Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q9SN68 (RAF2B_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ras-related protein RABF2b

Short name=AtRABF2b
Alternative name(s):
Ras-related protein Ara-7
Ras-related protein Rab5B
Short name=AtRab5B
Gene names
Name:RABF2B
Synonyms:ARA-7, RAB5B
Ordered Locus Names:At4g19640
ORF Names:F24J7.190
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length200 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Endosomal protein that may be involved in endocytosis. Ref.11

Subunit structure

Interacts with VPS9A homodimer. Ref.9 Ref.11

Subcellular location

Early endosome membrane. Endosome membrane. Vacuole membrane. Cell membrane; Lipid-anchor Probable. Note: Prevacuolar compartment. Ref.1 Ref.6 Ref.7 Ref.8 Ref.10

Tissue specificity

Expressed in roots and actively dividing cells. Ref.1

Induction

Activated by VPS9A. Ref.9

Sequence similarities

Belongs to the small GTPase superfamily. Rab family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 200200Ras-related protein RABF2b
PRO_0000406605

Regions

Nucleotide binding17 – 248GTP
Nucleotide binding65 – 695GTP By similarity
Nucleotide binding123 – 1264GTP
Nucleotide binding153 – 1542GTP
Motif39 – 479Effector region By similarity

Amino acid modifications

Lipidation1981S-geranylgeranyl cysteine By similarity
Lipidation1991S-geranylgeranyl cysteine By similarity

Experimental info

Mutagenesis191V → T: Loss of interaction with VPS9A. Ref.11
Mutagenesis241S → N: Dominant negative (GDP-bound form); no effect on the interaction with VPS9A. Ref.11
Mutagenesis361V → P: No effect on the interaction with VPS9A. Ref.11
Mutagenesis421T → A: No effect on the interaction with VPS9A. Ref.11
Mutagenesis441G → P: No effect on the interaction with VPS9A. Ref.11
Mutagenesis461A → D: Loss of interaction with VPS9A. Ref.11
Mutagenesis471F → A: Loss of interaction with VPS9A. Ref.11
Mutagenesis641W → A: Loss of interaction with VPS9A. Ref.11
Mutagenesis671A → G: Loss of interaction with VPS9A. Ref.11
Mutagenesis691Q → E: Loss of interaction with VPS9A. Ref.1 Ref.11
Mutagenesis691Q → L: Constitutively active (GTP-bound form); loss of targeting to plasma membrane and interaction with VPS9A. Ref.1 Ref.11
Mutagenesis741S → A: Loss of interaction with VPS9A. Ref.11
Mutagenesis751L → A: Loss of interaction with VPS9A. Ref.11
Mutagenesis781M → A: Loss of interaction with VPS9A. Ref.11
Mutagenesis791Y → A: Loss of interaction with VPS9A. Ref.11
Mutagenesis1231N → I: Blocks nucleotide binding; no effect on the interaction with VPS9A. Ref.11

Secondary structure

................................ 200
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9SN68 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: 769F75CFC708C6D0

FASTA20021,873
        10         20         30         40         50         60 
MAAAGNKSIN AKLVLLGDVG AGKSSLVLRF VKDQFVEFQE STIGAAFFSQ TLAVNDATVK 

        70         80         90        100        110        120 
FEIWDTAGQE RYHSLAPMYY RGAAAAIIVF DVTNQASFER AKKWVQELQA QGNPNMVMAL 

       130        140        150        160        170        180 
AGNKSDLLDA RKVTAEDAQT YAQENGLFFM ETSAKTATNV KEIFYEIARR LPRVQPTENP 

       190        200 
TGMVLPDRAM DRAVSSSCCA 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRT06157.
RefSeqNP_193699.1. NM_118084.4.
UniGeneAt.2030.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ9SN68.
SMRQ9SN68. Positions 8-172.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid12999. 1 interaction.
IntActQ9SN68. 2 interactions.

Proteomic databases

PaxDbQ9SN68.
PRIDEQ9SN68.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT4G19640.1; AT4G19640.1; AT4G19640.
GeneID827706.
KEGGath:AT4G19640.

Organism-specific databases

TAIRAT4G19640.

Phylogenomic databases

eggNOGCOG1100.
HOGENOMHOG000233968.
InParanoidQ9SN68.
OMAANLLFFE.
PhylomeDBQ9SN68.
ProtClustDBCLSN2685695.

Gene expression databases

ArrayExpressQ9SN68.
GenevestigatorQ9SN68.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
InterProIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]
PfamPF00071. Ras. 1 hit.
[Graphical view]
PRINTSPR00449. RASTRNSFRMNG.
SMARTSM00175. RAB. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR00231. small_GTP. 1 hit.
PROSITEPS51419. RAB. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9SN68.

Entry information

Entry nameRAF2B_ARATH
AccessionPrimary (citable) accession number: Q9SN68
Entry history
Integrated into UniProtKB/Swiss-Prot: April 5, 2011
Last sequence update: May 1, 2000
Last modified: April 16, 2014
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names