ID   VPS53_YEAST             Reviewed;         822 AA.
AC   P47061; D6VWF3;
DT   01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1996, sequence version 1.
DT   04-NOV-2026, entry version 169.
DE   RecName: Full=Vacuolar protein sorting-associated protein 53;
GN   Name=VPS53; OrderedLocusNames=YJL029C; ORFNames=J1258;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA   Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA   Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA   Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA   Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA   Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA   Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA   Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA   Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA   Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA   To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA   von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT   "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL   EMBO J. 15:2031-2049(1996).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [3]
RP   FUNCTION, AND INTERACTION WITH VPS52 AND VPS54.
RX   PubMed=10637310; DOI=10.1091/mbc.11.1.305;
RA   Conibear E., Stevens T.H.;
RT   "Vps52p, Vps53p, and Vps54p form a novel multisubunit complex required for
RT   protein sorting at the yeast late Golgi.";
RL   Mol. Biol. Cell 11:305-323(2000).
RN   [4]
RP   FUNCTION, AND INTERACTION WITH TLG1 AND YPT6.
RX   PubMed=11689439; DOI=10.1093/emboj/20.21.5991;
RA   Siniossoglou S., Pelham H.R.B.;
RT   "An effector of Ypt6p binds the SNARE Tlg1p and mediates selective fusion
RT   of vesicles with late Golgi membranes.";
RL   EMBO J. 20:5991-5998(2001).
RN   [5]
RP   FUNCTION, AND SUBCELLULAR LOCATION.
RX   PubMed=12377769; DOI=10.1074/jbc.m209428200;
RA   Siniossoglou S., Pelham H.R.B.;
RT   "Vps51p links the VFT complex to the SNARE Tlg1p.";
RL   J. Biol. Chem. 277:48318-48324(2002).
RN   [6]
RP   INTERACTION WITH ARL1.
RX   PubMed=12620189; DOI=10.1016/s0960-9822(03)00091-5;
RA   Panic B., Whyte J.R.C., Munro S.;
RT   "The ARF-like GTPases Arl1p and Arl3p act in a pathway that interacts with
RT   vesicle-tethering factors at the Golgi apparatus.";
RL   Curr. Biol. 13:405-410(2003).
RN   [7]
RP   FUNCTION, AND INTERACTION WITH VPS51; VPS52 AND VPS54.
RX   PubMed=12446664; DOI=10.1074/jbc.m210436200;
RA   Reggiori F., Wang C.-W., Stromhaug P.E., Shintani T., Klionsky D.J.;
RT   "Vps51 is part of the yeast Vps fifty-three tethering complex essential for
RT   retrograde traffic from the early endosome and Cvt vesicle completion.";
RL   J. Biol. Chem. 278:5009-5020(2003).
RN   [8]
RP   FUNCTION, AND INTERACTION WITH VPS51; VPS52; VPS54 AND TLG1.
RX   PubMed=12686613; DOI=10.1091/mbc.e02-10-0654;
RA   Conibear E., Cleck J.N., Stevens T.H.;
RT   "Vps51p mediates the association of the GARP (Vps52/53/54) complex with the
RT   late Golgi t-SNARE Tlg1p.";
RL   Mol. Biol. Cell 14:1610-1623(2003).
RN   [9]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=14562095; DOI=10.1038/nature02026;
RA   Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA   Weissman J.S., O'Shea E.K.;
RT   "Global analysis of protein localization in budding yeast.";
RL   Nature 425:686-691(2003).
RN   [10]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA   Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA   Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT   "Analysis of phosphorylation sites on proteins from Saccharomyces
RT   cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL   Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN   [11]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA   Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT   "A multidimensional chromatography technology for in-depth phosphoproteome
RT   analysis.";
RL   Mol. Cell. Proteomics 7:1389-1396(2008).
CC   -!- FUNCTION: Involved in retrograde transport from early and late
CC       endosomes to late Golgi by linking the vesicle through the t-SNARE TGL1
CC       to the Golgi, leading to the membrane fusion between late Golgi and
CC       endosomal vesicles. {ECO:0000269|PubMed:10637310,
CC       ECO:0000269|PubMed:11689439, ECO:0000269|PubMed:12377769,
CC       ECO:0000269|PubMed:12446664, ECO:0000269|PubMed:12686613}.
CC   -!- SUBUNIT: Component of the Golgi-associated retrograde protein (GARP)
CC       complex, also called VFT (VPS fifty-three) complex, composed of VPS51,
CC       VPS52, VPS53 and VPS54. Also interacts with TLG1, YPT6 and ARL1.
CC       {ECO:0000269|PubMed:10637310, ECO:0000269|PubMed:11689439,
CC       ECO:0000269|PubMed:12446664, ECO:0000269|PubMed:12620189,
CC       ECO:0000269|PubMed:12686613}.
CC   -!- INTERACTION:
CC       P47061; P38116: ARL1; NbExp=3; IntAct=EBI-25828, EBI-2869;
CC       P47061; P36116: VPS51; NbExp=4; IntAct=EBI-25828, EBI-26352;
CC       P47061; P39904: VPS52; NbExp=8; IntAct=EBI-25828, EBI-16418;
CC       P47061; Q12071: VPS54; NbExp=10; IntAct=EBI-25828, EBI-36751;
CC   -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane;
CC       Peripheral membrane protein. Endosome membrane; Peripheral membrane
CC       protein.
CC   -!- SIMILARITY: Belongs to the VPS53 family. {ECO:0000305}.
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DR   EMBL; Z49304; CAA89320.1; -; Genomic_DNA.
DR   EMBL; BK006943; DAA08769.1; -; Genomic_DNA.
DR   PIR; S56801; S56801.
DR   RefSeq; NP_012505.1; NM_001181463.1.
DR   PDB; 3NS4; X-ray; 2.90 A; A=554-822.
DR   AlphaFoldDB; P47061; -.
DR   SMR; P47061; -.
DR   BioGRID; 33730; 720.
DR   ComplexPortal; CPX-1718; GARP tethering complex.
DR   DIP; DIP-5902N; -.
DR   FunCoup; P47061; 905.
DR   IntAct; P47061; 8.
DR   STRING; 4932.YJL029C; -.
DR   iPTMnet; P47061; -.
DR   PaxDb; 4932-YJL029C; -.
DR   PeptideAtlas; P47061; -.
DR   EnsemblFungi; YJL029C_mRNA; YJL029C; YJL029C.
DR   GeneID; 853423; -.
DR   KEGG; sce:YJL029C; -.
DR   AGR; SGD:S000003566; -.
DR   SGD; S000003566; VPS53.
DR   VEuPathDB; FungiDB:YJL029C; -.
DR   eggNOG; KOG2180; Eukaryota.
DR   HOGENOM; CLU_358642_0_0_1; -.
DR   InParanoid; P47061; -.
DR   OMA; ADMFRTY; -.
DR   OrthoDB; 10261632at2759; -.
DR   BioCyc; YEAST:G3O-31498-MONOMER; -.
DR   BioGRID-ORCS; 853423; 7 hits in 10 CRISPR screens.
DR   EvolutionaryTrace; P47061; -.
DR   PRO; PR:P47061; -.
DR   Proteomes; UP000002311; Chromosome X.
DR   RNAct; P47061; protein.
DR   GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR   GO; GO:0005829; C:cytosol; HDA:SGD.
DR   GO; GO:0010008; C:endosome membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0000938; C:GARP complex; IPI:SGD.
DR   GO; GO:0005794; C:Golgi apparatus; IDA:SGD.
DR   GO; GO:0006896; P:Golgi to vacuole transport; IMP:SGD.
DR   GO; GO:0090156; P:intracellular sphingolipid homeostasis; IMP:SGD.
DR   GO; GO:0006623; P:protein targeting to vacuole; IDA:ComplexPortal.
DR   GO; GO:0042147; P:retrograde transport, endosome to Golgi; IDA:SGD.
DR   Gene3D; 1.10.357.110; Vacuolar protein sorting-associated protein 53, C-terminus; 1.
DR   InterPro; IPR039766; Vps53.
DR   InterPro; IPR031745; Vps53_C.
DR   InterPro; IPR038260; Vps53_C_sf.
DR   InterPro; IPR007234; Vps53_N.
DR   PANTHER; PTHR12820:SF0; VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 53 HOMOLOG; 1.
DR   PANTHER; PTHR12820; VACUOLAR SORTING PROTEIN 53; 1.
DR   Pfam; PF16854; VPS53_C; 1.
DR   Pfam; PF04100; Vps53_N; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Coiled coil; Endosome; Golgi apparatus; Membrane;
KW   Protein transport; Reference proteome; Transport.
FT   CHAIN           1..822
FT                   /note="Vacuolar protein sorting-associated protein 53"
FT                   /id="PRO_0000215193"
FT   COILED          34..58
FT                   /evidence="ECO:0000255"
FT   COILED          460..484
FT                   /evidence="ECO:0000255"
FT   HELIX           567..569
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           571..598
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   STRAND          605..608
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           615..638
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           639..643
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           653..676
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           683..693
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           700..710
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           716..729
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           746..750
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           752..763
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           768..772
FT                   /evidence="ECO:0007829|PDB:3NS4"
FT   HELIX           773..778
FT                   /evidence="ECO:0007829|PDB:3NS4"
SQ   SEQUENCE   822 AA;  95449 MW;  C75F19FA57157481 CRC64;
     MLEGTVDYDP LEDITNILFS KESLNNIDEL ISITRSYKKQ LQEDILKEEN ELKEHPKNSA
     EIEASLRKVF QDFKETQDVS ASTELTISNL TEGISYLDIA KKNLTHSLTL FQNLKILTDS
     YIQCNELLSQ GSFKKMVSPY KIMCSLAENT FISYKSLDEI NYLLSSISRL KGDTLSKIKQ
     NYNALFSGGN ISEHDTALTM ELREGACELL DCDTSTRAQM IDWCLDKLLF EMKEIFRVDD
     EAGSLENLSR RYIYFKKILN NFNSKFADYF LKDWEMAVRL TTTFYHITHK DLQTLLKREF
     KDKNPSIDLF MTALQSTLDF EKYIDVRFSK KIKEPKLSSC FEPYLTLWVS HQNQMMEKKF
     LSYMSEPKYP SNETESLVLP SSADLFRTYR SVLTQTLELI DNNANDSILT SLANFFSRWL
     QTYSQKILLP LLLPDNIEVQ DKLEAAKYTV LLINTADYCA TTIDQLEDKL SEFSGNREKL
     ANSFTKTKNI YDDLLAKGTS FLLNRVIPLD LNFVWREFIN NDWSNAAIED YSRYMVTLKS
     VLKMPALTDA SIKQQQEQPS TLAFILSQFN RDVYKWNFLD KVIDIITTNF VSNTIRLLQP
     VPPFSLAGSK RKFETRTVVN IGEQLLLDLE LLKEIFHTLP ESVSNDSDLR ENTSYKRVKR
     HADNNIDQLL KFIKLLMAPL DSADDYYETY SKLTNNNPDS AVWSFVLALK GIPWDLALWK
     KLWSAYNLET DDTDEGSRPD SNRDLFIFKW DKVLLGQFEN NLARMQDPNW SKFVRQDLKI
     SPPVMKRIVS TPQIQQQKEE QKKQSLSVKD FVSHSRFFNR GT
//