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Aliases for VPS4B Gene

Aliases for VPS4B Gene

  • Vacuolar Protein Sorting 4 Homolog B (S. Cerevisiae) 2 3
  • SKD1 3 4 6
  • Suppressor Of K(+) Transport Growth Defect 1 3 4
  • Cell Migration-Inducing Gene 1 Protein 3 4
  • Suppressor Of K+ Transport Defect 1 2 3
  • Vacuolar Protein Sorting-Associated Protein 4B 3
  • Vacuolar Protein Sorting 4B (Yeast) 2
  • Vacuolar Protein Sorting 4B 3
  • Cell Migration-Inducing 1 3
  • Protein SKD1 4
  • EC 3.6.4.6 4
  • VPS4-2 3
  • SKD1B 3
  • VPS42 4
  • MIG1 3

External Ids for VPS4B Gene

Previous HGNC Symbols for VPS4B Gene

  • SKD1

Previous GeneCards Identifiers for VPS4B Gene

  • GC18M060895
  • GC18M061029
  • GC18M060841
  • GC18M059205
  • GC18M059207
  • GC18M057754
  • GC18M061056

Summaries for VPS4B Gene

Entrez Gene Summary for VPS4B Gene

  • The protein encoded by this gene is a member of the AAA protein family (ATPases associated with diverse cellular activities), and is the homolog of the yeast Vps4 protein. In humans, two paralogs of the yeast protein have been identified. The former share a high degree of aa sequence similarity with each other, and also with yeast Vps4 and mouse Skd1 proteins. Mouse Skd1 (suppressor of K+ transport defect 1) has been shown to be a yeast Vps4 ortholog. Functional studies indicate that both human paralogs associate with the endosomal compartments, and are involved in intracellular protein trafficking, similar to Vps4 protein in yeast. The gene encoding this paralog has been mapped to chromosome 18; the gene for the other resides on chromosome 16. [provided by RefSeq, Jul 2008]

GeneCards Summary for VPS4B Gene

VPS4B (Vacuolar Protein Sorting 4 Homolog B (S. Cerevisiae)) is a Protein Coding gene. Among its related pathways are Disease and Endocytosis. GO annotations related to this gene include protein C-terminus binding and ATPase activity, coupled. An important paralog of this gene is KATNA1.

UniProtKB/Swiss-Prot for VPS4B Gene

  • Involved in late steps of the endosomal multivesicular bodies (MVB) pathway. Recognizes membrane-associated ESCRT-III assemblies and catalyzes their disassembly, possibly in combination with membrane fission. Redistributes the ESCRT-III components to the cytoplasm for further rounds of MVB sorting. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. In conjunction with the ESCRT machinery also appears to function in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (HIV-1 and other lentiviruses).

Gene Wiki entry for VPS4B Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS4B Gene

Genomics for VPS4B Gene

Regulatory Elements for VPS4B Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for VPS4B Gene

Start:
63,389,190 bp from pter
End:
63,422,519 bp from pter
Size:
33,330 bases
Orientation:
Minus strand

Genomic View for VPS4B Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VPS4B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS4B Gene

Proteins for VPS4B Gene

  • Protein details for VPS4B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75351-VPS4B_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 4B
    Protein Accession:
    O75351
    Secondary Accessions:
    • Q69HW4
    • Q9GZS7

    Protein attributes for VPS4B Gene

    Size:
    444 amino acids
    Molecular mass:
    49302 Da
    Quaternary structure:
    • Proposed to be monomeric or homodimeric in nucleotide-free form and to oligomerize upon binding to ATP to form two stacked hexameric or heptameric rings with a central pore through which ESCRT-III substrates are translocated in an ATP-dependent manner. In vitro, associates on the inside of a helical tubular structure formed by a CHMP2A-CHMP3 polymer. Interacts with CHMP1A, CHMP1B, CHMP2A, CHMP4B and CHMP6. Interacts with VPS4A; the interaction suggests a heteromeric assembly with VPS4A. Interacts with VTA1.

    Three dimensional structures from OCA and Proteopedia for VPS4B Gene

neXtProt entry for VPS4B Gene

Proteomics data for VPS4B Gene at MOPED

Post-translational modifications for VPS4B Gene

  • Ubiquitination at Lys147, Lys155, Lys163, and Lys217
  • Modification sites at PhosphoSitePlus

Other Protein References for VPS4B Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for VPS4B Gene

Domains for VPS4B Gene

Gene Families for VPS4B Gene

HGNC:
  • AATP :ATPases / AAA-type

Protein Domains for VPS4B Gene

Suggested Antigen Peptide Sequences for VPS4B Gene

Graphical View of Domain Structure for InterPro Entry

O75351

UniProtKB/Swiss-Prot:

VPS4B_HUMAN :
  • O75351
Domain:
  • The MIT domain serves as an adapter for ESCRT-III proteins. It forms an asymmetric three-helix bundle that binds amphipathic MIM (MIT interacting motif) helices along the groove between MIT helices 2 and 3 present in a subset of ESCRT-III proteins thus establishing the canonical MIM-MIT interaction. In an extended conformation along the groove between helices 1 and 3, also binds to a type-2 MIT interacting motif (MIM2).
  • Contains 1 MIT domain.
Family:
  • Belongs to the AAA ATPase family.
genes like me logo Genes that share domains with VPS4B: view

Function for VPS4B Gene

Molecular function for VPS4B Gene

UniProtKB/Swiss-Prot CatalyticActivity: ATP + H(2)O = ADP + phosphate
UniProtKB/Swiss-Prot Function: Involved in late steps of the endosomal multivesicular bodies (MVB) pathway. Recognizes membrane-associated ESCRT-III assemblies and catalyzes their disassembly, possibly in combination with membrane fission. Redistributes the ESCRT-III components to the cytoplasm for further rounds of MVB sorting. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. In conjunction with the ESCRT machinery also appears to function in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (HIV-1 and other lentiviruses).

Enzyme Numbers (IUBMB) for VPS4B Gene

Gene Ontology (GO) - Molecular Function for VPS4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11563910
GO:0005524 ATP binding IEA --
GO:0008022 protein C-terminus binding IPI 17928862
GO:0008568 NOT microtubule-severing ATPase activity IBA --
GO:0009378 four-way junction helicase activity --
genes like me logo Genes that share ontologies with VPS4B: view

Phenotypes for VPS4B Gene

genes like me logo Genes that share phenotypes with VPS4B: view

Animal Model Products

CRISPR Products

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for VPS4B Gene

Localization for VPS4B Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS4B Gene

Prevacuolar compartment membrane; Peripheral membrane protein. Late endosome membrane; Peripheral membrane protein. Note=Membrane-associated in the prevacuolar endosomal compartment. Localized in HIV-1 particles purified from acutely infected cells.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VPS4B Gene COMPARTMENTS Subcellular localization image for VPS4B gene
Compartment Confidence
cytosol 5
endosome 5
lysosome 5
nucleus 5
vacuole 5
plasma membrane 1

Gene Ontology (GO) - Cellular Components for VPS4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000922 spindle pole IDA 20616062
GO:0005634 nucleus IDA 16757520
GO:0005737 cytoplasm IDA 16757520
GO:0005764 lysosome --
GO:0005768 endosome IDA 11563910
genes like me logo Genes that share ontologies with VPS4B: view

Pathways for VPS4B Gene

genes like me logo Genes that share pathways with VPS4B: view

Pathways by source for VPS4B Gene

1 BioSystems pathway for VPS4B Gene
1 KEGG pathway for VPS4B Gene

Gene Ontology (GO) - Biological Process for VPS4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000920 cell separation after cytokinesis IMP 20616062
GO:0006200 obsolete ATP catabolic process --
GO:0006281 DNA repair --
GO:0006310 DNA recombination --
GO:0006813 potassium ion transport IEA --
genes like me logo Genes that share ontologies with VPS4B: view

Compounds for VPS4B Gene

(1) Novoseek inferred chemical compound relationships for VPS4B Gene

Compound -log(P) Hits PubMed IDs
glucose 4.72 2
genes like me logo Genes that share compounds with VPS4B: view

Transcripts for VPS4B Gene

Unigene Clusters for VPS4B Gene

Vacuolar protein sorting 4 homolog B (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VPS4B

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS4B Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
SP1: - - -
SP2:
SP3:
SP4:
SP5: - -
SP6:

Relevant External Links for VPS4B Gene

GeneLoc Exon Structure for
VPS4B
ECgene alternative splicing isoforms for
VPS4B

Expression for VPS4B Gene

mRNA expression in normal human tissues for VPS4B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for VPS4B Gene

SOURCE GeneReport for Unigene cluster for VPS4B Gene Hs.126550

mRNA Expression by UniProt/SwissProt for VPS4B Gene

O75351-VPS4B_HUMAN
Tissue specificity: Ubiquitously expressed.
genes like me logo Genes that share expressions with VPS4B: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for VPS4B Gene

Orthologs for VPS4B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS4B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS4B 35
  • 99.62 (n)
  • 100 (a)
VPS4B 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS4B 35
  • 88.74 (n)
  • 96.62 (a)
VPS4B 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS4B 35
  • 91.59 (n)
  • 96.4 (a)
VPS4B 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vps4b 35
  • 88.44 (n)
  • 95.5 (a)
Vps4b 16
Vps4b 36
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VPS4B 36
  • 93 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS4B 36
  • 82 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps4b 35
  • 87.31 (n)
  • 95.27 (a)
chicken
(Gallus gallus)
Aves VPS4B 35
  • 80.24 (n)
  • 90.62 (a)
VPS4B 36
  • 90 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS4B 36
  • 90 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.7085 35
vps4b 35
  • 77.5 (n)
  • 87.81 (a)
zebrafish
(Danio rerio)
Actinopterygii vps4b 35
  • 75.54 (n)
  • 88.89 (a)
vps4b 36
  • 88 (a)
OneToOne
zgc63682 35
fruit fly
(Drosophila melanogaster)
Insecta Vps4 36
  • 75 (a)
OneToMany
CG10793 37
  • 40 (a)
BG:DS06874.3 37
  • 41 (a)
BcDNA:GH02678 37
  • 74 (a)
worm
(Caenorhabditis elegans)
Secernentea vps-4 35
  • 62.9 (n)
  • 70.82 (a)
vps-4 36
  • 69 (a)
OneToMany
K04D7.2b 37
  • 37 (a)
Y34D9A.10 37
  • 53 (a)
K04D7.2a 37
  • 37 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL265W 35
  • 59.11 (n)
  • 62.85 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS4 35
  • 59.74 (n)
  • 63.32 (a)
VPS4 36
  • 61 (a)
OneToMany
VPS4 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B10846g 35
  • 60.58 (n)
  • 63.93 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.814 35
thale cress
(Arabidopsis thaliana)
eudicotyledons SKD1 35
  • 58.97 (n)
  • 57.86 (a)
corn
(Zea mays)
Liliopsida Zm.12751 35
rice
(Oryza sativa)
Liliopsida Os.7385 35
Os01g0141100 35
  • 61.24 (n)
  • 62.88 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU06942 35
  • 58.56 (n)
  • 61.57 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vps4 35
  • 59.39 (n)
  • 60.33 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3900 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10007 36
  • 72 (a)
OneToMany
Species with no ortholog for VPS4B:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS4B Gene

ENSEMBL:
Gene Tree for VPS4B (if available)
TreeFam:
Gene Tree for VPS4B (if available)

Paralogs for VPS4B Gene

Paralogs for VPS4B Gene

Selected SIMAP similar genes for VPS4B Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VPS4B: view

Variants for VPS4B Gene

Sequence variations from dbSNP and Humsavar for VPS4B Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type MAF
rs746987 -- 63,409,797(-) AACAA(C/T)GTAAA intron-variant
rs747027 -- 63,394,989(-) TACTA(A/G)TATTT intron-variant
rs898890 -- 63,393,640(+) TAATA(A/G)TTTTG intron-variant
rs952245 -- 63,400,726(-) ATGAC(A/G)TTTTT intron-variant
rs962296 -- 63,408,860(-) TTCTG(A/G)GATGA intron-variant

Relevant External Links for VPS4B Gene

HapMap Linkage Disequilibrium report
VPS4B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for VPS4B Gene

Disorders for VPS4B Gene

Relevant External Links for VPS4B

Genetic Association Database (GAD)
VPS4B
Human Genome Epidemiology (HuGE) Navigator
VPS4B
genes like me logo Genes that share disorders with VPS4B: view

No data available for UniProtKB/Swiss-Prot for VPS4B Gene

Publications for VPS4B Gene

  1. Mammalian cells express two VPS4 proteins both of which are involved in intracellular protein trafficking. (PMID: 11563910) Scheuring S. … Koehrer K. (J. Mol. Biol. 2001) 2 3 4 23
  2. Comparative sequence and expression analyses of four mammalian VPS4 genes. (PMID: 12594041) Beyer A. … Koehrer K. (Gene 2003) 3 4 23
  3. Mammalian class E Vps proteins, SBP1 and mVps2/CHMP2A, interact with and regulate the function of an AAA-ATPase SKD1/Vps4B. (PMID: 15173323) Fujita H. … Himeno M. (J. Cell. Sci. 2004) 3 23
  4. Identification of genes expressed in human CD34(+) hematopoietic stem/progenitor cells by expressed sequence tags and efficient full- length cDNA cloning. (PMID: 9653160) Mao M. … Chen Z. (Proc. Natl. Acad. Sci. U.S.A. 1998) 3 4
  5. CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins. (PMID: 11559748) Howard T.L. … Hollenberg S.M. (J. Cell Sci. 2001) 3 4

Products for VPS4B Gene

Sources for VPS4B Gene

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