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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)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi173 – 1808ATPSequence analysis

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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi64 – 641L → D: Inhibits membrane protein sorting to the vacuole. 1 Publication
Mutagenesisi179 – 1791K → A: No ATP hydrolysis. Missorting of vacuolar proteins. 1 Publication
Mutagenesisi216 – 2161Q → A: Abolishes oligomerization. 1 Publication
Mutagenesisi233 – 2331E → Q: Defective in ATP hydrolysis. Missorting of vacuolar proteins. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 437437Vacuolar protein sorting-associated protein 4PRO_0000084760Add
BLAST

Proteomic databases

MaxQBiP52917.

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 interactions.
DIPiDIP-1746N.
IntActiP52917. 18 interactions.
MINTiMINT-389240.

Structurei

Secondary structure

1
437
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 2220Combined sources
Helixi26 – 4621Combined sources
Helixi50 – 8132Combined sources
Beta strandi123 – 1264Combined sources
Helixi132 – 1343Combined sources
Helixi139 – 14810Combined sources
Helixi150 – 1545Combined sources
Helixi156 – 1583Combined sources
Beta strandi168 – 1725Combined sources
Beta strandi174 – 1774Combined sources
Helixi179 – 19012Combined sources
Beta strandi193 – 1986Combined sources
Helixi199 – 2035Combined sources
Turni204 – 2063Combined sources
Helixi207 – 2093Combined sources
Helixi210 – 22314Combined sources
Beta strandi225 – 2328Combined sources
Helixi234 – 2374Combined sources
Turni244 – 2496Combined sources
Helixi250 – 26011Combined sources
Helixi261 – 2644Combined sources
Beta strandi270 – 2778Combined sources
Helixi279 – 2813Combined sources
Helixi284 – 2896Combined sources
Beta strandi292 – 2954Combined sources
Helixi301 – 31212Combined sources
Beta strandi313 – 3153Combined sources
Helixi321 – 3299Combined sources
Turni330 – 3334Combined sources
Helixi336 – 34611Combined sources
Helixi349 – 3568Combined sources
Beta strandi358 – 3625Combined sources
Beta strandi373 – 3753Combined sources
Beta strandi378 – 3803Combined sources
Beta strandi383 – 3875Combined sources
Helixi388 – 3903Combined sources
Helixi393 – 3953Combined sources
Helixi403 – 41210Combined sources
Helixi421 – 43212Combined sources
Beta strandi433 – 4353Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-82, 119-437.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP52917.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 8078MITAdd
BLAST

Sequence similaritiesi

Belongs to the AAA ATPase family.Curated
Contains 1 MIT domain.Curated

Phylogenomic databases

GeneTreeiENSGT00550000074466.
HOGENOMiHOG000225146.
InParanoidiP52917.
KOiK12196.
OMAiPNCIVND.
OrthoDBiEOG72JWRT.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti32 – 321A → S in CAA63364 (PubMed:11329380).Curated

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
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. Positions 1-82, 119-437.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiP52917.

Proteomic databases

MaxQBiP52917.

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.
OMAiPNCIVND.
OrthoDBiEOG72JWRT.

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...

Publicationsi

« Hide 'large scale' publications
  1. "End13p/Vps4p is required for efficient transport from early to late endosomes in Saccharomyces cerevisiae."
    Zahn R., Stevenson B.J., Schroeder-Koehne S., Zanolari B., Riezman H., Munn A.L.
    J. Cell Sci. 114:1935-1947(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    Strain: ATCC 200060 / W303.
  2. "Endosomal transport function in yeast requires a novel AAA-type ATPase, Vps4p."
    Babst M., Sato T.K., Banta L.M., Emr S.D.
    EMBO J. 16:1820-1831(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, MUTAGENESIS OF LYS-179 AND GLU-233.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "The Vps4p AAA ATPase regulates membrane association of a Vps protein complex required for normal endosome function."
    Babst M., Wendland B., Estepa E.J., Emr S.D.
    EMBO J. 17:2982-2993(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  6. "Vps20p and Vta1p interact with Vps4p and function in multivesicular body sorting and endosomal transport in Saccharomyces cerevisiae."
    Yeo S.C.L., Xu L., Ren J., Boulton V.J., Wagle M.D., Liu C., Ren G., Wong P., Zahn R., Sasajala P., Yang H., Piper R.C., Munn A.L.
    J. Cell Sci. 116:3957-3970(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VPS20 AND VTA1.
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "Protein-protein interactions of ESCRT complexes in the yeast Saccharomyces cerevisiae."
    Bowers K., Lottridge J., Helliwell S.B., Goldthwaite L.M., Luzio J.P., Stevens T.H.
    Traffic 5:194-210(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH DID2.
  9. "Recycling of ESCRTs by the AAA-ATPase Vps4 is regulated by a conserved VSL region in Vta1."
    Azmi I., Davies B., Dimaano C., Payne J., Eckert D., Babst M., Katzmann D.J.
    J. Cell Biol. 172:705-717(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VTA1, OLIGOMERIZATION.
  10. "Did2 coordinates Vps4-mediated dissociation of ESCRT-III from endosomes."
    Nickerson D.P., West M., Odorizzi G.
    J. Cell Biol. 175:715-720(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH DID2.
  11. Erratum
    Nickerson D.P., West M., Odorizzi G.
    J. Cell Biol. 175:1043-1043(2006)
  12. "Vta1p and Vps46p regulate the membrane association and ATPase activity of Vps4p at the yeast multivesicular body."
    Lottridge J.M., Flannery A.R., Vincelli J.L., Stevens T.H.
    Proc. Natl. Acad. Sci. U.S.A. 103:6202-6207(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH DID2.
  13. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  14. Cited for: MUTAGENESIS OF LEU-64.
  15. "Cryo-EM structure of dodecameric Vps4p and its 2:1 complex with Vta1p."
    Yu Z., Gonciarz M.D., Sundquist W.I., Hill C.P., Jensen G.J.
    J. Mol. Biol. 377:364-377(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VTA1, SUBUNIT.
  16. "Novel Ist1-Did2 complex functions at a late step in multivesicular body sorting."
    Rue S.M., Mattei S., Saksena S., Emr S.D.
    Mol. Biol. Cell 19:475-484(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH IST1.
  17. "Structural characterization of the ATPase reaction cycle of endosomal AAA protein Vps4."
    Xiao J., Xia H., Yoshino-Koh K., Zhou J., Xu Z.
    J. Mol. Biol. 374:655-670(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 83-437, OLIGOMERIZATION, INTERACTION WITH VPS20 AND DID4.
  18. "Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4."
    Obita T., Saksena S., Ghazi-Tabatabai S., Gill D.J., Perisic O., Emr S.D., Williams R.L.
    Nature 449:735-739(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS) OF 1-82 IN COMPLEX WITH DID4, INTERACTION WITH DID2.
  19. "Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p."
    Hartmann C., Chami M., Zachariae U., de Groot B.L., Engel A., Grutter M.G.
    J. Mol. Biol. 377:352-363(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.35 ANGSTROMS) OF 116-437, OLIGOMERIZATION, MUTAGENESIS OF GLN-216.

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: July 6, 2016
This is version 151 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.