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Protein

Vacuolar protein sorting-associated protein 53

Gene

VPS53

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in retrograde transport from early and late endosomes to late Golgi by linking the vesicle through the t-SNARE TGL1 to the Golgi, leading to the membrane fusion between late Golgi and endosomal vesicles.5 Publications

GO - Biological processi

  1. Golgi to vacuole transport Source: SGD
  2. protein transport Source: UniProtKB-KW
  3. retrograde transport, endosome to Golgi Source: SGD
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Enzyme and pathway databases

BioCyciYEAST:G3O-31498-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 53
Gene namesi
Name:VPS53
Ordered Locus Names:YJL029C
ORF Names:J1258
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome X

Organism-specific databases

CYGDiYJL029c.
SGDiS000003566. VPS53.

Subcellular locationi

GO - Cellular componenti

  1. endosome membrane Source: UniProtKB-SubCell
  2. GARP complex Source: SGD
  3. Golgi apparatus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Endosome, Golgi apparatus, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 822822Vacuolar protein sorting-associated protein 53PRO_0000215193Add
BLAST

Proteomic databases

MaxQBiP47061.
PaxDbiP47061.

Expressioni

Gene expression databases

GenevestigatoriP47061.

Interactioni

Subunit structurei

Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54. Interacts also with TLG1, YPT6 and ARL1.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ARL1P381163EBI-25828,EBI-2869
VPS52P399048EBI-25828,EBI-16418
VPS54Q1207110EBI-25828,EBI-36751

Protein-protein interaction databases

BioGridi33730. 81 interactions.
DIPiDIP-5902N.
IntActiP47061. 8 interactions.
MINTiMINT-619612.
STRINGi4932.YJL029C.

Structurei

Secondary structure

1
822
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi567 – 5693Combined sources
Helixi571 – 59828Combined sources
Beta strandi605 – 6084Combined sources
Helixi615 – 63824Combined sources
Helixi639 – 6435Combined sources
Helixi653 – 67624Combined sources
Helixi683 – 69311Combined sources
Helixi700 – 71011Combined sources
Helixi716 – 72914Combined sources
Helixi746 – 7505Combined sources
Helixi752 – 76312Combined sources
Helixi768 – 7769Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3NS4X-ray2.90A554-822[»]
ProteinModelPortaliP47061.
SMRiP47061. Positions 564-779.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP47061.

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili34 – 5825Sequence AnalysisAdd
BLAST
Coiled coili460 – 48425Sequence AnalysisAdd
BLAST

Sequence similaritiesi

Belongs to the VPS53 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiNOG327715.
GeneTreeiENSGT00390000015165.
HOGENOMiHOG000000812.
InParanoidiP47061.
OMAiRRYIYFK.
OrthoDBiEOG7NKKTQ.

Family and domain databases

InterProiIPR007234. Vps53_N.
[Graphical view]
PfamiPF04100. Vps53_N. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P47061-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLEGTVDYDP LEDITNILFS KESLNNIDEL ISITRSYKKQ LQEDILKEEN
60 70 80 90 100
ELKEHPKNSA EIEASLRKVF QDFKETQDVS ASTELTISNL TEGISYLDIA
110 120 130 140 150
KKNLTHSLTL FQNLKILTDS YIQCNELLSQ GSFKKMVSPY KIMCSLAENT
160 170 180 190 200
FISYKSLDEI NYLLSSISRL KGDTLSKIKQ NYNALFSGGN ISEHDTALTM
210 220 230 240 250
ELREGACELL DCDTSTRAQM IDWCLDKLLF EMKEIFRVDD EAGSLENLSR
260 270 280 290 300
RYIYFKKILN NFNSKFADYF LKDWEMAVRL TTTFYHITHK DLQTLLKREF
310 320 330 340 350
KDKNPSIDLF MTALQSTLDF EKYIDVRFSK KIKEPKLSSC FEPYLTLWVS
360 370 380 390 400
HQNQMMEKKF LSYMSEPKYP SNETESLVLP SSADLFRTYR SVLTQTLELI
410 420 430 440 450
DNNANDSILT SLANFFSRWL QTYSQKILLP LLLPDNIEVQ DKLEAAKYTV
460 470 480 490 500
LLINTADYCA TTIDQLEDKL SEFSGNREKL ANSFTKTKNI YDDLLAKGTS
510 520 530 540 550
FLLNRVIPLD LNFVWREFIN NDWSNAAIED YSRYMVTLKS VLKMPALTDA
560 570 580 590 600
SIKQQQEQPS TLAFILSQFN RDVYKWNFLD KVIDIITTNF VSNTIRLLQP
610 620 630 640 650
VPPFSLAGSK RKFETRTVVN IGEQLLLDLE LLKEIFHTLP ESVSNDSDLR
660 670 680 690 700
ENTSYKRVKR HADNNIDQLL KFIKLLMAPL DSADDYYETY SKLTNNNPDS
710 720 730 740 750
AVWSFVLALK GIPWDLALWK KLWSAYNLET DDTDEGSRPD SNRDLFIFKW
760 770 780 790 800
DKVLLGQFEN NLARMQDPNW SKFVRQDLKI SPPVMKRIVS TPQIQQQKEE
810 820
QKKQSLSVKD FVSHSRFFNR GT
Length:822
Mass (Da):95,449
Last modified:February 1, 1996 - v1
Checksum:iC75F19FA57157481
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49304 Genomic DNA. Translation: CAA89320.1.
BK006943 Genomic DNA. Translation: DAA08769.1.
PIRiS56801.
RefSeqiNP_012505.1. NM_001181463.1.

Genome annotation databases

EnsemblFungiiYJL029C; YJL029C; YJL029C.
GeneIDi853423.
KEGGisce:YJL029C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49304 Genomic DNA. Translation: CAA89320.1.
BK006943 Genomic DNA. Translation: DAA08769.1.
PIRiS56801.
RefSeqiNP_012505.1. NM_001181463.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3NS4X-ray2.90A554-822[»]
ProteinModelPortaliP47061.
SMRiP47061. Positions 564-779.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33730. 81 interactions.
DIPiDIP-5902N.
IntActiP47061. 8 interactions.
MINTiMINT-619612.
STRINGi4932.YJL029C.

Proteomic databases

MaxQBiP47061.
PaxDbiP47061.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYJL029C; YJL029C; YJL029C.
GeneIDi853423.
KEGGisce:YJL029C.

Organism-specific databases

CYGDiYJL029c.
SGDiS000003566. VPS53.

Phylogenomic databases

eggNOGiNOG327715.
GeneTreeiENSGT00390000015165.
HOGENOMiHOG000000812.
InParanoidiP47061.
OMAiRRYIYFK.
OrthoDBiEOG7NKKTQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-31498-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP47061.
NextBioi973951.
PROiP47061.

Gene expression databases

GenevestigatoriP47061.

Family and domain databases

InterProiIPR007234. Vps53_N.
[Graphical view]
PfamiPF04100. Vps53_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
    Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Vps52p, Vps53p, and Vps54p form a novel multisubunit complex required for protein sorting at the yeast late Golgi."
    Conibear E., Stevens T.H.
    Mol. Biol. Cell 11:305-323(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH VPS52 AND VPS54.
  4. "An effector of Ypt6p binds the SNARE Tlg1p and mediates selective fusion of vesicles with late Golgi membranes."
    Siniossoglou S., Pelham H.R.B.
    EMBO J. 20:5991-5998(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH TLG1 AND YPT6.
  5. "Vps51p links the VFT complex to the SNARE Tlg1p."
    Siniossoglou S., Pelham H.R.B.
    J. Biol. Chem. 277:48318-48324(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  6. "The ARF-like GTPases Arl1p and Arl3p act in a pathway that interacts with vesicle-tethering factors at the Golgi apparatus."
    Panic B., Whyte J.R.C., Munro S.
    Curr. Biol. 13:405-410(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ARL1.
  7. "Vps51 is part of the yeast Vps fifty-three tethering complex essential for retrograde traffic from the early endosome and Cvt vesicle completion."
    Reggiori F., Wang C.-W., Stromhaug P.E., Shintani T., Klionsky D.J.
    J. Biol. Chem. 278:5009-5020(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH VPS51; VPS52 AND VPS54.
  8. "Vps51p mediates the association of the GARP (Vps52/53/54) complex with the late Golgi t-SNARE Tlg1p."
    Conibear E., Cleck J.N., Stevens T.H.
    Mol. Biol. Cell 14:1610-1623(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH VPS51; VPS52; VPS54 AND TLG1.
  9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  10. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
    Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
    Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "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(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiVPS53_YEAST
AccessioniPrimary (citable) accession number: P47061
Secondary accession number(s): D6VWF3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: January 7, 2015
This is version 104 of the entry and version 1 of the sequence. [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 X
    Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

External Data

Dasty 3

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 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.