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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: Annotation score: 5 out of 5-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

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
  • vacuole organization Source: GO_Central
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Keywords - Ligandi

ATP-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

GO - Cellular componenti

  • endosome Source: SGD
  • membrane Source: SGD
  • nucleus Source: GO_Central
  • Vps4-Vta1 complex Source: FlyBase
Complete GO annotation...

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.
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

WithEntry#Exp.IntActNotes
SNF7P399294EBI-20475,EBI-17554
VPS20Q042726EBI-20475,EBI-28157
VTA1Q062637EBI-20475,EBI-37098

GO - Molecular functioni

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

Protein-protein interaction databases

BioGridi36346. 158 interactors.
DIPiDIP-1746N.
IntActiP52917. 18 interactors.
MINTiMINT-389240.

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
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
Turni244 – 249Combined sources6
Helixi250 – 260Combined sources11
Helixi261 – 264Combined sources4
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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2QP9X-ray2.90X83-437[»]
2QPAX-ray3.20A/B/C83-437[»]
2RKOX-ray3.35A124-437[»]
2V6XX-ray1.98A1-82[»]
3EIEX-ray2.70A122-437[»]
3EIHX-ray3.25A/B/C104-437[»]
3MHVX-ray3.10C299-413[»]
4NIQX-ray2.30A/B1-82[»]
5FVKX-ray1.66A/B1-82[»]
5FVLX-ray1.97A/B1-82[»]
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
Contains 1 MIT domain.Curated

Phylogenomic databases

GeneTreeiENSGT00550000074466.
HOGENOMiHOG000225146.
InParanoidiP52917.
KOiK12196.
OMAiTILLKRD.
OrthoDBiEOG092C2QJ3.

Family and domain databases

Gene3Di1.20.58.280. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR003959. ATPase_AAA_core.
IPR003960. ATPase_AAA_CS.
IPR007330. MIT.
IPR027417. P-loop_NTPase.
IPR015415. Vps4_C.
[Graphical view]
PfamiPF00004. AAA. 1 hit.
PF04212. MIT. 1 hit.
PF09336. Vps4_C. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
SM00745. MIT. 1 hit.
[Graphical view]
SUPFAMiSSF116846. SSF116846. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS00674. AAA. 1 hit.
[Graphical view]

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.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2QP9X-ray2.90X83-437[»]
2QPAX-ray3.20A/B/C83-437[»]
2RKOX-ray3.35A124-437[»]
2V6XX-ray1.98A1-82[»]
3EIEX-ray2.70A122-437[»]
3EIHX-ray3.25A/B/C104-437[»]
3MHVX-ray3.10C299-413[»]
4NIQX-ray2.30A/B1-82[»]
5FVKX-ray1.66A/B1-82[»]
5FVLX-ray1.97A/B1-82[»]
ProteinModelPortaliP52917.
SMRiP52917.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36346. 158 interactors.
DIPiDIP-1746N.
IntActiP52917. 18 interactors.
MINTiMINT-389240.

PTM databases

iPTMnetiP52917.

Proteomic databases

MaxQBiP52917.
PRIDEiP52917.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPR173C; YPR173C; YPR173C.
GeneIDi856303.
KEGGisce:YPR173C.

Organism-specific databases

EuPathDBiFungiDB:YPR173C.
SGDiS000006377. VPS4.

Phylogenomic databases

GeneTreeiENSGT00550000074466.
HOGENOMiHOG000225146.
InParanoidiP52917.
KOiK12196.
OMAiTILLKRD.
OrthoDBiEOG092C2QJ3.

Enzyme and pathway databases

BioCyciYEAST:G3O-34300-MONOMER.
BRENDAi3.6.4.6. 984.

Miscellaneous databases

EvolutionaryTraceiP52917.
PROiP52917.

Family and domain databases

Gene3Di1.20.58.280. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR003959. ATPase_AAA_core.
IPR003960. ATPase_AAA_CS.
IPR007330. MIT.
IPR027417. P-loop_NTPase.
IPR015415. Vps4_C.
[Graphical view]
PfamiPF00004. AAA. 1 hit.
PF04212. MIT. 1 hit.
PF09336. Vps4_C. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
SM00745. MIT. 1 hit.
[Graphical view]
SUPFAMiSSF116846. SSF116846. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS00674. AAA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiVPS4_YEAST
AccessioniPrimary (citable) accession number: P52917
Secondary accession number(s): D6W4H4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: November 2, 2016
This is version 154 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

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

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.