VPS54_YEAST
ID VPS54_YEAST Reviewed; 889 AA.
AC Q12071; D6VS12;
DT 26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Vacuolar protein sorting-associated protein 54;
DE AltName: Full=CPF1 genetically-interacting protein 1;
DE AltName: Full=Temperature-sensitive clathrin synthetic mutation protein 3;
GN Name=VPS54; Synonyms=CGP1, LUV1, RKI1, TCS3; OrderedLocusNames=YDR027C;
GN ORFNames=PZF889, YD9813.05C;
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 [GENOMIC DNA].
RX PubMed=8896275;
RX DOI=10.1002/(sici)1097-0061(199609)12:10b<1085::aid-yea9>3.3.co;2-s;
RA Eide L.G., Sander C., Prydz H.;
RT "Sequencing and analysis of a 35.4 kb region on the right arm of chromosome
RT IV from Saccharomyces cerevisiae reveal 23 open reading frames.";
RL Yeast 12:1085-1090(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [3]
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 [4]
RP INTERACTION WITH RBL2.
RX PubMed=9914379; DOI=10.1007/s004120050331;
RA Smith A.M., Archer J.E., Solomon F.;
RT "Regulation of tubulin polypeptides and microtubule function: Luv1p
RT interacts with the beta-tubulin binding protein Rbl2p.";
RL Chromosoma 107:471-478(1998).
RN [5]
RP FUNCTION.
RX PubMed=10628971; DOI=10.1093/genetics/154.1.83;
RA Bensen E.S., Costaguta G., Payne G.S.;
RT "Synthetic genetic interactions with temperature-sensitive clathrin in
RT Saccharomyces cerevisiae. Roles for synaptojanin-like Inp53p and dynamin-
RT related Vps1p in clathrin-dependent protein sorting at the trans-Golgi
RT network.";
RL Genetics 154:83-97(2000).
RN [6]
RP FUNCTION, AND INTERACTION WITH VSP52 AND VSP53.
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 [7]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=10888679; DOI=10.1091/mbc.11.7.2429;
RA Conboy M.J., Cyert M.S.;
RT "Luv1p/Rki1p/Tcs3p/Vps54p, a yeast protein that localizes to the late Golgi
RT and early endosome, is required for normal vacuolar morphology.";
RL Mol. Biol. Cell 11:2429-2443(2000).
RN [8]
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 [9]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH VPS51; VSP52 AND
RP VSP53.
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 [10]
RP FUNCTION, AND INTERACTION WITH VPS52; SEC10; SEC15 AND EXO84.
RX PubMed=12395193; DOI=10.1007/s00438-002-0748-4;
RA Fiedler T.A., Karpova T.S., Fleig U., Young M.E., Cooper J.A.,
RA Hegemann J.H.;
RT "The vesicular transport protein Cgp1p/Vps54p/Tcs3p/Luv1p is required for
RT the integrity of the actin cytoskeleton.";
RL Mol. Genet. Genomics 268:190-205(2002).
RN [11]
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 [12]
RP FUNCTION, AND INTERACTION WITH VPS51; VPS52 AND VPS53.
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 [13]
RP FUNCTION, AND INTERACTION WITH VPS51; VPS52 AND VPS53.
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 [14]
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 [15]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [16]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 76625 / YPH499;
RX PubMed=14576278; DOI=10.1073/pnas.2135385100;
RA Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E.,
RA Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P.,
RA Pfanner N., Meisinger C.;
RT "The proteome of Saccharomyces cerevisiae mitochondria.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003).
RN [17]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-69 AND SER-72, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [18]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-69 AND THR-74, AND
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).
RN [19]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-69, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
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. Seems also to be involved in protein transport from
CC Golgi to the plasma membrane and is required for the integrity of the
CC actin cytoskeleton. {ECO:0000269|PubMed:10628971,
CC ECO:0000269|PubMed:10637310, ECO:0000269|PubMed:10888679,
CC ECO:0000269|PubMed:11689439, ECO:0000269|PubMed:12377769,
CC ECO:0000269|PubMed:12395193, ECO:0000269|PubMed:12446664,
CC 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. Interacts also with YPT6, TLG1, RBL2, SEC10,
CC SEC15, EXO84 and ARL1. {ECO:0000269|PubMed:10637310,
CC ECO:0000269|PubMed:11689439, ECO:0000269|PubMed:12377769,
CC ECO:0000269|PubMed:12395193, ECO:0000269|PubMed:12446664,
CC ECO:0000269|PubMed:12620189, ECO:0000269|PubMed:12686613,
CC ECO:0000269|PubMed:9914379}.
CC -!- INTERACTION:
CC Q12071; P38116: ARL1; NbExp=3; IntAct=EBI-36751, EBI-2869;
CC Q12071; P36116: VPS51; NbExp=3; IntAct=EBI-36751, EBI-26352;
CC Q12071; P39904: VPS52; NbExp=8; IntAct=EBI-36751, EBI-16418;
CC Q12071; P47061: VPS53; NbExp=9; IntAct=EBI-36751, EBI-25828;
CC -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane;
CC Peripheral membrane protein. Endosome membrane; Peripheral membrane
CC protein. Mitochondrion membrane {ECO:0000305}; Peripheral membrane
CC protein {ECO:0000305}. Note=May also be mitochondrial.
CC -!- MISCELLANEOUS: Present with 2540 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the VPS54 family. {ECO:0000305}.
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DR EMBL; X95966; CAA65220.1; -; Genomic_DNA.
DR EMBL; Z47814; CAA87806.1; -; Genomic_DNA.
DR EMBL; Z74323; CAA98849.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11872.1; -; Genomic_DNA.
DR PIR; S50934; S50934.
DR RefSeq; NP_010310.1; NM_001180335.1.
DR AlphaFoldDB; Q12071; -.
DR SMR; Q12071; -.
DR BioGRID; 32077; 235.
DR ComplexPortal; CPX-1718; GARP complex.
DR DIP; DIP-5903N; -.
DR IntAct; Q12071; 17.
DR MINT; Q12071; -.
DR STRING; 4932.YDR027C; -.
DR iPTMnet; Q12071; -.
DR MaxQB; Q12071; -.
DR PaxDb; Q12071; -.
DR PRIDE; Q12071; -.
DR EnsemblFungi; YDR027C_mRNA; YDR027C; YDR027C.
DR GeneID; 851591; -.
DR KEGG; sce:YDR027C; -.
DR SGD; S000002434; VPS54.
DR VEuPathDB; FungiDB:YDR027C; -.
DR eggNOG; KOG2115; Eukaryota.
DR GeneTree; ENSGT00390000000583; -.
DR HOGENOM; CLU_324701_0_0_1; -.
DR InParanoid; Q12071; -.
DR OMA; IRIVQLR; -.
DR BioCyc; YEAST:G3O-29643-MON; -.
DR PRO; PR:Q12071; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q12071; protein.
DR GO; GO:0005829; C:cytosol; IEA:GOC.
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:0031966; C:mitochondrial membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0019905; F:syntaxin binding; IBA:GO_Central.
DR GO; GO:0030476; P:ascospore wall assembly; IMP:SGD.
DR GO; GO:0090156; P:cellular sphingolipid homeostasis; IMP:SGD.
DR GO; GO:0006896; P:Golgi to vacuole transport; 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 InterPro; IPR039745; Vps54.
DR PANTHER; PTHR12965; PTHR12965; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Endosome; Golgi apparatus; Membrane; Mitochondrion;
KW Phosphoprotein; Protein transport; Reference proteome; Transport.
FT CHAIN 1..889
FT /note="Vacuolar protein sorting-associated protein 54"
FT /id="PRO_0000148737"
FT REGION 1..44
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 729..748
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 286..321
FT /evidence="ECO:0000255"
FT COMPBIAS 29..44
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 730..748
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 69
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 72
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950"
FT MOD_RES 74
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:18407956"
SQ SEQUENCE 889 AA; 101520 MW; 67E930C34E8CC5AA CRC64;
MSISETPHNK SQGLQKAAGR PKIVVPEGSP SRNSDSGSFT IEGDTSLNDD LLSISGSVTP
RARRSSRLSL DSITPRRSFD SRTLSVANSR SFGFENETHS GSMDFSPLGN NSIYEIVMNT
RRKNWLNYPT VADIPQVSLS KNDLDDHWKT HVIEYVKNIK SDYQIFQSTN NIRNMNQMEQ
LKELREGENM HEESFEANLR QGDAELINSI PDFYFSDKFQ LDNPRTFHKV LDAIDLFLTK
LDMKRQAERD EAFSELRDRL NDFLDIVETL LVTEISKSSH KFFHALSEVD NIQKRALDTM
SELKELAQNI KTIDAENIRK KISHLEMIFK RKNVEKLEQG LLQAKLVLNK TDECKSMYEE
NKLDNCLELI KSIDYLIKGD DSINEDVQSW TRCWPYKLSN LRTIPALSAT REFLTNMKIE
IGGKFSLQLS ILLIDDLRSF CKSIKPKETL HRIQTGSNDK KQTIFTDNFS SKITELIVRL
NRCEELTSAF DLYREKSITE LKSIIKIYLP TENAHADNNH DEKHLNNGST SGSKLSRLIK
EQTPAEFQSM LVNIFTHALE ALRRLYGHQK LLLDISLNEL ASVKSPNENQ HNMITQLDIR
TGINEIIRII QLRTGKIIAV RRELNLSLRY DYFLKFYAIC VIFIQECEVL SGEFLTKYLS
NVLASQIKHY ANAQSSKNYR NIKKKIDAEE WIPYIVDSSI QSDVNDIVSS IDIDPLSWTT
ILDMVGGSHD CENGRSEDKE KDEGNETYQG HRKSVVVGDK TFVASSSLLA TIEVIKELMV
LSINLPSIYL SNFEKLCYDA LQYYNSSAMA SVTQPGNSLL KTGRNLSIMG ESLDCLAEFV
IIVQRFYQRL SNSNRDFEPF DASHYTTLLG QFQASSNKIY MANAPPPPV
