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Q9UJ41 (RABX5_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 117. 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·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Rab5 GDP/GTP exchange factor
Alternative name(s):
RAP1
Rabaptin-5-associated exchange factor for Rab5
Rabex-5
Gene names
Name:RABGEF1
Synonyms:RABEX5
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length708 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Rab effector protein acting as linker between gamma-adaptin, RAB4A or RAB5A. Involved in endocytic membrane fusion and membrane trafficking of recycling endosomes. Stimulates nucleotide exchange on RAB5A. Can act as a ubiquitin ligase By similarity. Ref.8 Ref.9 Ref.11

Subunit structure

Interacts with RGS14; the interaction is GTP-dependent By similarity. Heterodimer with RABEP1. The heterodimer binds RAB4A and RAB5A that have been activated by GTP-binding. Interacts with RAB21, and with 100-fold lower affinity also with RAB22. Binds TSC2, GGA1, GGA2, GGA3, AP1G1 and AP1G2. Interacts with ubiquitinated EGFR. Ref.8 Ref.9 Ref.10 Ref.11

Subcellular location

Cytoplasm. Early endosome. Recycling endosome Ref.10.

Post-translational modification

Monoubiquitinated.

Sequence similarities

Contains 1 A20-type zinc finger.

Contains 1 VPS9 domain.

Binary interactions

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9UJ41-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Note: No experimental confirmation available.
Isoform 2 (identifier: Q9UJ41-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-138: Missing.
     199-238: Missing.
     377-415: Missing.
Isoform 3 (identifier: Q9UJ41-3)

Also known as: Long;

The sequence of this isoform differs from the canonical sequence as follows:
     1-138: Missing.
     377-415: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 708708Rab5 GDP/GTP exchange factor
PRO_0000191315

Regions

Domain449 – 592144VPS9
Zinc finger151 – 18535A20-type
Region139 – 252114Interaction with ubiquitinated proteins
Coiled coil624 – 66542 Potential

Natural variations

Alternative sequence1 – 138138Missing in isoform 2 and isoform 3.
VSP_010690
Alternative sequence199 – 23840Missing in isoform 2.
VSP_010691
Alternative sequence377 – 41539Missing in isoform 2 and isoform 3.
VSP_010692

Experimental info

Mutagenesis1961A → G: Reduces affinity for ubiquitin 3-fold. Ref.12
Mutagenesis5301D → A: Strongly reduced activity. Ref.11
Mutagenesis5341P → A: Strongly reduced activity. Ref.11
Mutagenesis5711Y → A: Strongly reduced activity. Ref.11
Mutagenesis5741T → A: Strongly reduced activity. Ref.11
Sequence conflict1991V → A in ABA64474. Ref.2
Sequence conflict2031C → Y in ABA64474. Ref.2
Sequence conflict4761E → D in BAC87138. Ref.3
Sequence conflict4871K → R in BAD97049. Ref.5

Secondary structure

........................................ 708
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 5, 2004. Version 2.
Checksum: 007E404F13AC91D8

FASTA70879,371
        10         20         30         40         50         60 
MVVVTGREPD SRRQDGAMSS SDAEDDFLEP ATPTATQAGH ALPLLPQERC AEFPALRGPP 

        70         80         90        100        110        120 
TQGACSSCVQ RGPVLCHRAP PGAAGEHAAT EGREGAPSVS GTHALLQRPL GADCGDRPAA 

       130        140        150        160        170        180 
CGPAEGPLCQ AQVVSRKKMS LKSERRGIHV DQSDLLCKKG CGYYGNPAWQ GFCSKCWREE 

       190        200        210        220        230        240 
YHKARQKQIQ EDWELAERVL LCCPGWSAMV QFQLTATSAS WAQVILLLQP PKWLGLQKLQ 

       250        260        270        280        290        300 
REEEEAFASS QSSQGAQSLT FSKFEEKKTN EKTRKVTTVK KFFSASSRVG SKKEIQEAKA 

       310        320        330        340        350        360 
PSPSINRQTS IETDRVSKEF IEFLKTFHKT GQEIYKQTKL FLEGMHYKRD LSIEEQSECA 

       370        380        390        400        410        420 
QDFYHNVAER MQTRGKERRF HHVGQAGLEL LTSGDPPASA SQSAGNTGVE PPHPAVPPER 

       430        440        450        460        470        480 
VEKIMDQIEK YIMTRLYKYV FCPETTDDEK KDLAIQKRIR ALRWVTPQML CVPVNEDIPE 

       490        500        510        520        530        540 
VSDMVVKAIT DIIEMDSKRV PRDKLACITK CSKHIFNAIK ITKNEPASAD DFLPTLIYIV 

       550        560        570        580        590        600 
LKGNPPRLQS NIQYITRFCN PSRLMTGEDG YYFTNLCCAV AFIEKLDAQS LNLSQEDFDR 

       610        620        630        640        650        660 
YMSGQTSPRK QEAESWSPDA CLGVKQMYKN LDLLSQLNER QERIMNEAKK LEKDLIDWTD 

       670        680        690        700 
GIAREVQDIV EKYPLEIKPP NQPLAAIDSE NVENDKLPPP LQPQVYAG 

« Hide

Isoform 2 [UniParc].

Checksum: 49ACABA276E65E91
Show »

FASTA49156,891
Isoform 3 (Long) [UniParc].

Checksum: 3C21934AA5ABBF9A
Show »

FASTA53161,300

References

« Hide 'large scale' references
[1]"Seven genes that are differentially transcribed in colorectal tumor cell lines."
Nimmrich I., Erdmann S., Melchers U., Finke U., Hentsch S., Moyer M.P., Hoffmann I., Mueller O.
Cancer Lett. 160:37-43(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
[2]Barbieri M.A., Hunker C.M.
Submitted (OCT-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2 AND 3).
Tissue: Cervix carcinoma.
[3]"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] (ISOFORM 1).
Tissue: Brain.
[4]"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
[5]Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Testis.
[6]"The DNA sequence of human chromosome 7."
Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L. expand/collapse author list , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
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] (ISOFORM 2).
Tissue: Lymph.
[8]"A novel Rab5 GDP/GTP exchange factor complexed to Rabaptin-5 links nucleotide exchange to effector recruitment and function."
Horiuchi H., Lippe R., McBride H.M., Rubino M., Woodman P., Stenmark H., Rybin V., Wilm M., Ashman K., Mann M., Zerial M.
Cell 90:1149-1159(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH RABEP1.
[9]"Functional synergy between Rab5 effector Rabaptin-5 and exchange factor Rabex-5 when physically associated in a complex."
Lippe R., Miaczynska M., Rybin V., Runge A., Zerial M.
Mol. Biol. Cell 12:2219-2228(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH RABEP1.
[10]"Divalent interaction of the GGAs with the Rabaptin-5-Rabex-5 complex."
Mattera R., Arighi C.N., Lodge R., Zerial M., Bonifacino J.S.
EMBO J. 22:78-88(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH GGA1; GGA2; GGA3; AP1G1 AND AP1G2, SUBCELLULAR LOCATION.
[11]"Structure, exchange determinants, and family-wide rab specificity of the tandem helical bundle and Vps9 domains of Rabex-5."
Delprato A., Merithew E., Lambright D.G.
Cell 118:607-617(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 310-611, FUNCTION, INTERACTION WITH RAB5; RAB21 AND RAB22, MUTAGENESIS OF ASP-530; PRO-534; TYR-571 AND THR-574.
[12]"Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin."
Penengo L., Mapelli M., Murachelli A.G., Confalonieri S., Magri L., Musacchio A., Di Fiore P.P., Polo S., Schneider T.R.
Cell 124:1183-1195(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 139-252 IN COMPLEX WITH UBIQUITIN, UBIQUITINATION, MUTAGENESIS OF ALA-196.
[13]"Structural basis for Rab GTPase activation by VPS9 domain exchange factors."
Delprato A., Lambright D.G.
Nat. Struct. Mol. Biol. 14:406-412(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 310-614 IN COMPLEX WITH RAB21.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ250042 mRNA. Translation: CAB57359.1.
DQ230533 mRNA. Translation: ABA64473.1.
DQ230534 mRNA. Translation: ABA64474.1.
AK127790 mRNA. Translation: BAC87138.1.
BT007107 mRNA. Translation: AAP35771.1.
AK223329 mRNA. Translation: BAD97049.1.
AC027644 Genomic DNA. Translation: AAQ93362.1.
BC015330 mRNA. Translation: AAH15330.1.
RefSeqNP_001273989.1. NM_001287060.1.
NP_001273990.1. NM_001287061.1.
NP_001273991.1. NM_001287062.1.
NP_055319.1. NM_014504.2.
UniGeneHs.530053.
Hs.662268.
Hs.733181.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1TXUX-ray2.35A310-611[»]
2C7MX-ray2.40A139-252[»]
2C7NX-ray2.10A/C/E/G/I/K139-252[»]
2OT3X-ray2.10A310-614[»]
ProteinModelPortalQ9UJ41.
SMRQ9UJ41. Positions 155-252, 312-604.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid118154. 25 interactions.
DIPDIP-29348N.
IntActQ9UJ41. 11 interactions.
MINTMINT-1189235.
STRING9606.ENSP00000284957.

PTM databases

PhosphoSiteQ9UJ41.

Polymorphism databases

DMDM56405102.

Proteomic databases

PaxDbQ9UJ41.
PRIDEQ9UJ41.

Protocols and materials databases

DNASU27342.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000284957; ENSP00000284957; ENSG00000154710. [Q9UJ41-2]
ENST00000450873; ENSP00000415815; ENSG00000154710. [Q9UJ41-2]
GeneID27342.
KEGGhsa:27342.
UCSCuc003tvf.3. human. [Q9UJ41-1]
uc003tvh.3. human. [Q9UJ41-2]

Organism-specific databases

CTD27342.
GeneCardsGC07P066205.
HGNCHGNC:17676. RABGEF1.
HPAHPA001407.
MIM609700. gene.
neXtProtNX_Q9UJ41.
PharmGKBPA134946532.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG301606.
HOGENOMHOG000070180.
HOVERGENHBG062584.
PhylomeDBQ9UJ41.
TreeFamTF321331.

Gene expression databases

CleanExHS_RABGEF1.
GenevestigatorQ9UJ41.

Family and domain databases

InterProIPR003123. VPS9.
IPR013995. VPS9_subgr.
IPR002653. Znf_A20.
[Graphical view]
PfamPF02204. VPS9. 1 hit.
PF01754. zf-A20. 1 hit.
[Graphical view]
SMARTSM00167. VPS9. 1 hit.
SM00259. ZnF_A20. 1 hit.
[Graphical view]
PROSITEPS51205. VPS9. 1 hit.
PS51036. ZF_A20. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSRABGEF1. human.
EvolutionaryTraceQ9UJ41.
GeneWikiRABGEF1.
GenomeRNAi27342.
NextBio50418.
PROQ9UJ41.
SOURCESearch...

Entry information

Entry nameRABX5_HUMAN
AccessionPrimary (citable) accession number: Q9UJ41
Secondary accession number(s): Q3HKR2, Q3HKR3, Q53FG0
Entry history
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: April 16, 2014
This is version 117 of the entry and version 2 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 7

Human chromosome 7: entries, gene names and cross-references to MIM