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Protein

Rab5 GDP/GTP exchange factor

Gene

RABGEF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).By similarity3 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri151 – 185A20-typePROSITE-ProRule annotationAdd BLAST35

GO - Molecular functioni

  • DNA binding Source: InterPro
  • Rab GTPase binding Source: UniProtKB
  • Rab guanyl-nucleotide exchange factor activity Source: UniProtKB
  • ubiquitin protein ligase activity Source: Ensembl
  • zinc ion binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Endocytosis, Protein transport, Transport, Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000154710-MONOMER.
ReactomeiR-HSA-8876198. RAB GEFs exchange GTP for GDP on RABs.
SIGNORiQ9UJ41.

Names & Taxonomyi

Protein namesi
Recommended name:
Rab5 GDP/GTP exchange factor
Alternative name(s):
RAP1
Rabaptin-5-associated exchange factor for Rab5
Rabex-5
Gene namesi
Name:RABGEF1
Synonyms:RABEX5
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:17676. RABGEF1.

Subcellular locationi

GO - Cellular componenti

  • early endosome Source: UniProtKB
  • recycling endosome Source: UniProtKB-SubCell
  • vesicle Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi196A → G: Reduces affinity for ubiquitin 3-fold. 1 Publication1
Mutagenesisi530D → A: Strongly reduced activity. 1 Publication1
Mutagenesisi534P → A: Strongly reduced activity. 1 Publication1
Mutagenesisi571Y → A: Strongly reduced activity. 1 Publication1
Mutagenesisi574T → A: Strongly reduced activity. 1 Publication1

Organism-specific databases

DisGeNETi27342.
OpenTargetsiENSG00000154710.
PharmGKBiPA134946532.

Polymorphism and mutation databases

BioMutaiRABGEF1.
DMDMi56405102.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001913151 – 708Rab5 GDP/GTP exchange factorAdd BLAST708

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei302PhosphoserineCombined sources1
Modified residuei310PhosphoserineCombined sources1
Modified residuei329N6-acetyllysineCombined sources1
Modified residuei348N6-acetyllysineCombined sources1
Modified residuei590PhosphoserineCombined sources1
Modified residuei594PhosphoserineCombined sources1
Modified residuei607PhosphoserineBy similarity1
Modified residuei617PhosphoserineCombined sources1

Post-translational modificationi

Monoubiquitinated.

Keywords - PTMi

Acetylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9UJ41.
PeptideAtlasiQ9UJ41.
PRIDEiQ9UJ41.

PTM databases

iPTMnetiQ9UJ41.
PhosphoSitePlusiQ9UJ41.

Expressioni

Gene expression databases

BgeeiENSG00000154710.
CleanExiHS_RABGEF1.
ExpressionAtlasiQ9UJ41. baseline and differential.
GenevisibleiQ9UJ41. HS.

Organism-specific databases

HPAiCAB037056.
HPA001407.

Interactioni

Subunit structurei

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.By similarity6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
BLOC1S6Q9UL453EBI-913954,EBI-465781
CIPCQ9C0C63EBI-913954,EBI-5654244
DAZAP2Q150383EBI-913954,EBI-724310
EGFRP005334EBI-913954,EBI-297353
KXD1Q9BQD32EBI-913954,EBI-739657
TEAD4D3DUQ63EBI-913954,EBI-10176734
THOC1Q96FV93EBI-913954,EBI-1765605
TRIM15Q9C0193EBI-913954,EBI-2342111
TRIM54Q9BYV23EBI-913954,EBI-2130429
TXN2Q997573EBI-913954,EBI-2932492
UBBP0CG476EBI-913954,EBI-413034
UBCP629902EBI-913954,EBI-413053From a different organism.
UBCQ96C323EBI-913954,EBI-745483
ZC2HC1CQ53FD03EBI-913954,EBI-740767

GO - Molecular functioni

  • Rab GTPase binding Source: UniProtKB

Protein-protein interaction databases

BioGridi118154. 58 interactors.
DIPiDIP-29348N.
IntActiQ9UJ41. 23 interactors.
MINTiMINT-1189235.

Structurei

Secondary structure

1708
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi161 – 163Combined sources3
Helixi167 – 169Combined sources3
Helixi174 – 198Combined sources25
Helixi239 – 248Combined sources10
Helixi318 – 325Combined sources8
Helixi328 – 346Combined sources19
Turni347 – 350Combined sources4
Helixi353 – 372Combined sources20
Helixi418 – 440Combined sources23
Helixi448 – 461Combined sources14
Turni462 – 464Combined sources3
Turni467 – 471Combined sources5
Helixi479 – 494Combined sources16
Helixi495 – 497Combined sources3
Helixi501 – 523Combined sources23
Helixi529 – 543Combined sources15
Helixi548 – 558Combined sources11
Turni561 – 565Combined sources5
Helixi568 – 585Combined sources18
Helixi589 – 591Combined sources3
Helixi595 – 602Combined sources8
Helixi626 – 632Combined sources7
Helixi634 – 669Combined sources36

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TXUX-ray2.35A311-611[»]
2C7MX-ray2.40A139-252[»]
2C7NX-ray2.10A/C/E/G/I/K139-252[»]
2OT3X-ray2.10A310-614[»]
4N3XX-ray2.00A/B/C/D626-672[»]
4N3YX-ray2.20A630-672[»]
4N3ZX-ray3.10A310-672[»]
4Q9UX-ray4.62A/E310-672[»]
ProteinModelPortaliQ9UJ41.
SMRiQ9UJ41.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UJ41.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini449 – 592VPS9PROSITE-ProRule annotationAdd BLAST144

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni139 – 252Interaction with ubiquitinated proteinsAdd BLAST114

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili624 – 665Sequence analysisAdd BLAST42

Sequence similaritiesi

Contains 1 A20-type zinc finger.PROSITE-ProRule annotation
Contains 1 VPS9 domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri151 – 185A20-typePROSITE-ProRule annotationAdd BLAST35

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00530000063341.
HOGENOMiHOG000070180.
HOVERGENiHBG062584.
InParanoidiQ9UJ41.
KOiK20131.
OMAiWTDGIAR.
OrthoDBiEOG091G059N.
PhylomeDBiQ9UJ41.
TreeFamiTF321331.

Family and domain databases

InterProiIPR003123. VPS9.
IPR002653. Znf_A20.
[Graphical view]
PfamiPF02204. VPS9. 1 hit.
PF01754. zf-A20. 1 hit.
[Graphical view]
SMARTiSM00167. VPS9. 1 hit.
SM00259. ZnF_A20. 1 hit.
[Graphical view]
PROSITEiPS51205. VPS9. 1 hit.
PS51036. ZF_A20. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UJ41-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MVVVTGREPD SRRQDGAMSS SDAEDDFLEP ATPTATQAGH ALPLLPQERC
60 70 80 90 100
AEFPALRGPP TQGACSSCVQ RGPVLCHRAP PGAAGEHAAT EGREGAPSVS
110 120 130 140 150
GTHALLQRPL GADCGDRPAA CGPAEGPLCQ AQVVSRKKMS LKSERRGIHV
160 170 180 190 200
DQSDLLCKKG CGYYGNPAWQ GFCSKCWREE YHKARQKQIQ EDWELAERVL
210 220 230 240 250
LCCPGWSAMV QFQLTATSAS WAQVILLLQP PKWLGLQKLQ REEEEAFASS
260 270 280 290 300
QSSQGAQSLT FSKFEEKKTN EKTRKVTTVK KFFSASSRVG SKKEIQEAKA
310 320 330 340 350
PSPSINRQTS IETDRVSKEF IEFLKTFHKT GQEIYKQTKL FLEGMHYKRD
360 370 380 390 400
LSIEEQSECA QDFYHNVAER MQTRGKERRF HHVGQAGLEL LTSGDPPASA
410 420 430 440 450
SQSAGNTGVE PPHPAVPPER VEKIMDQIEK YIMTRLYKYV FCPETTDDEK
460 470 480 490 500
KDLAIQKRIR ALRWVTPQML CVPVNEDIPE VSDMVVKAIT DIIEMDSKRV
510 520 530 540 550
PRDKLACITK CSKHIFNAIK ITKNEPASAD DFLPTLIYIV LKGNPPRLQS
560 570 580 590 600
NIQYITRFCN PSRLMTGEDG YYFTNLCCAV AFIEKLDAQS LNLSQEDFDR
610 620 630 640 650
YMSGQTSPRK QEAESWSPDA CLGVKQMYKN LDLLSQLNER QERIMNEAKK
660 670 680 690 700
LEKDLIDWTD GIAREVQDIV EKYPLEIKPP NQPLAAIDSE NVENDKLPPP

LQPQVYAG
Note: No experimental confirmation available.
Length:708
Mass (Da):79,371
Last modified:July 5, 2004 - v2
Checksum:i007E404F13AC91D8
GO
Isoform 2 (identifier: Q9UJ41-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-138: Missing.
     199-238: Missing.
     377-415: Missing.

Show »
Length:491
Mass (Da):56,891
Checksum:i49ACABA276E65E91
GO
Isoform 3 (identifier: Q9UJ41-3) [UniParc]FASTAAdd to basket
Also known as: Long

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

Show »
Length:531
Mass (Da):61,300
Checksum:i3C21934AA5ABBF9A
GO
Isoform 4 (identifier: Q9UJ41-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-8: MVVVTGRE → MMASSYHE
     9-132: Missing.
     199-238: Missing.
     377-415: Missing.

Note: No experimental confirmation available.
Show »
Length:505
Mass (Da):58,526
Checksum:i655A49886ADE2891
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti199V → A in ABA64474 (Ref. 2) Curated1
Sequence conflicti203C → Y in ABA64474 (Ref. 2) Curated1
Sequence conflicti476E → D in BAC87138 (PubMed:14702039).Curated1
Sequence conflicti487K → R in BAD97049 (Ref. 5) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0106901 – 138Missing in isoform 2 and isoform 3. 5 PublicationsAdd BLAST138
Alternative sequenceiVSP_0546431 – 8MVVVTGRE → MMASSYHE in isoform 4. 1 Publication8
Alternative sequenceiVSP_0546449 – 132Missing in isoform 4. 1 PublicationAdd BLAST124
Alternative sequenceiVSP_010691199 – 238Missing in isoform 2 and isoform 4. 6 PublicationsAdd BLAST40
Alternative sequenceiVSP_010692377 – 415Missing in isoform 2, isoform 3 and isoform 4. 6 PublicationsAdd BLAST39

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ250042 mRNA. Translation: CAB57359.1.
DQ230533 mRNA. Translation: ABA64473.1.
DQ230534 mRNA. Translation: ABA64474.1.
BT007107 mRNA. Translation: AAP35771.1.
AK127790 mRNA. Translation: BAC87138.1.
AK303006 mRNA. Translation: BAG64139.1.
AK223329 mRNA. Translation: BAD97049.1.
AC027644 Genomic DNA. Translation: AAQ93362.1.
AC079588 Genomic DNA. No translation available.
BC015330 mRNA. Translation: AAH15330.1.
CCDSiCCDS5535.1. [Q9UJ41-2]
CCDS69308.1. [Q9UJ41-4]
RefSeqiNP_001273989.1. NM_001287060.1.
NP_001273990.1. NM_001287061.1. [Q9UJ41-4]
NP_001273991.1. NM_001287062.1. [Q9UJ41-2]
NP_055319.1. NM_014504.2. [Q9UJ41-2]
UniGeneiHs.530053.
Hs.662268.
Hs.733181.

Genome annotation databases

EnsembliENST00000284957; ENSP00000284957; ENSG00000154710. [Q9UJ41-2]
ENST00000380828; ENSP00000370208; ENSG00000154710. [Q9UJ41-4]
ENST00000450873; ENSP00000415815; ENSG00000154710. [Q9UJ41-2]
GeneIDi27342.
KEGGihsa:27342.
UCSCiuc003tvh.4. human. [Q9UJ41-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ250042 mRNA. Translation: CAB57359.1.
DQ230533 mRNA. Translation: ABA64473.1.
DQ230534 mRNA. Translation: ABA64474.1.
BT007107 mRNA. Translation: AAP35771.1.
AK127790 mRNA. Translation: BAC87138.1.
AK303006 mRNA. Translation: BAG64139.1.
AK223329 mRNA. Translation: BAD97049.1.
AC027644 Genomic DNA. Translation: AAQ93362.1.
AC079588 Genomic DNA. No translation available.
BC015330 mRNA. Translation: AAH15330.1.
CCDSiCCDS5535.1. [Q9UJ41-2]
CCDS69308.1. [Q9UJ41-4]
RefSeqiNP_001273989.1. NM_001287060.1.
NP_001273990.1. NM_001287061.1. [Q9UJ41-4]
NP_001273991.1. NM_001287062.1. [Q9UJ41-2]
NP_055319.1. NM_014504.2. [Q9UJ41-2]
UniGeneiHs.530053.
Hs.662268.
Hs.733181.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TXUX-ray2.35A311-611[»]
2C7MX-ray2.40A139-252[»]
2C7NX-ray2.10A/C/E/G/I/K139-252[»]
2OT3X-ray2.10A310-614[»]
4N3XX-ray2.00A/B/C/D626-672[»]
4N3YX-ray2.20A630-672[»]
4N3ZX-ray3.10A310-672[»]
4Q9UX-ray4.62A/E310-672[»]
ProteinModelPortaliQ9UJ41.
SMRiQ9UJ41.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi118154. 58 interactors.
DIPiDIP-29348N.
IntActiQ9UJ41. 23 interactors.
MINTiMINT-1189235.

PTM databases

iPTMnetiQ9UJ41.
PhosphoSitePlusiQ9UJ41.

Polymorphism and mutation databases

BioMutaiRABGEF1.
DMDMi56405102.

Proteomic databases

EPDiQ9UJ41.
PeptideAtlasiQ9UJ41.
PRIDEiQ9UJ41.

Protocols and materials databases

DNASUi27342.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000284957; ENSP00000284957; ENSG00000154710. [Q9UJ41-2]
ENST00000380828; ENSP00000370208; ENSG00000154710. [Q9UJ41-4]
ENST00000450873; ENSP00000415815; ENSG00000154710. [Q9UJ41-2]
GeneIDi27342.
KEGGihsa:27342.
UCSCiuc003tvh.4. human. [Q9UJ41-1]

Organism-specific databases

CTDi27342.
DisGeNETi27342.
GeneCardsiRABGEF1.
HGNCiHGNC:17676. RABGEF1.
HPAiCAB037056.
HPA001407.
MIMi609700. gene.
neXtProtiNX_Q9UJ41.
OpenTargetsiENSG00000154710.
PharmGKBiPA134946532.
GenAtlasiSearch...

Phylogenomic databases

GeneTreeiENSGT00530000063341.
HOGENOMiHOG000070180.
HOVERGENiHBG062584.
InParanoidiQ9UJ41.
KOiK20131.
OMAiWTDGIAR.
OrthoDBiEOG091G059N.
PhylomeDBiQ9UJ41.
TreeFamiTF321331.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000154710-MONOMER.
ReactomeiR-HSA-8876198. RAB GEFs exchange GTP for GDP on RABs.
SIGNORiQ9UJ41.

Miscellaneous databases

ChiTaRSiRABGEF1. human.
EvolutionaryTraceiQ9UJ41.
GeneWikiiRABGEF1.
GenomeRNAii27342.
PROiQ9UJ41.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000154710.
CleanExiHS_RABGEF1.
ExpressionAtlasiQ9UJ41. baseline and differential.
GenevisibleiQ9UJ41. HS.

Family and domain databases

InterProiIPR003123. VPS9.
IPR002653. Znf_A20.
[Graphical view]
PfamiPF02204. VPS9. 1 hit.
PF01754. zf-A20. 1 hit.
[Graphical view]
SMARTiSM00167. VPS9. 1 hit.
SM00259. ZnF_A20. 1 hit.
[Graphical view]
PROSITEiPS51205. VPS9. 1 hit.
PS51036. ZF_A20. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRABX5_HUMAN
AccessioniPrimary (citable) accession number: Q9UJ41
Secondary accession number(s): B4DZM7
, Q3HKR2, Q3HKR3, Q53FG0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: November 30, 2016
This is version 146 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.