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Q9SN68

- RAF2B_ARATH

UniProt

Q9SN68 - RAF2B_ARATH

Protein

Ras-related protein RABF2b

Gene

RABF2B

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 105 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    Functioni

    Endosomal protein that may be involved in endocytosis.1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi17 – 248GTP
    Nucleotide bindingi65 – 695GTPBy similarity
    Nucleotide bindingi123 – 1264GTP
    Nucleotide bindingi153 – 1542GTP

    GO - Molecular functioni

    1. GTP binding Source: UniProtKB
    2. protein binding Source: UniProtKB

    GO - Biological processi

    1. endocytosis Source: UniProtKB-KW
    2. protein transport Source: InterPro
    3. small GTPase mediated signal transduction Source: InterPro

    Keywords - Biological processi

    Endocytosis

    Keywords - Ligandi

    GTP-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ras-related protein RABF2b
    Short name:
    AtRABF2b
    Alternative name(s):
    Ras-related protein Ara-7
    Ras-related protein Rab5B
    Short name:
    AtRab5B
    Gene namesi
    Name:RABF2B
    Synonyms:ARA-7, RAB5B
    Ordered Locus Names:At4g19640
    ORF Names:F24J7.190
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 4

    Organism-specific databases

    TAIRiAT4G19640.

    Subcellular locationi

    Early endosome membrane. Endosome membrane. Vacuole membrane. Cell membrane Curated; Lipid-anchor Curated
    Note: Prevacuolar compartment.

    GO - Cellular componenti

    1. early endosome Source: UniProtKB
    2. early endosome membrane Source: UniProtKB-SubCell
    3. endoplasmic reticulum Source: TAIR
    4. endosome Source: TAIR
    5. plasma membrane Source: TAIR
    6. vacuolar membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cell membrane, Endosome, Membrane, Vacuole

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi19 – 191V → T: Loss of interaction with VPS9A. 1 Publication
    Mutagenesisi24 – 241S → N: Dominant negative (GDP-bound form); no effect on the interaction with VPS9A. 1 Publication
    Mutagenesisi36 – 361V → P: No effect on the interaction with VPS9A. 1 Publication
    Mutagenesisi42 – 421T → A: No effect on the interaction with VPS9A. 1 Publication
    Mutagenesisi44 – 441G → P: No effect on the interaction with VPS9A. 1 Publication
    Mutagenesisi46 – 461A → D: Loss of interaction with VPS9A. 1 Publication
    Mutagenesisi47 – 471F → A: Loss of interaction with VPS9A. 1 Publication
    Mutagenesisi64 – 641W → A: Loss of interaction with VPS9A. 1 Publication
    Mutagenesisi67 – 671A → G: Loss of interaction with VPS9A. 1 Publication
    Mutagenesisi69 – 691Q → E: Loss of interaction with VPS9A. 2 Publications
    Mutagenesisi69 – 691Q → L: Constitutively active (GTP-bound form); loss of targeting to plasma membrane and interaction with VPS9A. 2 Publications
    Mutagenesisi74 – 741S → A: Loss of interaction with VPS9A. 1 Publication
    Mutagenesisi75 – 751L → A: Loss of interaction with VPS9A. 1 Publication
    Mutagenesisi78 – 781M → A: Loss of interaction with VPS9A. 1 Publication
    Mutagenesisi79 – 791Y → A: Loss of interaction with VPS9A. 1 Publication
    Mutagenesisi123 – 1231N → I: Blocks nucleotide binding; no effect on the interaction with VPS9A. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 200200Ras-related protein RABF2bPRO_0000406605Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi198 – 1981S-geranylgeranyl cysteineBy similarity
    Lipidationi199 – 1991S-geranylgeranyl cysteineBy similarity

    Keywords - PTMi

    Lipoprotein, Prenylation

    Proteomic databases

    PaxDbiQ9SN68.
    PRIDEiQ9SN68.

    Expressioni

    Tissue specificityi

    Expressed in roots and actively dividing cells.1 Publication

    Inductioni

    Activated by VPS9A.1 Publication

    Gene expression databases

    ArrayExpressiQ9SN68.
    GenevestigatoriQ9SN68.

    Interactioni

    Subunit structurei

    Interacts with VPS9A homodimer.2 Publications

    Protein-protein interaction databases

    BioGridi12999. 1 interaction.
    IntActiQ9SN68. 2 interactions.

    Structurei

    Secondary structure

    1
    200
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 168
    Helixi23 – 3210
    Turni36 – 383
    Beta strandi41 – 433
    Beta strandi46 – 549
    Beta strandi57 – 659
    Helixi70 – 767
    Helixi77 – 804
    Beta strandi84 – 918
    Helixi95 – 11117
    Beta strandi117 – 1237
    Turni128 – 1303
    Helixi135 – 14410
    Beta strandi148 – 1514
    Beta strandi154 – 1563
    Helixi160 – 16910

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2EFCX-ray2.09B/D1-179[»]
    2EFDX-ray3.00B/D1-179[»]
    2EFEX-ray2.08B/D1-179[»]
    2EFHX-ray2.10B/D1-179[»]
    4G01X-ray2.20B1-179[»]
    ProteinModelPortaliQ9SN68.
    SMRiQ9SN68. Positions 8-172.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9SN68.

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi39 – 479Effector regionBy similarity

    Sequence similaritiesi

    Belongs to the small GTPase superfamily. Rab family.Curated

    Phylogenomic databases

    eggNOGiCOG1100.
    HOGENOMiHOG000233968.
    InParanoidiQ9SN68.
    OMAiTNVKEIF.
    PhylomeDBiQ9SN68.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR027417. P-loop_NTPase.
    IPR005225. Small_GTP-bd_dom.
    IPR001806. Small_GTPase.
    IPR003579. Small_GTPase_Rab_type.
    [Graphical view]
    PfamiPF00071. Ras. 1 hit.
    [Graphical view]
    PRINTSiPR00449. RASTRNSFRMNG.
    SMARTiSM00175. RAB. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00231. small_GTP. 1 hit.
    PROSITEiPS51419. RAB. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9SN68-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAAAGNKSIN AKLVLLGDVG AGKSSLVLRF VKDQFVEFQE STIGAAFFSQ    50
    TLAVNDATVK FEIWDTAGQE RYHSLAPMYY RGAAAAIIVF DVTNQASFER 100
    AKKWVQELQA QGNPNMVMAL AGNKSDLLDA RKVTAEDAQT YAQENGLFFM 150
    ETSAKTATNV KEIFYEIARR LPRVQPTENP TGMVLPDRAM DRAVSSSCCA 200
    Length:200
    Mass (Da):21,873
    Last modified:May 1, 2000 - v1
    Checksum:i769F75CFC708C6D0
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB038491 mRNA. Translation: BAB32669.1.
    AL021768 Genomic DNA. Translation: CAA16940.1.
    AL161551 Genomic DNA. Translation: CAB78966.1.
    CP002687 Genomic DNA. Translation: AEE84207.1.
    AF370309 mRNA. Translation: AAK44124.1.
    AY052670 mRNA. Translation: AAK96574.1.
    AY063095 mRNA. Translation: AAL34269.1.
    PIRiT06157.
    RefSeqiNP_193699.1. NM_118084.4.
    UniGeneiAt.2030.

    Genome annotation databases

    EnsemblPlantsiAT4G19640.1; AT4G19640.1; AT4G19640.
    GeneIDi827706.
    KEGGiath:AT4G19640.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB038491 mRNA. Translation: BAB32669.1 .
    AL021768 Genomic DNA. Translation: CAA16940.1 .
    AL161551 Genomic DNA. Translation: CAB78966.1 .
    CP002687 Genomic DNA. Translation: AEE84207.1 .
    AF370309 mRNA. Translation: AAK44124.1 .
    AY052670 mRNA. Translation: AAK96574.1 .
    AY063095 mRNA. Translation: AAL34269.1 .
    PIRi T06157.
    RefSeqi NP_193699.1. NM_118084.4.
    UniGenei At.2030.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2EFC X-ray 2.09 B/D 1-179 [» ]
    2EFD X-ray 3.00 B/D 1-179 [» ]
    2EFE X-ray 2.08 B/D 1-179 [» ]
    2EFH X-ray 2.10 B/D 1-179 [» ]
    4G01 X-ray 2.20 B 1-179 [» ]
    ProteinModelPortali Q9SN68.
    SMRi Q9SN68. Positions 8-172.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 12999. 1 interaction.
    IntActi Q9SN68. 2 interactions.

    Proteomic databases

    PaxDbi Q9SN68.
    PRIDEi Q9SN68.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT4G19640.1 ; AT4G19640.1 ; AT4G19640 .
    GeneIDi 827706.
    KEGGi ath:AT4G19640.

    Organism-specific databases

    TAIRi AT4G19640.

    Phylogenomic databases

    eggNOGi COG1100.
    HOGENOMi HOG000233968.
    InParanoidi Q9SN68.
    OMAi TNVKEIF.
    PhylomeDBi Q9SN68.

    Miscellaneous databases

    EvolutionaryTracei Q9SN68.

    Gene expression databases

    ArrayExpressi Q9SN68.
    Genevestigatori Q9SN68.

    Family and domain databases

    Gene3Di 3.40.50.300. 1 hit.
    InterProi IPR027417. P-loop_NTPase.
    IPR005225. Small_GTP-bd_dom.
    IPR001806. Small_GTPase.
    IPR003579. Small_GTPase_Rab_type.
    [Graphical view ]
    Pfami PF00071. Ras. 1 hit.
    [Graphical view ]
    PRINTSi PR00449. RASTRNSFRMNG.
    SMARTi SM00175. RAB. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 1 hit.
    TIGRFAMsi TIGR00231. small_GTP. 1 hit.
    PROSITEi PS51419. RAB. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Ara6, a plant-unique novel type Rab GTPase, functions in the endocytic pathway of Arabidopsis thaliana."
      Ueda T., Yamaguchi M., Uchimiya H., Nakano A.
      EMBO J. 20:4730-4741(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, TISSUE SPECIFICITY, MUTAGENESIS OF GLN-69.
    2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
      Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
      , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
      Nature 402:769-777(1999) [PubMed] [Europe PMC] [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. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Analysis of the small GTPase gene superfamily of Arabidopsis."
      Vernoud V., Horton A.C., Yang Z., Nielsen E.
      Plant Physiol. 131:1191-1208(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY, NOMENCLATURE.
    6. "The Arabidopsis rab5 homologs rha1 and ara7 localize to the prevacuolar compartment."
      Lee G.J., Sohn E.J., Lee M.H., Hwang I.
      Plant Cell Physiol. 45:1211-1220(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    7. "Two plant-viral movement proteins traffic in the endocytic recycling pathway."
      Haupt S., Cowan G.H., Ziegler A., Roberts A.G., Oparka K.J., Torrance L.
      Plant Cell 17:164-181(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    8. "Endocytosis and degradation of BOR1, a boron transporter of Arabidopsis thaliana, regulated by boron availability."
      Takano J., Miwa K., Yuan L., von Wiren N., Fujiwara T.
      Proc. Natl. Acad. Sci. U.S.A. 102:12276-12281(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    9. "VPS9a, the common activator for two distinct types of Rab5 GTPases, is essential for the development of Arabidopsis thaliana."
      Goh T., Uchida W., Arakawa S., Ito E., Dainobu T., Ebine K., Takeuchi M., Sato K., Ueda T., Nakano A.
      Plant Cell 19:3504-3515(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH VPS9A, INDUCTION.
    10. "PROTEIN S-ACYL TRANSFERASE10 Is Critical for Development and Salt Tolerance in Arabidopsis."
      Zhou L.Z., Li S., Feng Q.N., Zhang Y.L., Zhao X., Zeng Y.L., Wang H., Jiang L., Zhang Y.
      Plant Cell 25:1093-1107(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    11. "GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5.Vps9 system."
      Uejima T., Ihara K., Goh T., Ito E., Sunada M., Ueda T., Nakano A., Wakatsuki S.
      J. Biol. Chem. 285:36689-36697(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF 1-179 IN COMPLEX WITH GDP, FUNCTION, INTERACTION WITH VPS9A, MUTAGENESIS OF VAL-19; SER-24; VAL-36; THR-42; GLY-44; ALA-46; PHE-47; TRP-64; ALA-67; GLN-69; SER-74; LEU-75; MET-78; TYR-79 AND ASN-123.

    Entry informationi

    Entry nameiRAF2B_ARATH
    AccessioniPrimary (citable) accession number: Q9SN68
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 5, 2011
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 105 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3