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Protein

Vacuolar protein sorting-associated protein 21

Gene

VPS21

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

Required for protein transport to the vacuole. Involved in two vesicle trafficking steps to the prevacuolar compartment (PVC), regulating the docking of endosomes and Golgi vesicles to the PVC by interacting with PEP7/VAC1 on the PVC membrane and promoting SNARE complex formation.2 Publications

Enzyme regulationi

Alternates between an inactive form bound to GDP and an active form bound to GTP. Activated by the guanine nucleotide-exchange factor (GEF) VPS9 and inactivated by GTPase-activating proteins (GAPs) GYP1 and GYP3.3 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi14 – 218GTP
Nucleotide bindingi62 – 665GTP
Nucleotide bindingi120 – 1234GTP

GO - Molecular functioni

  • GTPase activity Source: SGD
  • GTP binding Source: UniProtKB-KW

GO - Biological processi

  • endocytosis Source: SGD
  • Golgi to endosome transport Source: SGD
  • late endosome to vacuole transport via multivesicular body sorting pathway Source: SGD
  • multivesicular body assembly Source: SGD
  • protein localization to endosome Source: SGD
  • protein targeting to vacuole Source: SGD
  • reticulophagy Source: SGD
  • small GTPase mediated signal transduction Source: InterPro
  • vacuole inheritance Source: SGD
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33623-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 21
Alternative name(s):
GTP-binding protein YPT51
Vacuolar protein-targeting protein 12
Gene namesi
Name:VPS21
Synonyms:VPS12, VPT12, YPT21, YPT51
Ordered Locus Names:YOR089C
ORF Names:YOR3154C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR089C.
SGDiS000005615. VPS21.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: GOC
  • early endosome Source: GO_Central
  • endocytic vesicle Source: GO_Central
  • endosome membrane Source: UniProtKB-SubCell
  • late endosome Source: SGD
  • mitochondrial membrane Source: UniProtKB-SubCell
  • plasma membrane Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Endosome, Membrane, Mitochondrion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi21 – 211S → L or N: Locks VPS21 in its GDP-bound form by abolishing binding to GTP. 3 Publications
Mutagenesisi66 – 661Q → L: Abolishes GTP hydrolysis. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 210210Vacuolar protein sorting-associated protein 21PRO_0000121325Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei188 – 1881PhosphoserineCombined sources
Lipidationi208 – 2081S-geranylgeranyl cysteineBy similarity
Modified residuei210 – 2101Cysteine methyl esterBy similarity
Lipidationi210 – 2101S-geranylgeranyl cysteineBy similarity

Keywords - PTMi

Lipoprotein, Methylation, Phosphoprotein, Prenylation

Proteomic databases

MaxQBiP36017.
PRIDEiP36017.

PTM databases

iPTMnetiP36017.

Interactioni

Subunit structurei

Interacts in its active GTP-bound form with PEP7/VAC1.2 Publications

Protein-protein interaction databases

BioGridi34487. 292 interactions.
DIPiDIP-3801N.
IntActiP36017. 12 interactions.
MINTiMINT-507539.

Structurei

Secondary structure

1
210
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 138Combined sources
Helixi20 – 2910Combined sources
Beta strandi40 – 5112Combined sources
Beta strandi54 – 6310Combined sources
Helixi67 – 726Combined sources
Helixi73 – 775Combined sources
Beta strandi81 – 888Combined sources
Helixi92 – 10817Combined sources
Beta strandi114 – 1207Combined sources
Helixi122 – 1265Combined sources
Helixi135 – 14511Combined sources
Beta strandi148 – 1514Combined sources
Turni154 – 1563Combined sources
Helixi160 – 1689Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EK0X-ray1.48A5-174[»]
ProteinModelPortaliP36017.
SMRiP36017. Positions 5-174.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36017.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi36 – 449Effector regionSequence analysis

Sequence similaritiesi

Belongs to the small GTPase superfamily. Rab family.Curated

Phylogenomic databases

GeneTreeiENSGT00760000119101.
HOGENOMiHOG000233968.
InParanoidiP36017.
KOiK07889.
OMAiTREATGY.
OrthoDBiEOG7BGHXR.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51419. RAB. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P36017-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNTSVTSIKL VLLGEAAVGK SSIVLRFVSN DFAENKEPTI GAAFLTQRVT
60 70 80 90 100
INEHTVKFEI WDTAGQERFA SLAPMYYRNA QAALVVYDVT KPQSFIKARH
110 120 130 140 150
WVKELHEQAS KDIIIALVGN KIDMLQEGGE RKVAREEGEK LAEEKGLLFF
160 170 180 190 200
ETSAKTGENV NDVFLGIGEK IPLKTAEEQN SASNERESNN QRVDLNAAND
210
GTSANSACSC
Length:210
Mass (Da):23,081
Last modified:June 1, 1994 - v1
Checksum:i34D7DA0090C33F09
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76173 Genomic DNA. Translation: CAA53769.1.
Z29338 Genomic DNA. Translation: CAA82543.1.
X94335 Genomic DNA. Translation: CAA64010.1.
Z74997 Genomic DNA. Translation: CAA99285.1.
BK006948 Genomic DNA. Translation: DAA10866.1.
PIRiS43399.
RefSeqiNP_014732.1. NM_001183508.1.

Genome annotation databases

EnsemblFungiiYOR089C; YOR089C; YOR089C.
GeneIDi854256.
KEGGisce:YOR089C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76173 Genomic DNA. Translation: CAA53769.1.
Z29338 Genomic DNA. Translation: CAA82543.1.
X94335 Genomic DNA. Translation: CAA64010.1.
Z74997 Genomic DNA. Translation: CAA99285.1.
BK006948 Genomic DNA. Translation: DAA10866.1.
PIRiS43399.
RefSeqiNP_014732.1. NM_001183508.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EK0X-ray1.48A5-174[»]
ProteinModelPortaliP36017.
SMRiP36017. Positions 5-174.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34487. 292 interactions.
DIPiDIP-3801N.
IntActiP36017. 12 interactions.
MINTiMINT-507539.

PTM databases

iPTMnetiP36017.

Proteomic databases

MaxQBiP36017.
PRIDEiP36017.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOR089C; YOR089C; YOR089C.
GeneIDi854256.
KEGGisce:YOR089C.

Organism-specific databases

EuPathDBiFungiDB:YOR089C.
SGDiS000005615. VPS21.

Phylogenomic databases

GeneTreeiENSGT00760000119101.
HOGENOMiHOG000233968.
InParanoidiP36017.
KOiK07889.
OMAiTREATGY.
OrthoDBiEOG7BGHXR.

Enzyme and pathway databases

BioCyciYEAST:G3O-33623-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP36017.
PROiP36017.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51419. RAB. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Role of three rab5-like GTPases, Ypt51p, Ypt52p, and Ypt53p, in the endocytic and vacuolar protein sorting pathways of yeast."
    Singer-Krueger B., Stenmark H., Duesterhoeft A., Philippsen P., Yoo J.-S., Gallwitz D., Zerial M.
    J. Cell Biol. 125:283-298(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "VPS21 encodes a rab5-like GTP binding protein that is required for the sorting of yeast vacuolar proteins."
    Horazdovsky B.F., Busch G.R., Emr S.D.
    EMBO J. 13:1297-1309(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, MUTAGENESIS OF SER-21.
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. Bienvenut W.V., Peters C.
    Submitted (MAY-2005) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 10-20; 27-97; 112-131 AND 146-186, IDENTIFICATION BY MASS SPECTROMETRY.
  7. "Vac1p coordinates Rab and phosphatidylinositol 3-kinase signaling in Vps45p-dependent vesicle docking/fusion at the endosome."
    Peterson M.R., Burd C.G., Emr S.D.
    Curr. Biol. 9:159-162(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PEP7, MUTAGENESIS OF SER-21 AND GLN-66.
  8. "Vps9p is a guanine nucleotide exchange factor involved in vesicle-mediated vacuolar protein transport."
    Hama H., Tall G.G., Horazdovsky B.F.
    J. Biol. Chem. 274:15284-15291(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION, MUTAGENESIS OF SER-21.
  9. "Two new members of a family of Ypt/Rab GTPase activating proteins. Promiscuity of substrate recognition."
    Albert S., Gallwitz D.
    J. Biol. Chem. 274:33186-33189(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  10. "The phosphatidylinositol 3-phosphate binding protein Vac1p interacts with a Rab GTPase and a Sec1p homologue to facilitate vesicle-mediated vacuolar protein sorting."
    Tall G.G., Hama H., DeWald D.B., Horazdovsky B.F.
    Mol. Biol. Cell 10:1873-1889(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PEP7.
  11. "VPS21 controls entry of endocytosed and biosynthetic proteins into the yeast prevacuolar compartment."
    Gerrard S.R., Bryant N.J., Stevens T.H.
    Mol. Biol. Cell 11:613-626(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  12. "Yeast rab GTPase-activating protein Gyp1p localizes to the Golgi apparatus and is a negative regulator of Ypt1p."
    Du L.-L., Novick P.
    Mol. Biol. Cell 12:1215-1226(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  13. "Cdc50p, a conserved endosomal membrane protein, controls polarized growth in Saccharomyces cerevisiae."
    Misu K., Fujimura-Kamada K., Ueda T., Nakano A., Katoh H., Tanaka K.
    Mol. Biol. Cell 14:730-747(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  14. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  15. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Strain: ATCC 76625 / YPH499.
  16. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-188, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. "High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis."
    Esters H., Alexandrov K., Constantinescu A.-T., Goody R.S., Scheidig A.J.
    J. Mol. Biol. 298:111-121(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 1-195.

Entry informationi

Entry nameiVPS21_YEAST
AccessioniPrimary (citable) accession number: P36017
Secondary accession number(s): D6W2F0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: July 6, 2016
This is version 159 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 8759 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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 XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: 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.