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P20338 (RAB4A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 158. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ras-related protein Rab-4A
Gene names
Name:RAB4A
Synonyms:RAB4
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length218 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Protein transport. Probably involved in vesicular traffic By similarity.

Subunit structure

Interacts with SGSM1, SGSM2 and SGSM3 By similarity. Interacts with RAB11FIP1, RABEP1, ZFYVE20 and RUFY1. Interacts (membrane-bound form) with NDRG1; the interaction involves NDRG1 in vesicular recycling of E-cadherin. Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15 Ref.18

Subcellular location

Membrane; Peripheral membrane protein. Cytoplasm. Note: Generally associated with membranes. Cytoplasmic when phosphorylated by CDK1.

Post-translational modification

Phosphorylated by CDK1 kinase during mitosis. Ref.8 Ref.9

Sequence similarities

Belongs to the small GTPase superfamily. Rab family.

Caution

It is uncertain whether Met-1 or Met-6 is the initiator.

Sequence caution

The sequence AAA60244.1 differs from that shown. Reason: Frameshift at position 6.

Ontologies

Keywords
   Biological processProtein transport
Transport
   Cellular componentCytoplasm
Membrane
   LigandGTP-binding
Nucleotide-binding
   PTMLipoprotein
Methylation
Phosphoprotein
Prenylation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processGTP catabolic process

Inferred from direct assay Ref.17Ref.18. Source: GOC

antigen processing and presentation

Inferred from mutant phenotype PubMed 19717423. Source: UniProtKB

membrane organization

Traceable author statement. Source: Reactome

regulation of endocytosis

Inferred from electronic annotation. Source: Ensembl

small GTPase mediated signal transduction

Inferred from electronic annotation. Source: InterPro

   Cellular_componentendosome

Inferred from electronic annotation. Source: Ensembl

extracellular vesicular exosome

Inferred from direct assay PubMed 15326289. Source: UniProtKB

membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

perinuclear region of cytoplasm

Inferred from direct assay PubMed 19590752. Source: UniProtKB

vesicle

Inferred from direct assay PubMed 19590752. Source: UniProtKB

   Molecular_functionGDP binding

Inferred from direct assay Ref.17Ref.18. Source: UniProtKB

GTP binding

Inferred from direct assay Ref.17Ref.18. Source: UniProtKB

GTPase activity

Inferred from direct assay Ref.17Ref.18. Source: UniProtKB

protein binding

Inferred from physical interaction Ref.18PubMed 18227069. Source: UniProtKB

protein transporter activity

Inferred from electronic annotation. Source: Ensembl

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 218218Ras-related protein Rab-4A
PRO_0000121093

Regions

Nucleotide binding20 – 289GTP
Nucleotide binding68 – 725GTP
Nucleotide binding126 – 1294GTP
Nucleotide binding156 – 1583GTP
Motif42 – 509Effector region By similarity

Amino acid modifications

Modified residue2041Phosphoserine; by CDK1 Ref.9
Modified residue2181Cysteine methyl ester By similarity
Lipidation2161S-geranylgeranyl cysteine By similarity
Lipidation2181S-geranylgeranyl cysteine By similarity

Experimental info

Mutagenesis511G → A: 10-fold decrease in ZFYVE20 binding affinity. Ref.18
Mutagenesis511G → L: 10-fold decrease in ZFYVE20 binding affinity. Ref.18
Sequence conflict1621N → D in AAA60244. Ref.1
Sequence conflict2081A → T in AAA60244. Ref.1

Secondary structure

.............................. 218
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P20338 [UniParc].

Last modified March 6, 2013. Version 3.
Checksum: 983D65E1162741B0

FASTA21824,390
        10         20         30         40         50         60 
MSQTAMSETY DFLFKFLVIG NAGTGKSCLL HQFIEKKFKD DSNHTIGVEF GSKIINVGGK 

        70         80         90        100        110        120 
YVKLQIWDTA GQERFRSVTR SYYRGAAGAL LVYDITSRET YNALTNWLTD ARMLASQNIV 

       130        140        150        160        170        180 
IILCGNKKDL DADREVTFLE ASRFAQENEL MFLETSALTG ENVEEAFVQC ARKILNKIES 

       190        200        210 
GELDPERMGS GIQYGDAALR QLRSPRRAQA PNAQECGC 

« Hide

References

« Hide 'large scale' references
[1]"The human Rab genes encode a family of GTP-binding proteins related to yeast YPT1 and SEC4 products involved in secretion."
Zahraoui A., Touchot N., Chardin P., Tavitian A.
J. Biol. Chem. 264:12394-12401(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Regulation of CD4 expression via recycling by HRES-1/RAB4 controls susceptibility to HIV infection."
Nagy G., Ward J., Mosser D.D., Koncz A., Gergely P. Jr., Stancato C., Qian Y., Fernandez D., Niland B., Grossman C.E., Telarico T., Banki K., Perl A.
J. Biol. Chem. 281:34574-34591(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]"cDNA clones of human proteins involved in signal transduction sequenced by the Guthrie cDNA resource center (www.cdna.org)."
Puhl H.L. III, Ikeda S.R., Aronstam R.S.
Submitted (APR-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Brain.
[4]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Caudate nucleus.
[5]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Skin and Uterus.
[8]"Phosphorylation of two small GTP-binding proteins of the Rab family by p34cdc2."
Bailly E., McCaffrey M., Touchot N., Zahraoui A., Goud B., Bornens M.
Nature 350:715-718(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION BY CDK1.
[9]"Reversible phosphorylation-dephosphorylation determines the localization of rab4 during the cell cycle."
van der Sluijs P., Hull M., Huber L.A., Male P., Goud B., Mellman I.
EMBO J. 11:4379-4389(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT SER-204 BY CDK1.
[10]"Rabaptin4, a novel effector of the small GTPase rab4a, is recruited to perinuclear recycling vesicles."
Nagelkerken B., van Anken E., van Raak M., Gerez L., Mohrmann K., van Uden N., Holthuizen J., Pelkmans L., van der Sluijs P.
Biochem. J. 346:593-601(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RABEP1.
[11]"Rab coupling protein (RCP), a novel Rab4 and Rab11 effector protein."
Lindsay A.J., Hendrick A.G., Cantalupo G., Senic-Matuglia F., Goud B., Bucci C., McCaffrey M.W.
J. Biol. Chem. 277:12190-12199(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RAB11FIP1.
Tissue: Cervix carcinoma.
[12]"Divalent Rab effectors regulate the sub-compartmental organization and sorting of early endosomes."
de Renzis S., Soennichsen B., Zerial M.
Nat. Cell Biol. 4:124-133(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH ZFYVE20.
[13]"Characterisation of the Rab binding properties of Rab coupling protein (RCP) by site-directed mutagenesis."
Lindsay A.J., McCaffrey M.W.
FEBS Lett. 571:86-92(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RAB11FIP1.
[14]"Rabip4' is an effector of rab5 and rab4 and regulates transport through early endosomes."
Fouraux M.A., Deneka M., Ivan V., van der Heijden A., Raymackers J., van Suylekom D., van Venrooij W.J., van der Sluijs P., Pruijn G.J.M.
Mol. Biol. Cell 15:611-624(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RUFY1.
[15]"The N-Myc down regulated Gene1 (NDRG1) is a Rab4a effector involved in vesicular recycling of E-cadherin."
Kachhap S.K., Faith D., Qian D.Z., Shabbeer S., Galloway N.L., Pili R., Denmeade S.R., DeMarzo A.M., Carducci M.A.
PLoS ONE 2:E844-E844(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH NDRG1.
[16]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[17]"High resolution crystal structures of human Rab4a in its active and inactive conformations."
Huber S.K., Scheidig A.J.
FEBS Lett. 579:2821-2829(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.57 ANGSTROMS) OF 6-189 IN COMPLEX WITH GTP ANALOG AND GDP.
[18]"Structural basis of family-wide Rab GTPase recognition by rabenosyn-5."
Eathiraj S., Pan X., Ritacco C., Lambright D.G.
Nature 436:415-419(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) OF 7-177 IN COMPLEX WITH GTP, INTERACTION WITH ZFYVE20, MUTAGENESIS OF GLY-51.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M28211 mRNA. Translation: AAA60244.1. Frameshift.
AY585832 mRNA. Translation: AAT91347.1.
AF498934 mRNA. Translation: AAM21082.1.
AK313807 mRNA. Translation: BAG36543.1.
AL162595, AL117350 Genomic DNA. Translation: CAI19037.1.
AL117350, AL162595 Genomic DNA. Translation: CAI22870.1.
CH471098 Genomic DNA. Translation: EAW69890.1.
BC002438 mRNA. Translation: AAH02438.1.
BC004309 mRNA. Translation: AAH04309.1.
CCDSCCDS31050.1.
PIRE34323.
RefSeqNP_001258927.1. NM_001271998.1.
NP_004569.2. NM_004578.3.
UniGeneHs.296169.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1YU9X-ray2.07A7-177[»]
1Z0KX-ray1.92A/C7-177[»]
2BMDX-ray1.80A6-189[»]
2BMEX-ray1.57A/B/C/D6-189[»]
ProteinModelPortalP20338.
SMRP20338. Positions 7-182.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid111805. 31 interactions.
DIPDIP-372N.
IntActP20338. 14 interactions.
MINTMINT-1376149.
STRING9606.ENSP00000355651.

PTM databases

PhosphoSiteP20338.

Polymorphism databases

DMDM460018296.

Proteomic databases

MaxQBP20338.
PaxDbP20338.
PRIDEP20338.

Protocols and materials databases

DNASU5867.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000366690; ENSP00000355651; ENSG00000168118.
GeneID5867.
KEGGhsa:5867.
UCSCuc001hth.4. human.

Organism-specific databases

CTD5867.
GeneCardsGC01P229406.
HGNCHGNC:9781. RAB4A.
HPACAB004990.
MIM179511. gene.
neXtProtNX_P20338.
PharmGKBPA34141.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1100.
HOVERGENHBG009351.
InParanoidP20338.
KOK07879.
OMADESNHTI.
OrthoDBEOG7QK0CV.
PhylomeDBP20338.
TreeFamTF300032.

Enzyme and pathway databases

ReactomeREACT_11123. Membrane Trafficking.
SignaLinkP20338.

Gene expression databases

BgeeP20338.
CleanExHS_RAB4A.
GenevestigatorP20338.

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

EvolutionaryTraceP20338.
GeneWikiRAB4A.
GenomeRNAi5867.
NextBio22786.
PROP20338.
SOURCESearch...

Entry information

Entry nameRAB4A_HUMAN
AccessionPrimary (citable) accession number: P20338
Secondary accession number(s): Q5T7P7, Q9BQ44
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: March 6, 2013
Last modified: July 9, 2014
This is version 158 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM