Vps4b vacuolar protein sorting 4B [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Vps4bprovided by MGI
Official Full Name: vacuolar protein sorting 4Bprovided by MGI
Primary source: MGI:MGI:1100499
See related: Ensembl:ENSMUSG00000009907 AllianceGenome:MGI:1100499
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Skd1; 8030489C12Rik
Summary: Predicted to enable ATP hydrolysis activity and protein homodimerization activity. Involved in late endosomal microautophagy; multivesicular body assembly; and viral budding from plasma membrane. Acts upstream of or within several processes, including canonical Wnt signaling pathway; establishment of blood-brain barrier; and potassium ion transport. Located in cytosol. Is expressed in central nervous system; head; and migrating neural crest. Orthologous to human VPS4B (vacuolar protein sorting 4 homolog B). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in bladder adult (RPKM 17.1), placenta adult (RPKM 16.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 E2.1; 1 50.1 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (106698518..106724455, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (106770788..106796725, complement)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of Rnf31 and Vps4b sensitizes pancreatic cancer to T cell-mediated killing.
Title: Loss of Rnf31 and Vps4b sensitizes pancreatic cancer to T cell-mediated killing.
VPS4B deficiency causes early embryonic lethality and induces signal transduction disorders of cell endocytosis.
Title: VPS4B deficiency causes early embryonic lethality and induces signal transduction disorders of cell endocytosis.
Expressions of cytokeratin 14 and proliferating cell nuclear antigen in the Hertwig's epithelial root sheath of a Vps4b knockout mouse.
Title: Expressions of cytokeratin 14 and proliferating cell nuclear antigen in the Hertwig's epithelial root sheath of a Vps4b knockout mouse.
VPS4B, via Wnt-beta-catenin signalling, acts as a regulator of the proliferation and differentiation of hDPSCs
Title: Vacuolar protein sorting 4B regulates the proliferation and odontoblastic differentiation of human dental pulp stem cells through the Wnt-β-catenin signalling pathway.
Gene vps4b plays a significant role in the development of tooth germ. The expression of DSPP and COL- may be controlled by gene vps4b and regulates the development of tooth dentin and cementum together with vps4b.
Title: [Spatio-temporal expression of dentin sialophosphoprotein and collagen Ⅰ during molar tooth germ development in vps4b knockout mouse].
a dominant negative form of the CHMP2B-interacting protein VPS4A, which alters multivesicular bodies, leads to accumulation and aggregation of Abeta as well as tau phosphorylation, mimicking the cellular changes in Alzheimer's disease
Title: Aβ accumulation causes MVB enlargement and is modelled by dominant negative VPS4A.
ATP hydrolysis would eliminate this interaction and subsequent nucleotide release causes the domains to rotate, which together lead to the disassembly of the SKD1 oligomer
Title: Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (5) 1 citation
Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info	PubMed
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in ESCRT III complex disassembly	IEA Inferred from Electronic Annotation more info
involved_in ESCRT III complex disassembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagosome maturation	NAS Non-traceable Author Statement more info	PubMed
involved_in autophagy	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within canonical Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within central nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in endosomal transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within endosomal transport	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within endosome organization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within endosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosome to lysosome transport via multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of blood-brain barrier	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in late endosomal microautophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in late endosome to lysosome transport via multivesicular body sorting pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in membrane fission	NAS Non-traceable Author Statement more info	PubMed
involved_in midbody abscission	ISO Inferred from Sequence Orthology more info
involved_in midbody abscission	NAS Non-traceable Author Statement more info	PubMed
involved_in mitotic metaphase chromosome alignment	IEA Inferred from Electronic Annotation more info
involved_in mitotic metaphase chromosome alignment	ISO Inferred from Sequence Orthology more info
involved_in multivesicular body assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in multivesicular body assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in multivesicular body sorting pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of exosomal secretion	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of exosomal secretion	ISO Inferred from Sequence Orthology more info
involved_in nuclear membrane reassembly	NAS Non-traceable Author Statement more info	PubMed
involved_in nucleus organization	ISO Inferred from Sequence Orthology more info
involved_in nucleus organization	NAS Non-traceable Author Statement more info	PubMed
involved_in plasma membrane repair	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of G2/M transition of mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of G2/M transition of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of centriole elongation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of centriole elongation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of exosomal secretion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of exosomal secretion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within potassium ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in protein depolymerization	IEA Inferred from Electronic Annotation more info
involved_in protein depolymerization	ISO Inferred from Sequence Orthology more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of centrosome duplication	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitotic spindle assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of mitotic spindle assembly	ISO Inferred from Sequence Orthology more info
involved_in response to lipid	IEA Inferred from Electronic Annotation more info
involved_in response to lipid	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within vacuolar transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vacuole organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in viral budding from plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in viral budding from plasma membrane	ISO Inferred from Sequence Orthology more info
involved_in viral budding via host ESCRT complex	IEA Inferred from Electronic Annotation more info
involved_in viral budding via host ESCRT complex	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of ATPase complex	NAS Non-traceable Author Statement more info	PubMed
located_in Flemming body	IEA Inferred from Electronic Annotation more info
located_in Flemming body	ISO Inferred from Sequence Orthology more info
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	ISO Inferred from Sequence Orthology more info	PubMed
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in midbody	NAS Non-traceable Author Statement more info	PubMed
part_of nuclear pore	NAS Non-traceable Author Statement more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in spindle pole	IEA Inferred from Electronic Annotation more info
located_in spindle pole	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 4B

Names: suppressor of K(+) transport growth defect 1; suppressor of K+ transport defect 1

NP_033216.2

EC 3.6.4.6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_009190.2 → NP_033216.2 vacuolar protein sorting-associated protein 4B

See identical proteins and their annotated locations for NP_033216.2

Status: VALIDATED

Source sequence(s)

AK034641, AK151023, BY126089

Consensus CDS

CCDS15211.1

UniProtKB/Swiss-Prot

P46467, Q91W22, Q9R1C9

UniProtKB/TrEMBL

Q3TN07, Q3U8P5

Related

ENSMUSP00000092230.6, ENSMUST00000094646.6

Conserved Domains (4) summary

cd02678
Location:7 → 69

MIT_VPS4; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.

pfam09336
Location:381 → 441

Vps4_C; Vps4 C terminal oligomerization domain

pfam17862
Location:325 → 366

AAA_lid_3; AAA+ lid domain

cd19521
Location:128 → 298

RecA-like_VPS4; ATPase domain of vacuolar protein sorting-associated protein 4