VPS4 AAA family ATPase VPS4 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: VPS4
Official Full Name: AAA family ATPase VPS4
Primary source: SGD:S000006377
Locus tag: YPR173C
See related: AllianceGenome:SGD:S000006377; FungiDB:YPR173C; VEuPathDB:YPR173C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: CSC1; DID6; END13; GRD13; VPL4; VPT10
Summary: Enables ATP binding activity and ATP hydrolysis activity. Involved in several processes, including intralumenal vesicle formation; protein retention in Golgi apparatus; and reticulophagy. Located in endosome and membrane. Orthologous to several human genes including VPS4B (vacuolar protein sorting 4 homolog B). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See VPS4 in Genome Data Viewer

Location:: chromosome: XVI

Exon count:: 1

Sequence:: Chromosome: XVI; NC_001148.4 (886524..887837, complement)

Chromosome XVI - NC_001148.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001148.4

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Bro1 stimulates Vps4 to promote intralumenal vesicle formation during multivesicular body biogenesis.
Title: Bro1 stimulates Vps4 to promote intralumenal vesicle formation during multivesicular body biogenesis.
Data show that linear and cyclic versions of peptides bind to the S. cerevisiae AAA+ ATPase Vps4 (Vps4 ) with similar affinities
Title: Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases.
we review recent advances in our understanding of the structures, activities, and mechanisms of the ESCRT-III and Vps4 machinery, including the first high-resolution structures of ESCRT-III filaments, the assembled Vps4 enzyme in complex with an ESCRT-III substrate, the discovery that ESCRT-III/Vps4 complexes can promote both inside-out and outside-in membrane fission reactions
Title: Structures, Functions, and Dynamics of ESCRT-III/Vps4 Membrane Remodeling and Fission Complexes.
These observations directly verify long-standing predictions that ATP-hydrolyzing assemblies of ESCRT-III and Vps4 sever membranes.
Title: ATP-dependent force generation and membrane scission by ESCRT-III and Vps4.
The authors now report a 3.2 A structure of Vps4 bound to an ESCRT-III peptide substrate. The new structure reveals that the peptide approximates a beta-strand conformation whose helical symmetry matches that of the five Vps4 subunits it contacts directly.
Title: The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.
The authors propose a model in which multiple Vps4 hexamers (four or more) draw together several ESCRT-III filaments. This process induces cargo crowding and inward membrane buckling, followed by constriction of the nascent bud neck and ultimately intraluminal vesicle generation by vesicle fission.
Title: Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding.
Four Vps4 subunits form a helix whose interfaces are consistent with ATP binding, is stabilized by Vta1, and binds the substrate peptide.
Title: Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase.
The major ESCRT-III subunit Snf7 localizes transiently to vesicles and tubules surrounded by a cup-shaped membrane and this was accelerated in vps4Delta cells, correlating with increased Acb1 secretion.
Title: ESCRT-III drives the final stages of CUPS maturation for unconventional protein secretion.
data support a model in which Ist1-Did2 interactions during ESCRT-III polymerization coordinate Vps4 activity with the timing of ESCRT-III disassembly
Title: Conformational Changes in the Endosomal Sorting Complex Required for the Transport III Subunit Ist1 Lead to Distinct Modes of ATPase Vps4 Regulation.
These data support a mechanism in which Vps4 disassembles its substrates by completely unfolding them and threading them through the central pore.
Title: Vps4 disassembles an ESCRT-III filament by global unfolding and processive translocation.

Submit: New GeneRIF Correction See all GeneRIFs (29)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in endosomal transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intralumenal vesicle formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in late endosome to vacuole transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in late endosome to vacuole transport via multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in macroautophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein retention in Golgi apparatus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in reticulophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in sterol metabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in sterol metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vacuole organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasm	HDA more info	PubMed
located_in endoplasmic reticulum	HDA more info	PubMed
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: AAA family ATPase VPS4

NP_015499.1

AAA-ATPase involved in multivesicular body (MVB) protein sorting; ATP-bound Vps4p localizes to endosomes and catalyzes ESCRT-III disassembly and membrane release; ATPase activity is activated by Vta1p; regulates cellular sterol metabolism

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001148.4 Reference assembly

Range

886524..887837 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001184270.1 → NP_015499.1 TPA: AAA family ATPase VPS4 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_015499.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W4H4, P52917

UniProtKB/TrEMBL

A6ZX48, B3LKD3, B5VTV5, C7GP56, C8ZJK2, G2WPY5, N1NW67

Conserved Domains (3) summary

COG0464
Location:11 → 418

SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]

pfam09336
Location:373 → 433

Vps4_C; Vps4 C terminal oligomerization domain

cd19521
Location:127 → 296

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