMHYAG KWLPGLIKEG
     GVAIAPAMSS AIGGGLGLGG DEMSISCGSN SSGGSSGPDW KGGLHMVLSA GKTNGHQDSV
     ACLAGLGISP KDQRMIVESL ISIIPPQKDS VTCSFLLRLL RAANMLKVAP ALITELEKRV
     GMQFEQATLQ DLLIPGYNNK GETMYDVDLV QRLLEHFLVQ EQTEGSSPSR MSPSPSQSMY
     ADIPRGNNNN GGGGGGNNQN AKMRVARLVD SYLTEVARDR NLPLTKFQVL AEALPESART
     CDDGLYRAID SYLKAHPTLS EHERKRLCRV MDCQKLSMDA CMHAAQNERL PLRVVVQVLF
     SEQVKISNAL ANTSLKESTT LGEAMGTYQP MIPNRKTLIE ATPQSFQEGW AAAKKDINTL
     KFELETVKTK YVELQNEMEV MQRQFEKTGK VKNTPSSSAW TSGWKKLSKL TKMSGQESHD
     ISSGGEQAGV DHPPPRKPRR WRNSIS
//