RABF1_ARATH
ID RABF1_ARATH Reviewed; 202 AA.
AC Q9CB01; A8MRL2; Q9SV33;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Ras-related protein RABF1 {ECO:0000303|PubMed:12644670};
DE Short=AtRABF1 {ECO:0000303|PubMed:12644670};
DE AltName: Full=Ras-related protein Ara-6 {ECO:0000303|PubMed:11532937};
DE AltName: Full=Ras-related protein Rab5C {ECO:0000305|PubMed:12644670};
DE Short=AtRab5C {ECO:0000305|PubMed:12644670};
GN Name=RABF1 {ECO:0000303|PubMed:12644670};
GN Synonyms=ARA-6 {ECO:0000303|PubMed:11532937},
GN RAB5C {ECO:0000305|PubMed:12644670};
GN OrderedLocusNames=At3g54840 {ECO:0000312|Araport:AT3G54840};
GN ORFNames=F28P10.180 {ECO:0000312|EMBL:CAB41100.1};
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 TISSUE SPECIFICITY, MYRISTOYLATION AT GLY-2, PALMITOYLATION AT CYS-3, AND
RP MUTAGENESIS OF GLY-2; CYS-3; GLN-93 AND ASN-147.
RX PubMed=11532937; DOI=10.1093/emboj/20.17.4730;
RA Ueda T., Yamaguchi M., Uchimiya H., Nakano A.;
RT "Ara6, a plant-unique novel type Rab GTPase, functions in the endocytic
RT pathway of Arabidopsis thaliana.";
RL EMBO J. 20:4730-4741(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP FUNCTION, AND MUTAGENESIS OF SER-47.
RX PubMed=12724533; DOI=10.1105/tpc.009779;
RA Sohn E.J., Kim E.S., Zhao M., Kim S.J., Kim H., Kim Y.W., Lee Y.J.,
RA Hillmer S., Sohn U., Jiang L., Hwang I.;
RT "Rha1, an Arabidopsis Rab5 homolog, plays a critical role in the vacuolar
RT trafficking of soluble cargo proteins.";
RL Plant Cell 15:1057-1070(2003).
RN [7]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=12644670; DOI=10.1104/pp.013052;
RA Vernoud V., Horton A.C., Yang Z., Nielsen E.;
RT "Analysis of the small GTPase gene superfamily of Arabidopsis.";
RL Plant Physiol. 131:1191-1208(2003).
RN [8]
RP INTERACTION WITH VPS9A, INDUCTION, AND MUTAGENESIS OF SER-47; GLN-93 AND
RP ASN-147.
RX PubMed=18055610; DOI=10.1105/tpc.107.053876;
RA Goh T., Uchida W., Arakawa S., Ito E., Dainobu T., Ebine K., Takeuchi M.,
RA Sato K., Ueda T., Nakano A.;
RT "VPS9a, the common activator for two distinct types of Rab5 GTPases, is
RT essential for the development of Arabidopsis thaliana.";
RL Plant Cell 19:3504-3515(2007).
RN [9]
RP INTERACTION WITH TCTP1.
RX PubMed=20736351; DOI=10.1073/pnas.1007926107;
RA Brioudes F., Thierry A.M., Chambrier P., Mollereau B., Bendahmane M.;
RT "Translationally controlled tumor protein is a conserved mitotic growth
RT integrator in animals and plants.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:16384-16389(2010).
RN [10]
RP SUBCELLULAR LOCATION, AND PALMITOYLATION.
RX PubMed=23482856; DOI=10.1105/tpc.112.108829;
RA Zhou L.Z., Li S., Feng Q.N., Zhang Y.L., Zhao X., Zeng Y.L., Wang H.,
RA Jiang L., Zhang Y.;
RT "Protein S-acyl transferase10 is critical for development and salt
RT tolerance in Arabidopsis.";
RL Plant Cell 25:1093-1107(2013).
CC -!- FUNCTION: Endosomal protein probably involved in endocytosis. Probably
CC not involved in vacuolar trafficking. {ECO:0000269|PubMed:11532937,
CC ECO:0000269|PubMed:12724533}.
CC -!- SUBUNIT: Interacts with VPS9A (PubMed:18055610). Interacts with TCTP1
CC (PubMed:20736351). {ECO:0000269|PubMed:18055610,
CC ECO:0000269|PubMed:20736351}.
CC -!- SUBCELLULAR LOCATION: Early endosome membrane
CC {ECO:0000269|PubMed:11532937}. Endosome membrane
CC {ECO:0000269|PubMed:23482856}. Cell membrane
CC {ECO:0000269|PubMed:11532937}; Lipid-anchor
CC {ECO:0000269|PubMed:11532937}. Endoplasmic reticulum
CC {ECO:0000269|PubMed:11532937}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9CB01-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9CB01-2; Sequence=VSP_040836;
CC -!- TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:11532937}.
CC -!- INDUCTION: Activated by VPS9A. {ECO:0000269|PubMed:18055610}.
CC -!- PTM: Although this sequence lacks the C-terminal cysteine motifs
CC subject to isoprenylation in other Rab proteins, it does have N-
CC terminal N-myristoylation and S-palmitoylation.
CC {ECO:0000269|PubMed:11532937, ECO:0000269|PubMed:23482856}.
CC -!- SIMILARITY: Belongs to the small GTPase superfamily. Rab family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB41100.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB007766; BAB32953.1; -; mRNA.
DR EMBL; BT002860; AAO22677.1; -; mRNA.
DR EMBL; AL049655; CAB41100.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE79298.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79299.1; -; Genomic_DNA.
DR EMBL; BT004392; AAO42386.1; -; mRNA.
DR EMBL; AK316975; BAH19672.1; -; mRNA.
DR PIR; T06736; T06736.
DR RefSeq; NP_001078287.1; NM_001084818.1. [Q9CB01-2]
DR RefSeq; NP_567008.1; NM_115341.3. [Q9CB01-1]
DR AlphaFoldDB; Q9CB01; -.
DR SMR; Q9CB01; -.
DR BioGRID; 9965; 4.
DR IntAct; Q9CB01; 6.
DR STRING; 3702.AT3G54840.1; -.
DR iPTMnet; Q9CB01; -.
DR SwissPalm; Q9CB01; -.
DR PaxDb; Q9CB01; -.
DR PRIDE; Q9CB01; -.
DR ProteomicsDB; 236764; -. [Q9CB01-1]
DR EnsemblPlants; AT3G54840.1; AT3G54840.1; AT3G54840. [Q9CB01-1]
DR EnsemblPlants; AT3G54840.2; AT3G54840.2; AT3G54840. [Q9CB01-2]
DR GeneID; 824649; -.
DR Gramene; AT3G54840.1; AT3G54840.1; AT3G54840. [Q9CB01-1]
DR Gramene; AT3G54840.2; AT3G54840.2; AT3G54840. [Q9CB01-2]
DR KEGG; ath:AT3G54840; -.
DR Araport; AT3G54840; -.
DR TAIR; locus:2082672; AT3G54840.
DR eggNOG; KOG0092; Eukaryota.
DR HOGENOM; CLU_041217_10_2_1; -.
DR InParanoid; Q9CB01; -.
DR PhylomeDB; Q9CB01; -.
DR BioCyc; ARA:AT3G54840-MON; -.
DR PRO; PR:Q9CB01; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9CB01; baseline and differential.
DR Genevisible; Q9CB01; AT.
DR GO; GO:0010009; C:cytoplasmic side of endosome membrane; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005769; C:early endosome; IDA:TAIR.
DR GO; GO:0031901; C:early endosome membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell.
DR GO; GO:0005768; C:endosome; IDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003924; F:GTPase activity; IDA:TAIR.
DR GO; GO:0045022; P:early endosome to late endosome transport; IMP:TAIR.
DR GO; GO:0006897; P:endocytosis; IEA:UniProtKB-KW.
DR GO; GO:0006886; P:intracellular protein transport; IBA:GO_Central.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR005225; Small_GTP-bd_dom.
DR InterPro; IPR001806; Small_GTPase.
DR Pfam; PF00071; Ras; 1.
DR SMART; SM00174; RHO; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00231; small_GTP; 1.
DR PROSITE; PS51419; RAB; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cell membrane; Endocytosis; Endoplasmic reticulum;
KW Endosome; GTP-binding; Lipoprotein; Membrane; Myristate;
KW Nucleotide-binding; Palmitate; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..202
FT /note="Ras-related protein RABF1"
FT /id="PRO_0000406606"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 62..70
FT /note="Effector region"
FT /evidence="ECO:0000250"
FT BINDING 40..47
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 89..93
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 147..150
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 177..178
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT LIPID 2
FT /note="N-myristoyl glycine"
FT /evidence="ECO:0000269|PubMed:11532937"
FT LIPID 3
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000269|PubMed:11532937"
FT VAR_SEQ 190..202
FT /note="EIGKRLPRPAPSS -> CTHV (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:19423640"
FT /id="VSP_040836"
FT MUTAGEN 2
FT /note="G->A: Loss of myristoylation. Loss of targeting to
FT membrane."
FT /evidence="ECO:0000269|PubMed:11532937"
FT MUTAGEN 3
FT /note="C->S: Loss of palmitoylation."
FT /evidence="ECO:0000269|PubMed:11532937"
FT MUTAGEN 47
FT /note="S->N: Dominant negative (GDP-bound form); no effect
FT on vacuolar trafficking. No effect on the interaction with
FT VPS9A."
FT /evidence="ECO:0000269|PubMed:12724533,
FT ECO:0000269|PubMed:18055610"
FT MUTAGEN 93
FT /note="Q->L: Constitutively active (GTP-bound form); no
FT effect on targeting to plasma membrane. Loss of interaction
FT with VPS9A."
FT /evidence="ECO:0000269|PubMed:11532937,
FT ECO:0000269|PubMed:18055610"
FT MUTAGEN 147
FT /note="N->I: Blocks nucleotide binding; loss of targeting
FT to endosomal membrane. No effect on the interaction with
FT VPS9A."
FT /evidence="ECO:0000269|PubMed:11532937,
FT ECO:0000269|PubMed:18055610"
SQ SEQUENCE 202 AA; 21889 MW; 528D7DAD2AB58398 CRC64;
MGCASSLPDR NSGTLSGLSN SENAVPADAK NLRVKLVLLG DSGVGKSCIV LRFVRGQFDA
TSKVTVGASF LSQTIALQDS TTVKFEIWDT AGQERYSALA PLYYRGAGVA VIVYDITSPE
SFKKAQYWVK ELQKHGSPDI VMALVGNKAD LHEKREVPTE DGMELAEKNG MFFIETSAKT
ADNINQLFEE IGKRLPRPAP SS
