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Protein

Vacuolar protein sorting-associated protein 28

Gene

VPS28

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

Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for normal endocytic and biosynthetic traffic to the yeast vacuole.

GO - Molecular functioni

  • protein complex binding Source: SGD

GO - Biological processi

  • protein targeting to membrane Source: SGD
  • protein targeting to vacuole Source: SGD
  • ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Source: SGD
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Enzyme and pathway databases

BioCyciYEAST:G3O-33974-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 28
Alternative name(s):
ESCRT-I complex subunit VPS28
Gene namesi
Name:VPS28
Synonyms:VPT28
Ordered Locus Names:YPL065W
ORF Names:LPE5W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL065W.
SGDiS000005986. VPS28.

Subcellular locationi

GO - Cellular componenti

  • endosome Source: SGD
  • ESCRT I complex Source: SGD
  • late endosome membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi40 – 401L → D: Abolishes ESCRT-I complex assembly; class E phenotype (malformed late MVB); when associated with D-44. 1 Publication
Mutagenesisi44 – 441Y → D: Abolishes ESCRT-I complex assembly; class E phenotype (malformed late MVB); when associated with D-40. 1 Publication
Mutagenesisi228 – 2314FDLE → ASLA: Abolishes interaction with VPS20. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 242242Vacuolar protein sorting-associated protein 28PRO_0000120958Add
BLAST

Proteomic databases

MaxQBiQ02767.
PeptideAtlasiQ02767.

Interactioni

Subunit structurei

Component of the ESCRT-I complex (endosomal sorting complex required for transport I) which consists of STP22, VPS28, SRN2 and MVB12 in a 1:1:1:1 stoechiometry. Self-associates. Interacts with VPS27; the interaction mediates the association with the ESCRT-0 complex. Interacts with VPS20; the interaction mediates the association with the ESCRT-III complex.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
STP22P256042EBI-20387,EBI-411625
VPS36Q066966EBI-20387,EBI-36540

GO - Molecular functioni

  • protein complex binding Source: SGD

Protein-protein interaction databases

BioGridi36114. 75 interactions.
DIPiDIP-5828N.
IntActiQ02767. 6 interactions.
MINTiMINT-468379.

Structurei

Secondary structure

1
242
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 123Combined sources
Helixi14 – 174Combined sources
Beta strandi27 – 293Combined sources
Helixi31 – 5828Combined sources
Helixi64 – 8219Combined sources
Turni85 – 884Combined sources
Helixi89 – 10315Combined sources
Helixi109 – 1179Combined sources
Helixi150 – 16819Combined sources
Helixi174 – 19118Combined sources
Helixi199 – 21012Combined sources
Helixi220 – 24021Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CAZX-ray3.60B/E1-147[»]
2F66X-ray2.80B/E13-125[»]
2F6MX-ray2.10B/D13-118[»]
2G3KX-ray3.05A/B/C/D/E/F/G148-241[»]
2J9UX-ray2.00A/C148-242[»]
2J9VX-ray2.00A148-242[»]
2P22X-ray2.70B1-118[»]
ProteinModelPortaliQ02767.
SMRiQ02767. Positions 22-122, 148-242.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ02767.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini11 – 125115VPS28 N-terminalPROSITE-ProRule annotationAdd
BLAST
Domaini148 – 24295VPS28 C-terminalPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni148 – 24295Interaction with VSP36 and VPS20Add
BLAST

Sequence similaritiesi

Belongs to the VPS28 family.PROSITE-ProRule annotation
Contains 1 VPS28 C-terminal domain.PROSITE-ProRule annotation
Contains 1 VPS28 N-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000007486.
HOGENOMiHOG000203818.
InParanoidiQ02767.
KOiK12184.
OMAiKYRLDCP.
OrthoDBiEOG7J9W1T.

Family and domain databases

InterProiIPR007143. VPS28.
IPR017899. VPS28_C.
IPR017898. VPS28_N.
[Graphical view]
PANTHERiPTHR12937. PTHR12937. 1 hit.
PfamiPF03997. VPS28. 1 hit.
[Graphical view]
PIRSFiPIRSF017535. VPS28. 1 hit.
PROSITEiPS51310. VPS28_C. 1 hit.
PS51313. VPS28_N. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q02767-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQKHNIKLNQ NQDISQLFHD EVPLFDNSIT SKDKEVIETL SEIYSIVITL
60 70 80 90 100
DHVEKAYLKD SIDDTQYTNT VDKLLKQFKV YLNSQNKEEI NKHFQSIEAF
110 120 130 140 150
CDTYNITASN AITRLERGIP ITAEHAISTT TSAPSGDNKQ SSSSDKKFNA
160 170 180 190 200
KYVAEATGNF ITVMDALKLN YNAKDQLHPL LAELLISINR VTRDDFENRS
210 220 230 240
KLIDWIVRIN KLSIGDTLTE TQIRELLFDL ELAYKSFYAL LD
Length:242
Mass (Da):27,702
Last modified:November 1, 1996 - v1
Checksum:iDE091D3F60C9D132
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti193 – 1931R → K in AAT92809 (PubMed:17322287).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U50630 Genomic DNA. Translation: AAB40936.1.
U39205 Genomic DNA. Translation: AAB68300.1.
AY692790 Genomic DNA. Translation: AAT92809.1.
BK006949 Genomic DNA. Translation: DAA11366.1.
PIRiS60925.
RefSeqiNP_015260.1. NM_001183879.1.

Genome annotation databases

EnsemblFungiiYPL065W; YPL065W; YPL065W.
GeneIDi856040.
KEGGisce:YPL065W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U50630 Genomic DNA. Translation: AAB40936.1.
U39205 Genomic DNA. Translation: AAB68300.1.
AY692790 Genomic DNA. Translation: AAT92809.1.
BK006949 Genomic DNA. Translation: DAA11366.1.
PIRiS60925.
RefSeqiNP_015260.1. NM_001183879.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CAZX-ray3.60B/E1-147[»]
2F66X-ray2.80B/E13-125[»]
2F6MX-ray2.10B/D13-118[»]
2G3KX-ray3.05A/B/C/D/E/F/G148-241[»]
2J9UX-ray2.00A/C148-242[»]
2J9VX-ray2.00A148-242[»]
2P22X-ray2.70B1-118[»]
ProteinModelPortaliQ02767.
SMRiQ02767. Positions 22-122, 148-242.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36114. 75 interactions.
DIPiDIP-5828N.
IntActiQ02767. 6 interactions.
MINTiMINT-468379.

Proteomic databases

MaxQBiQ02767.
PeptideAtlasiQ02767.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL065W; YPL065W; YPL065W.
GeneIDi856040.
KEGGisce:YPL065W.

Organism-specific databases

EuPathDBiFungiDB:YPL065W.
SGDiS000005986. VPS28.

Phylogenomic databases

GeneTreeiENSGT00390000007486.
HOGENOMiHOG000203818.
InParanoidiQ02767.
KOiK12184.
OMAiKYRLDCP.
OrthoDBiEOG7J9W1T.

Enzyme and pathway databases

BioCyciYEAST:G3O-33974-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ02767.
PROiQ02767.

Family and domain databases

InterProiIPR007143. VPS28.
IPR017899. VPS28_C.
IPR017898. VPS28_N.
[Graphical view]
PANTHERiPTHR12937. PTHR12937. 1 hit.
PfamiPF03997. VPS28. 1 hit.
[Graphical view]
PIRSFiPIRSF017535. VPS28. 1 hit.
PROSITEiPS51310. VPS28_C. 1 hit.
PS51313. VPS28_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Multilamellar endosome-like compartment accumulates in the yeast vps28 vacuolar protein sorting mutant."
    Rieder S.E., Banta L.M., Koehrer K., McCaffery J.M., Emr S.D.
    Mol. Biol. Cell 7:985-999(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "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.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. "Vps27 recruits ESCRT machinery to endosomes during MVB sorting."
    Katzmann D.J., Stefan C.J., Babst M., Emr S.D.
    J. Cell Biol. 162:413-423(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, INTERACTION WITH VPS27.
  8. "ESCRT-I core and ESCRT-II GLUE domain structures reveal role for GLUE in linking to ESCRT-I and membranes."
    Teo H., Gill D.J., Sun J., Perisic O., Veprintsev D.B., Vallis Y., Emr S.D., Williams R.L.
    Cell 125:99-111(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.6 ANGSTROMS) OF 1-147 IN COMPLEX WITH STP22 AND SRN2, INTERACTION WITH VPS36.
  9. "Structural and functional organization of the ESCRT-I trafficking complex."
    Kostelansky M.S., Sun J., Lee S., Kim J., Ghirlando R., Hierro A., Emr S.D., Hurley J.H.
    Cell 125:113-126(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 13-125 IN COMPLEX WITH STP22 AND SRN2, MUTAGENESIS OF LEU-40 AND TYR-44.
  10. "The crystal structure of the C-terminal domain of Vps28 reveals a conserved surface required for Vps20 recruitment."
    Pineda-Molina E., Belrhali H., Piefer A.J., Akula I., Bates P., Weissenhorn W.
    Traffic 7:1007-1016(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.05 ANGSTROMS) OF 148-241, SELF-ASSOCIATION, INTERACTION WITH VPS20, MUTAGENESIS OF 228-PHE--GLU-231.
  11. "Structural insight into the ESCRT-I/-II link and its role in MVB trafficking."
    Gill D.J., Teo H., Sun J., Perisic O., Veprintsev D.B., Emr S.D., Williams R.L.
    EMBO J. 26:600-612(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 148-242, COMPOSITION OF THE ESCRT-I COMPLEX.
  12. "Molecular architecture and functional model of the complete yeast ESCRT-I heterotetramer."
    Kostelansky M.S., Schluter C., Tam Y.Y., Lee S., Ghirlando R., Beach B., Conibear E., Hurley J.H.
    Cell 129:485-498(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 1-118, COMPOSITION OF THE ESCRT-I COMPLEX.

Entry informationi

Entry nameiVPS28_YEAST
AccessioniPrimary (citable) accession number: Q02767
Secondary accession number(s): D6W3V0, E9P8X2, P87328
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 141 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 1420 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.