Q9SN68 (RAF2B_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	RABF2B
Synonyms:	ARA-7, RAB5B
Ordered Locus Names:	At4g19640
ORF Names:	F24J7.190

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	200 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Endosomal protein that may be involved in endocytosis. Ref.10
Subunit structure	Interacts with VPS9A homodimer. Ref.9 Ref.10
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
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.

Ontologies

Keywords
Biological process	Endocytosis
Cellular component	Cell membrane Endosome Membrane Vacuole
Ligand	GTP-binding Nucleotide-binding
PTM	Lipoprotein Prenylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	endocytosis Inferred from electronic annotation. Source: UniProtKB-KW protein transport Inferred from electronic annotation. Source: InterPro small GTPase mediated signal transduction Inferred from electronic annotation. Source: InterPro
Cellular_component	early endosome Inferred from direct assay Ref.1. Source: UniProtKB early endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell endoplasmic reticulum Inferred from direct assay PubMed 22923678. Source: TAIR plasma membrane Inferred from direct assay PubMed 17644812. Source: TAIR vacuolar membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	GTP binding Inferred from direct assay Ref.10. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 200

200

Ras-related protein RABF2b

PRO_0000406605

Regions

Nucleotide binding

17 – 24

8

GTP

Nucleotide binding

65 – 69

5

GTP By similarity

Nucleotide binding

123 – 126

4

GTP

Nucleotide binding

153 – 154

2

GTP

Motif

39 – 47

9

Effector region By similarity

Amino acid modifications

Lipidation

198

1

S-geranylgeranyl cysteine By similarity

Lipidation

199

1

S-geranylgeranyl cysteine By similarity

Experimental info

Mutagenesis

19

1

V → T: Loss of interaction with VPS9A. Ref.10

Mutagenesis

24

1

S → N: Dominant negative (GDP-bound form); no effect on the interaction with VPS9A. Ref.10

Mutagenesis

36

1

V → P: No effect on the interaction with VPS9A. Ref.10

Mutagenesis

42

1

T → A: No effect on the interaction with VPS9A. Ref.10

Mutagenesis

44

1

G → P: No effect on the interaction with VPS9A. Ref.10

Mutagenesis

46

1

A → D: Loss of interaction with VPS9A. Ref.10

Mutagenesis

47

1

F → A: Loss of interaction with VPS9A. Ref.10

Mutagenesis

64

1

W → A: Loss of interaction with VPS9A. Ref.10

Mutagenesis

67

1

A → G: Loss of interaction with VPS9A. Ref.10

Mutagenesis

69

1

Q → E: Loss of interaction with VPS9A. Ref.1 Ref.10

Mutagenesis

69

1

Q → L: Constitutively active (GTP-bound form); loss of targeting to plasma membrane and interaction with VPS9A. Ref.1 Ref.10

Mutagenesis

74

1

S → A: Loss of interaction with VPS9A. Ref.10

Mutagenesis

75

1

L → A: Loss of interaction with VPS9A. Ref.10

Mutagenesis

78

1

M → A: Loss of interaction with VPS9A. Ref.10

Mutagenesis

79

1

Y → A: Loss of interaction with VPS9A. Ref.10

Mutagenesis

123

1

N → I: Blocks nucleotide binding; no effect on the interaction with VPS9A. Ref.10

Secondary structure

1

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200

Helix Strand Turn

Details...

Beta strand

9 – 16

8

Helix

23 – 32

10

Turn

36 – 38

3

Beta strand

46 – 54

9

Beta strand

57 – 65

9

Helix

70 – 76

7

Helix

77 – 80

4

Beta strand

84 – 91

8

Helix

95 – 111

17

Beta strand

117 – 123

7

Turn

128 – 130

3

Helix

135 – 144

10

Beta strand

148 – 151

4

Beta strand

154 – 156

3

Helix

160 – 169

10

Sequences

	Sequence		Length	Mass (Da)
	Q9SN68 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 769F75CFC708C6D0	FASTA	200	21,873
	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

References

	« Hide 'large scale' referencesShow '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. , 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]	"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.

IPI

IPI00520138.

PIR

T06157.

RefSeq

NP_193699.1. NM_118084.4.

UniGene

At.2030.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q9SN68.

SMR

Q9SN68. Positions 8-172.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9SN68. 2 interactions.

Proteomic databases

PaxDb

Q9SN68.

PRIDE

Q9SN68.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT4G19640.1; AT4G19640.1; AT4G19640.

GeneID

827706.

KEGG

ath:AT4G19640.

Organism-specific databases

TAIR

At4g19640.

Phylogenomic databases

eggNOG

COG1100.

HOGENOM

HOG000233968.

InParanoid

Q9SN68.

KO

K07976.

OMA

VDLQESN.

PhylomeDB

Q9SN68.

ProtClustDB

CLSN2685695.

Gene expression databases

ArrayExpress

Q9SN68.

Genevestigator

Q9SN68.

Family and domain databases

InterPro

IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]

Pfam

PF00071. Ras. 1 hit.
[Graphical view]

PRINTS

PR00449. RASTRNSFRMNG.

SMART

SM00175. RAB. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00231. small_GTP. 1 hit.

PROSITE

PS51419. RAB. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9SN68.

Entry information

Entry name

RAF2B_ARATH

Accession

Primary (citable) accession number: Q9SN68

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 5, 2011
Last sequence update:	May 1, 2000
Last modified:	May 1, 2013
This is version 95 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program