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Protein

Vacuolar protein sorting-associated protein 4

Gene

VPS4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in the transport of biosynthetic membrane proteins from the prevacuolar/endosomal compartment to the vacuole. Required for multivesicular body (MVB) protein sorting. Catalyzes the ATP-dependent dissociation of class E VPS proteins from endosomal membranes, such as the disassembly of the ESCRT-III complex.3 Publications

Miscellaneous

Present with 5350 molecules/cell in log phase SD medium.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi173 – 180ATPSequence analysis8

GO - Molecular functioni

  • ATPase activity Source: SGD
  • ATP binding Source: SGD
  • identical protein binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

  • intralumenal vesicle formation Source: SGD
  • late endosome to vacuole transport Source: SGD
  • late endosome to vacuole transport via multivesicular body sorting pathway Source: SGD
  • macroautophagy Source: SGD
  • protein homooligomerization Source: SGD
  • protein retention in Golgi apparatus Source: SGD
  • protein transport Source: UniProtKB-KW
  • sterol metabolic process Source: SGD

Keywordsi

Biological processProtein transport, Transport
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-34300-MONOMER
BRENDAi3.6.4.6 984

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 4
Alternative name(s):
DOA4-independent degradation protein 6
Protein END13
Vacuolar protein-targeting protein 10
Gene namesi
Name:VPS4
Synonyms:CSC1, DID6, END13, GRD13, VPL4, VPT10
Ordered Locus Names:YPR173C
ORF Names:P9705.10
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPR173C
SGDiS000006377 VPS4

Subcellular locationi

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

Keywords - Cellular componenti

Endosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi64L → D: Inhibits membrane protein sorting to the vacuole. 1 Publication1
Mutagenesisi179K → A: No ATP hydrolysis. Missorting of vacuolar proteins. 1 Publication1
Mutagenesisi216Q → A: Abolishes oligomerization. 1 Publication1
Mutagenesisi233E → Q: Defective in ATP hydrolysis. Missorting of vacuolar proteins. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000847601 – 437Vacuolar protein sorting-associated protein 4Add BLAST437

Proteomic databases

MaxQBiP52917
PaxDbiP52917
PRIDEiP52917

PTM databases

iPTMnetiP52917

Interactioni

Subunit structurei

Monomer or homodimer (in nucleotide-free form). Decamer, dodecamer or tetradecamer of two stacked respective homooligomeric rings (when bound to ATP); the dodecameric form seems to be predominant. Interacts with VPS20. Interacts with VTA1; the interaction requires the dimeric structure of VTA1; 6 homodimers of VTA1 appear to associate with the dodecameric VSP4 complex. Interacts with DID2. Interacts with DID4. Interacts with IST1; IST1 competes with VTA1 for binding with VPS4.10 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • identical protein binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi36346, 586 interactors
ComplexPortaliCPX-334 VPS4 complex
DIPiDIP-1746N
IntActiP52917, 34 interactors
MINTiP52917
STRINGi4932.YPR173C

Structurei

Secondary structure

1437
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 22Combined sources20
Helixi26 – 46Combined sources21
Helixi50 – 81Combined sources32
Turni117 – 121Combined sources5
Beta strandi123 – 126Combined sources4
Helixi132 – 134Combined sources3
Helixi139 – 148Combined sources10
Helixi150 – 154Combined sources5
Helixi156 – 158Combined sources3
Beta strandi168 – 172Combined sources5
Beta strandi174 – 177Combined sources4
Helixi179 – 190Combined sources12
Beta strandi193 – 198Combined sources6
Helixi199 – 203Combined sources5
Turni204 – 206Combined sources3
Helixi207 – 209Combined sources3
Helixi210 – 223Combined sources14
Beta strandi225 – 232Combined sources8
Helixi234 – 237Combined sources4
Beta strandi241 – 244Combined sources4
Helixi250 – 260Combined sources11
Helixi261 – 264Combined sources4
Beta strandi267 – 269Combined sources3
Beta strandi270 – 277Combined sources8
Helixi279 – 281Combined sources3
Helixi284 – 289Combined sources6
Beta strandi292 – 295Combined sources4
Helixi301 – 312Combined sources12
Beta strandi313 – 315Combined sources3
Helixi321 – 329Combined sources9
Turni330 – 333Combined sources4
Helixi336 – 346Combined sources11
Helixi349 – 356Combined sources8
Beta strandi358 – 362Combined sources5
Beta strandi373 – 375Combined sources3
Beta strandi378 – 380Combined sources3
Beta strandi383 – 387Combined sources5
Helixi388 – 390Combined sources3
Helixi393 – 395Combined sources3
Helixi403 – 412Combined sources10
Helixi421 – 432Combined sources12
Beta strandi433 – 435Combined sources3

3D structure databases

ProteinModelPortaliP52917
SMRiP52917
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP52917

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 80MITAdd BLAST78

Sequence similaritiesi

Belongs to the AAA ATPase family.Curated

Phylogenomic databases

GeneTreeiENSGT00550000074466
HOGENOMiHOG000225146
InParanoidiP52917
KOiK12196
OMAiRAKCMQY
OrthoDBiEOG092C2QJ3

Family and domain databases

InterProiView protein in InterPro
IPR003593 AAA+_ATPase
IPR003959 ATPase_AAA_core
IPR003960 ATPase_AAA_CS
IPR007330 MIT
IPR036181 MIT_dom_sf
IPR027417 P-loop_NTPase
IPR015415 Vps4_C
PfamiView protein in Pfam
PF00004 AAA, 1 hit
PF04212 MIT, 1 hit
PF09336 Vps4_C, 1 hit
SMARTiView protein in SMART
SM00382 AAA, 1 hit
SM00745 MIT, 1 hit
SUPFAMiSSF116846 SSF116846, 1 hit
SSF52540 SSF52540, 2 hits
PROSITEiView protein in PROSITE
PS00674 AAA, 1 hit

Sequencei

Sequence statusi: Complete.

P52917-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTGDFLTKG IELVQKAIDL DTATQYEEAY TAYYNGLDYL MLALKYEKNP
60 70 80 90 100
KSKDLIRAKF TEYLNRAEQL KKHLESEEAN AAKKSPSAGS GSNGGNKKIS
110 120 130 140 150
QEEGEDNGGE DNKKLRGALS SAILSEKPNV KWEDVAGLEG AKEALKEAVI
160 170 180 190 200
LPVKFPHLFK GNRKPTSGIL LYGPPGTGKS YLAKAVATEA NSTFFSVSSS
210 220 230 240 250
DLVSKWMGES EKLVKQLFAM ARENKPSIIF IDEVDALTGT RGEGESEASR
260 270 280 290 300
RIKTELLVQM NGVGNDSQGV LVLGATNIPW QLDSAIRRRF ERRIYIPLPD
310 320 330 340 350
LAARTTMFEI NVGDTPCVLT KEDYRTLGAM TEGYSGSDIA VVVKDALMQP
360 370 380 390 400
IRKIQSATHF KDVSTEDDET RKLTPCSPGD DGAIEMSWTD IEADELKEPD
410 420 430
LTIKDFLKAI KSTRPTVNED DLLKQEQFTR DFGQEGN
Length:437
Mass (Da):48,172
Last modified:October 1, 1996 - v1
Checksum:iE65BCDB19C9510DD
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti32A → S in CAA63364 (PubMed:11329380).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X92680 Genomic DNA Translation: CAA63364.1
U25842 Genomic DNA Translation: AAB68107.1
BK006949 Genomic DNA Translation: DAA11590.1
PIRiS59831
RefSeqiNP_015499.1, NM_001184270.1

Genome annotation databases

EnsemblFungiiYPR173C; YPR173C; YPR173C
GeneIDi856303
KEGGisce:YPR173C

Similar proteinsi

Entry informationi

Entry nameiVPS4_YEAST
AccessioniPrimary (citable) accession number: P52917
Secondary accession number(s): D6W4H4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: July 18, 2018
This is version 170 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

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