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Protein

Rab5 GDP/GTP exchange factor

Gene

RABGEF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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
  • zinc ion binding Source: InterPro

GO - Biological processi

  • endocytosis Source: UniProtKB-KW
  • protein targeting to membrane Source: UniProtKB

Keywordsi

Biological processEndocytosis, Protein transport, Transport, Ubl conjugation pathway
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-8854214 TBC/RABGAPs
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
SIGNORiQ9UJ41

Protein family/group databases

TCDBi1.F.1.1.5 the synaptosomal vesicle fusion pore (svf-pore) family

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

EuPathDBiHostDB:ENSG00000154710.15
HGNCiHGNC:17676 RABGEF1
MIMi609700 gene
neXtProtiNX_Q9UJ41

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
ProteomicsDBi84583
84584 [Q9UJ41-2]
84585 [Q9UJ41-3]

PTM databases

iPTMnetiQ9UJ41
PhosphoSitePlusiQ9UJ41

Expressioni

Gene expression databases

BgeeiENSG00000154710 Expressed in 92 organ(s), highest expression level in ectocervix
CleanExiHS_RABGEF1
ExpressionAtlasiQ9UJ41 baseline and differential
GenevisibleiQ9UJ41 HS

Organism-specific databases

HPAiHPA001407

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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi118154, 94 interactors
DIPiDIP-29348N
IntActiQ9UJ41, 47 interactors
MINTiQ9UJ41

Structurei

Secondary structure

1708
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

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
OMAiRCCRHIF
OrthoDBiEOG091G059N
PhylomeDBiQ9UJ41
TreeFamiTF321331

Family and domain databases

Gene3Di1.20.1050.80, 1 hit
InterProiView protein in InterPro
IPR003123 VPS9
IPR037191 VPS9_dom_sf
IPR002653 Znf_A20
PfamiView protein in Pfam
PF02204 VPS9, 1 hit
PF01754 zf-A20, 1 hit
SMARTiView protein in SMART
SM00167 VPS9, 1 hit
SM00259 ZnF_A20, 1 hit
SUPFAMiSSF109993 SSF109993, 1 hit
PROSITEiView protein in PROSITE
PS51205 VPS9, 1 hit
PS51036 ZF_A20, 1 hit

Sequences (4+)i

Sequence statusi: Complete.

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

This entry has 4 described isoforms and 7 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 7 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
E9PFK9E9PFK9_HUMAN
Rab5 GDP/GTP exchange factor
RABGEF1
504Annotation score:
Q3HKR1Q3HKR1_HUMAN
RAP1 short isoform
RABGEF1
407Annotation score:
C9JDA2C9JDA2_HUMAN
Rab5 GDP/GTP exchange factor
RABGEF1
45Annotation score:
V9GYI8V9GYI8_HUMAN
Rab5 GDP/GTP exchange factor
RABGEF1
119Annotation score:
A0A0A0MSJ3A0A0A0MSJ3_HUMAN
RAB guanine nucleotide exchange fac...
RABGEF1 hCG_39434
299Annotation score:
A0A1W2PPY0A0A1W2PPY0_HUMAN
Rab5 GDP/GTP exchange factor
RABGEF1
94Annotation score:
E9PHB8E9PHB8_HUMAN
Uncharacterized protein
232Annotation score:

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

Similar proteinsi

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-ray2.40A139-199[»]
2C7NX-ray2.10A/C/E/G/I/K139-199[»]
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, 94 interactors
DIPiDIP-29348N
IntActiQ9UJ41, 47 interactors
MINTiQ9UJ41

Protein family/group databases

TCDBi1.F.1.1.5 the synaptosomal vesicle fusion pore (svf-pore) family

PTM databases

iPTMnetiQ9UJ41
PhosphoSitePlusiQ9UJ41

Polymorphism and mutation databases

BioMutaiRABGEF1
DMDMi56405102

Proteomic databases

EPDiQ9UJ41
PeptideAtlasiQ9UJ41
PRIDEiQ9UJ41
ProteomicsDBi84583
84584 [Q9UJ41-2]
84585 [Q9UJ41-3]

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
EuPathDBiHostDB:ENSG00000154710.15
GeneCardsiRABGEF1
HGNCiHGNC:17676 RABGEF1
HPAiHPA001407
MIMi609700 gene
neXtProtiNX_Q9UJ41
OpenTargetsiENSG00000154710
PharmGKBiPA134946532
GenAtlasiSearch...

Phylogenomic databases

GeneTreeiENSGT00530000063341
HOGENOMiHOG000070180
HOVERGENiHBG062584
InParanoidiQ9UJ41
KOiK20131
OMAiRCCRHIF
OrthoDBiEOG091G059N
PhylomeDBiQ9UJ41
TreeFamiTF321331

Enzyme and pathway databases

ReactomeiR-HSA-8854214 TBC/RABGAPs
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
SIGNORiQ9UJ41

Miscellaneous databases

ChiTaRSiRABGEF1 human
EvolutionaryTraceiQ9UJ41
GeneWikiiRABGEF1
GenomeRNAii27342
PROiPR:Q9UJ41
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000154710 Expressed in 92 organ(s), highest expression level in ectocervix
CleanExiHS_RABGEF1
ExpressionAtlasiQ9UJ41 baseline and differential
GenevisibleiQ9UJ41 HS

Family and domain databases

Gene3Di1.20.1050.80, 1 hit
InterProiView protein in InterPro
IPR003123 VPS9
IPR037191 VPS9_dom_sf
IPR002653 Znf_A20
PfamiView protein in Pfam
PF02204 VPS9, 1 hit
PF01754 zf-A20, 1 hit
SMARTiView protein in SMART
SM00167 VPS9, 1 hit
SM00259 ZnF_A20, 1 hit
SUPFAMiSSF109993 SSF109993, 1 hit
PROSITEiView protein in PROSITE
PS51205 VPS9, 1 hit
PS51036 ZF_A20, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRABX5_HUMAN
AccessioniPrimary (citable) accession number: Q9UJ41
Secondary accession number(s): B4DZM7
, Q3HKR2, Q3HKR3, Q53FG0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: November 7, 2018
This is version 163 of the entry and version 2 of the sequence. See 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. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
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