Q9FMF5 (RPT3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Root phototropism protein 3

Alternative name(s):
BTB/POZ domain-containing protein RPT3
Non-phototropic hypocotyl protein 3

Gene names

Name:	RPT3
Synonyms:	JK218, NPH3
Ordered Locus Names:	At5g64330
ORF Names:	MSJ1.17

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	746 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins By similarity. Signal transducer of the phototropic response and photo-induced movements. Involved in the phot1 pathway under low blue light (LBL) fluence rate and in the phot2 pathway under higher fluence rate of blue light (HBL). Necessary for root and hypocotyl phototropisms, but not for the regulation of stomata opening. Not involved in chloroplast accumulation and translocation. Ref.1 Ref.6 Ref.7 Ref.10 Ref.12
Pathway	Protein modification; protein ubiquitination.
Subunit structure	Interacts with PKS1, PKS2, RPT2, PHOT1 and PHOT2. Ref.1 Ref.7 Ref.10 Ref.12
Subcellular location	Cell membrane; Peripheral membrane protein Ref.1 Ref.10.
Tissue specificity	Expressed in hypocotyls, guard cells and mesophyll cells. Ref.7
Induction	In the root, up-regulated by red light. Ref.9
Domain	The BTB/POZ domain mediates the interaction with some component of ubiquitin ligase complexes. Ref.8
Post-translational modification	Phosphorylated in the dark Probable. Ref.1 Ref.5 Ref.11
Disruption phenotype	Impaired leaf flattening and slight epinasty when grown under blue light. Ref.12
Sequence similarities	Belongs to the NPH3 family. Contains 1 BTB (POZ) domain. Contains 1 NPH3 domain.
Sequence caution	The sequence BAB09864.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Cell membrane Membrane
Coding sequence diversity	Alternative splicing
Molecular function	Transducer
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	blue light signaling pathway Inferred from genetic interaction. Source: TAIR phototropism Inferred from mutant phenotype. Source: TAIR
Cellular component	plasma membrane Inferred from direct assay. Source: TAIR
Molecular function	protein binding Inferred from physical interaction Ref.1Ref.10. Source: IntAct signal transducer activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PHOT1	O48963	2	EBI-1553842,EBI-1553849
PUB35	Q9SW11	2	EBI-1553842,EBI-626181

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9FMF5-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q9FMF5-2)

The sequence of this isoform differs from the canonical sequence as follows:
     555-558: AHPT → VYIY
     559-746: Missing.

Note: May be due to an intron retention. No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 746	746	Root phototropism protein 3		PRO_0000097439
Regions
	Domain	54 – 122	69	BTB
	Domain	250 – 581	332	NPH3
	Compositional bias	9 – 18	10	Poly-Gly
Amino acid modifications
	Modified residue	237	1	Phosphoserine Ref.11
	Modified residue	467	1	Phosphoserine Ref.11
	Modified residue	546	1	Phosphotyrosine Probable
Natural variations
	Alternative sequence	555 – 558	4	AHPT → VYIY in isoform 2.		VSP_041384
	Alternative sequence	559 – 746	188	Missing in isoform 2.		VSP_041385
Experimental info
	Mutagenesis	546	1	Missing in nph3-2; loss of hypocotyl phototropism. Ref.1
	Sequence conflict	519	1	D → V in BAE99857. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified June 28, 2011. Version 2. Checksum: 7D91D4224A5F3549	FASTA	746	81,873
	10 20 30 40 50 60 MMWESESDGG VGVGGGGGRE YGDGVLSSNK HGGVKTDGFE LRGQSWFVAT DIPSDLLVKI 70 80 90 100 110 120 GDMNFHLHKY PLLSRSGKMN RLIYESRDPD PTILILDDLP GGPEAFELAS KFCYGVPVDL 130 140 150 160 170 180 TATNISGLRC AAEYLEMTED LEEGNLIFKT EAFLSYVVLS SWRDSILVLK SCEKLSPWAE 190 200 210 220 230 240 NLQIVRRCSE SIAWKACSNP KGIRWAYTGK APSPSTTNFA GSSPRWNESK DSSFYCSPSR 250 260 270 280 290 300 NTNSQPVPPD WWFEDVSILR IDHFVRVITA IKVKGMRFEL LGAVIMHYAG KWLPGLIKEG 310 320 330 340 350 360 GVAIAPAMSS AIGGGLGLGG DEMSISCGSN SSGGSSGPDW KGGLHMVLSA GKTNGHQDSV 370 380 390 400 410 420 ACLAGLGISP KDQRMIVESL ISIIPPQKDS VTCSFLLRLL RAANMLKVAP ALITELEKRV 430 440 450 460 470 480 GMQFEQATLQ DLLIPGYNNK GETMYDVDLV QRLLEHFLVQ EQTEGSSPSR MSPSPSQSMY 490 500 510 520 530 540 ADIPRGNNNN GGGGGGNNQN AKMRVARLVD SYLTEVARDR NLPLTKFQVL AEALPESART 550 560 570 580 590 600 CDDGLYRAID SYLKAHPTLS EHERKRLCRV MDCQKLSMDA CMHAAQNERL PLRVVVQVLF 610 620 630 640 650 660 SEQVKISNAL ANTSLKESTT LGEAMGTYQP MIPNRKTLIE ATPQSFQEGW AAAKKDINTL 670 680 690 700 710 720 KFELETVKTK YVELQNEMEV MQRQFEKTGK VKNTPSSSAW TSGWKKLSKL TKMSGQESHD 730 740 ISSGGEQAGV DHPPPRKPRR WRNSIS
	Isoform 2 [UniParc]. Checksum: 8E6673CB8BFBB4CF	FASTA	558	60,732
	10 20 30 40 50 60 MMWESESDGG VGVGGGGGRE YGDGVLSSNK HGGVKTDGFE LRGQSWFVAT DIPSDLLVKI 70 80 90 100 110 120 GDMNFHLHKY PLLSRSGKMN RLIYESRDPD PTILILDDLP GGPEAFELAS KFCYGVPVDL 130 140 150 160 170 180 TATNISGLRC AAEYLEMTED LEEGNLIFKT EAFLSYVVLS SWRDSILVLK SCEKLSPWAE 190 200 210 220 230 240 NLQIVRRCSE SIAWKACSNP KGIRWAYTGK APSPSTTNFA GSSPRWNESK DSSFYCSPSR 250 260 270 280 290 300 NTNSQPVPPD WWFEDVSILR IDHFVRVITA IKVKGMRFEL LGAVIMHYAG KWLPGLIKEG 310 320 330 340 350 360 GVAIAPAMSS AIGGGLGLGG DEMSISCGSN SSGGSSGPDW KGGLHMVLSA GKTNGHQDSV 370 380 390 400 410 420 ACLAGLGISP KDQRMIVESL ISIIPPQKDS VTCSFLLRLL RAANMLKVAP ALITELEKRV 430 440 450 460 470 480 GMQFEQATLQ DLLIPGYNNK GETMYDVDLV QRLLEHFLVQ EQTEGSSPSR MSPSPSQSMY 490 500 510 520 530 540 ADIPRGNNNN GGGGGGNNQN AKMRVARLVD SYLTEVARDR NLPLTKFQVL AEALPESART 550 CDDGLYRAID SYLKVYIY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Arabidopsis NPH3: a NPH1 photoreceptor-interacting protein essential for phototropism." Motchoulski A., Liscum E. Science 286:961-964(1999) [PubMed: 10542152] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH PHOT1, PHOSPHORYLATION, MUTAGENESIS OF TYR-546. Strain: cv. Columbia.
[2]	"Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones." Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N., Tabata S. DNA Res. 4:401-414(1997) [PubMed: 9501997] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs." Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K. , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K. Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Strain: cv. Columbia.
[5]	"Light-induced phosphorylation of a membrane protein plays an early role in signal transduction for phototropism in Arabidopsis thaliana." Reymond P., Short T.W., Briggs W.R., Poff K.L. Proc. Natl. Acad. Sci. U.S.A. 89:4718-4721(1992) [PubMed: 11537679] [Abstract] Cited for: PHOSPHORYLATION.
[6]	"RPT2: a signal transducer of the phototropic response in Arabidopsis." Sakai T., Wada T., Ishiguro S., Okada K. Plant Cell 12:225-236(2000) [PubMed: 10662859] [Abstract] Cited for: FUNCTION.
[7]	"RPT2 is a signal transducer involved in phototropic response and stomatal opening by association with phototropin 1 in Arabidopsis thaliana." Inada S., Ohgishi M., Mayama T., Okada K., Sakai T. Plant Cell 16:887-896(2004) [PubMed: 15031408] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY, INTERACTION WITH RPT2.
[8]	"Cullins 3a and 3b assemble with members of the broad complex/tramtrack/bric-a-brac (BTB) protein family to form essential ubiquitin-protein ligases (E3s) in Arabidopsis." Gingerich D.J., Gagne J.M., Salter D.W., Hellmann H., Estelle M., Ma L., Vierstra R.D. J. Biol. Chem. 280:18810-18821(2005) [PubMed: 15749712] [Abstract] Cited for: DOMAIN BTB.
[9]	"Gene profiling of the red light signalling pathways in roots." Molas M.L., Kiss J.Z., Correll M.J. J. Exp. Bot. 57:3217-3229(2006) [PubMed: 16908503] [Abstract] Cited for: INDUCTION.
[10]	"PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism." Lariguet P., Schepens I., Hodgson D., Pedmale U.V., Trevisan M., Kami C., de Carbonnel M., Alonso J.M., Ecker J.R., Liscum E., Fankhauser C. Proc. Natl. Acad. Sci. U.S.A. 103:10134-10139(2006) [PubMed: 16777956] [Abstract] Cited for: FUNCTION, INTERACTION WITH PKS1 AND PHOT1, SUBCELLULAR LOCATION.
[11]	"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S. Plant Physiol. 150:889-903(2009) [PubMed: 19376835] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-237 AND SER-467, MASS SPECTROMETRY. Strain: cv. Columbia. Tissue: Seedling.
[12]	"The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 protein is a phototropin signaling element that regulates leaf flattening and leaf positioning." de Carbonnel M., Davis P., Roelfsema M.R., Inoue S., Schepens I., Lariguet P., Geisler M., Shimazaki K., Hangarter R., Fankhauser C. Plant Physiol. 152:1391-1405(2010) [PubMed: 20071603] [Abstract] Cited for: FUNCTION, INTERACTION WITH PKS1; PKS2; PHOT1 AND PHOT2, DISRUPTION PHENOTYPE.
+	Additional computationally mapped references.

Web resources

PlantsUBQ

A functional genomics database for the ubiquitin/26S proteasome proteolytic pathway in plants

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF180390 mRNA. Translation: AAF05914.1. AB008268 Genomic DNA. Translation: BAB09864.1. Sequence problems. CP002688 Genomic DNA. Translation: AED97870.1. CP002688 Genomic DNA. Translation: AED97871.1. AK227884 mRNA. Translation: BAE99857.1.
IPI	IPI00542309. IPI00891244.
RefSeq	NP_001119489.1. NM_001126017.1. NP_568989.1. NM_125829.3.
UniGene	At.49218. At.71062.
3D structure databases
ProteinModelPortal	Q9FMF5.
SMR	Q9FMF5. Positions 50-139.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9FMF5. 3 interactions.
STRING	Q9FMF5.
Proteomic databases
PRIDE	Q9FMF5.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	836554.
GenomeReviews	Gene locus AT5G64330 in contig BA000015_GR.
KEGG	ath:AT5G64330.
Organism-specific databases
GeneFarm	5154.
TAIR	At5g64330.
Phylogenomic databases
GeneTree	EPGT00070000031143.
HOGENOM	HBG745678.
InParanoid	Q9FMF5.
Gene expression databases
Genevestigator	Q9FMF5.
GermOnline	AT5G64330. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR000210. BTB/POZ-like. IPR011333. BTB/POZ_fold. IPR004249. NPH3. [Graphical view]
Gene3D	G3DSA:3.30.710.10. BTB/POZ_fold. 1 hit.
Pfam	PF03000. NPH3. 1 hit. [Graphical view]
SMART	SM00225. BTB. 1 hit. [Graphical view]
SUPFAM	SSF54695. BTB/POZ_fold. 1 hit.
PROSITE	PS50097. BTB. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPT3_ARATH

Accession

Primary (citable) accession number: Q9FMF5
Secondary accession number(s): F4KDL6 , F4KDL7, Q0WSP1, Q9SPB4

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	June 28, 2011
Last modified:	December 14, 2011
This is version 68 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program