VPS74_YEAST
ID VPS74_YEAST Reviewed; 345 AA.
AC Q06385; D6VT03;
DT 19-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=Vacuolar protein sorting-associated protein 74;
GN Name=VPS74; OrderedLocusNames=YDR372C; ORFNames=D9481.15;
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=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 [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 INVOLVEMENT IN VPS.
RX PubMed=12134085; DOI=10.1091/mbc.02-01-0005;
RA Bonangelino C.J., Chavez E.M., Bonifacino J.S.;
RT "Genomic screen for vacuolar protein sorting genes in Saccharomyces
RT cerevisiae.";
RL Mol. Biol. Cell 13:2486-2501(2002).
RN [4]
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 [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14, AND IDENTIFICATION BY
RP 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 [6]
RP LIPID-BINDING, AND SUBCELLULAR LOCATION.
RX PubMed=19837035; DOI=10.1016/j.cell.2009.07.052;
RA Dippold H.C., Ng M.M., Farber-Katz S.E., Lee S.K., Kerr M.L.,
RA Peterman M.C., Sim R., Wiharto P.A., Galbraith K.A., Madhavarapu S.,
RA Fuchs G.J., Meerloo T., Farquhar M.G., Zhou H., Field S.J.;
RT "GOLPH3 bridges phosphatidylinositol-4- phosphate and actomyosin to stretch
RT and shape the Golgi to promote budding.";
RL Cell 139:337-351(2009).
RN [7]
RP FUNCTION IN GOLGI TRAFFICKING, SUBCELLULAR LOCATION, LIPID-BINDING, AND
RP MUTAGENESIS OF TRP-88; ARG-97; LYS-178 AND ARG-181.
RX PubMed=20026658; DOI=10.1083/jcb.200909063;
RA Wood C.S., Schmitz K.R., Bessman N.J., Setty T.G., Ferguson K.M.,
RA Burd C.G.;
RT "PtdIns4P recognition by Vps74/GOLPH3 links PtdIns 4-kinase signaling to
RT retrograde Golgi trafficking.";
RL J. Cell Biol. 187:967-975(2009).
RN [8]
RP FUNCTION, MUTAGENESIS OF 6-ARG--ARG-8, COATOMER-BINDING, PHOSPHORYLATION AT
RP SER-19, AND INTERACTION WITH ARF1.
RX PubMed=22889169; DOI=10.1111/j.1600-0854.2012.01403.x;
RA Tu L., Chen L., Banfield D.K.;
RT "A conserved N-terminal arginine-motif in GOLPH3-family proteins mediates
RT binding to coatomer.";
RL Traffic 13:1496-1507(2012).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), FUNCTION, OLIGOMERIZATION, AND
RP SUBCELLULAR LOCATION.
RX PubMed=18410729; DOI=10.1016/j.devcel.2008.02.016;
RA Schmitz K.R., Liu J., Li S., Setty T.G., Wood C.S., Burd C.G.,
RA Ferguson K.M.;
RT "Golgi localization of glycosyltransferases requires a Vps74p oligomer.";
RL Dev. Cell 14:523-534(2008).
CC -!- FUNCTION: Phosphatidylinositol-4-phosphate-binding protein that links
CC Golgi membranes to the cytoskeleton and may participate in the tensile
CC force required for vesicle budding from the Golgi. Thereby, may play a
CC role in Golgi membrane trafficking and could indirectly give its
CC flattened shape to the Golgi apparatus. May also bind to the coatomer
CC to regulate Golgi membrane trafficking. May play a role in anterograde
CC transport from the Golgi to the plasma membrane and regulate secretion.
CC Mediates the cis and medial Golgi localization of mannosyltransferases
CC through direct binding of their cytosolic domains. Involved in vacuolar
CC protein sorting. {ECO:0000269|PubMed:18410729,
CC ECO:0000269|PubMed:20026658, ECO:0000269|PubMed:22889169}.
CC -!- SUBUNIT: Homotetramer. Interacts with coatomer complex. May interact
CC with ARF1. {ECO:0000269|PubMed:22889169}.
CC -!- SUBCELLULAR LOCATION: Golgi apparatus, Golgi stack membrane
CC {ECO:0000269|PubMed:18410729, ECO:0000269|PubMed:19837035,
CC ECO:0000269|PubMed:20026658}; Peripheral membrane protein
CC {ECO:0000269|PubMed:18410729, ECO:0000269|PubMed:19837035,
CC ECO:0000269|PubMed:20026658}; Cytoplasmic side
CC {ECO:0000269|PubMed:18410729, ECO:0000269|PubMed:19837035,
CC ECO:0000269|PubMed:20026658}. Note=Phosphatidylinositol 4-phosphate-
CC binding and oligomerization participate in the recruitment onto Golgi
CC membranes.
CC -!- MISCELLANEOUS: Present with 1850 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the GOLPH3/VPS74 family. {ECO:0000305}.
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DR EMBL; U28373; AAB64808.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12213.1; -; Genomic_DNA.
DR PIR; S61167; S61167.
DR RefSeq; NP_010660.1; NM_001180680.1.
DR PDB; 2ZIH; X-ray; 2.80 A; A/B/C/D=1-345.
DR PDB; 2ZII; X-ray; 3.05 A; A/B/C/D=60-345.
DR PDB; 4TU3; X-ray; 3.19 A; A=1-345.
DR PDBsum; 2ZIH; -.
DR PDBsum; 2ZII; -.
DR PDBsum; 4TU3; -.
DR AlphaFoldDB; Q06385; -.
DR SMR; Q06385; -.
DR BioGRID; 32431; 225.
DR DIP; DIP-1768N; -.
DR IntAct; Q06385; 9.
DR MINT; Q06385; -.
DR STRING; 4932.YDR372C; -.
DR iPTMnet; Q06385; -.
DR MaxQB; Q06385; -.
DR PaxDb; Q06385; -.
DR PRIDE; Q06385; -.
DR EnsemblFungi; YDR372C_mRNA; YDR372C; YDR372C.
DR GeneID; 851978; -.
DR KEGG; sce:YDR372C; -.
DR SGD; S000002780; VPS74.
DR VEuPathDB; FungiDB:YDR372C; -.
DR eggNOG; KOG3983; Eukaryota.
DR GeneTree; ENSGT00390000007153; -.
DR HOGENOM; CLU_036311_1_0_1; -.
DR InParanoid; Q06385; -.
DR OMA; IANWIDL; -.
DR BioCyc; YEAST:G3O-29922-MON; -.
DR EvolutionaryTrace; Q06385; -.
DR PRO; PR:Q06385; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q06385; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0019898; C:extrinsic component of membrane; IDA:SGD.
DR GO; GO:0005794; C:Golgi apparatus; IDA:UniProtKB.
DR GO; GO:0031985; C:Golgi cisterna; IBA:GO_Central.
DR GO; GO:0032580; C:Golgi cisterna membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005797; C:Golgi medial cisterna; IDA:SGD.
DR GO; GO:0000139; C:Golgi membrane; IEA:GOC.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0005802; C:trans-Golgi network; IDA:CACAO.
DR GO; GO:0019899; F:enzyme binding; IPI:SGD.
DR GO; GO:0070273; F:phosphatidylinositol-4-phosphate binding; IDA:UniProtKB.
DR GO; GO:0030968; P:endoplasmic reticulum unfolded protein response; IMP:SGD.
DR GO; GO:0007030; P:Golgi organization; IBA:GO_Central.
DR GO; GO:0043001; P:Golgi to plasma membrane protein transport; IBA:GO_Central.
DR GO; GO:0048194; P:Golgi vesicle budding; IBA:GO_Central.
DR GO; GO:0006487; P:protein N-linked glycosylation; IMP:CACAO.
DR GO; GO:0035269; P:protein O-linked mannosylation; IMP:CACAO.
DR GO; GO:0045053; P:protein retention in Golgi apparatus; IMP:SGD.
DR GO; GO:0060304; P:regulation of phosphatidylinositol dephosphorylation; IMP:SGD.
DR GO; GO:0006890; P:retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum; IMP:SGD.
DR Gene3D; 1.10.3630.10; -; 1.
DR InterPro; IPR008628; GPP34-like.
DR InterPro; IPR038261; GPP34-like_sf.
DR PANTHER; PTHR12704; PTHR12704; 1.
DR Pfam; PF05719; GPP34; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Golgi apparatus; Lipid-binding; Membrane; Phosphoprotein;
KW Protein transport; Reference proteome; Transport.
FT CHAIN 1..345
FT /note="Vacuolar protein sorting-associated protein 74"
FT /id="PRO_0000123823"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 197..208
FT /note="Beta-hairpin required for oligomerization"
FT BINDING 88
FT /ligand="a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol
FT 4-phosphate)"
FT /ligand_id="ChEBI:CHEBI:58178"
FT /evidence="ECO:0000305"
FT BINDING 97
FT /ligand="a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol
FT 4-phosphate)"
FT /ligand_id="ChEBI:CHEBI:58178"
FT /evidence="ECO:0000305"
FT BINDING 178
FT /ligand="a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol
FT 4-phosphate)"
FT /ligand_id="ChEBI:CHEBI:58178"
FT /evidence="ECO:0000305"
FT BINDING 181
FT /ligand="a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol
FT 4-phosphate)"
FT /ligand_id="ChEBI:CHEBI:58178"
FT /evidence="ECO:0000305"
FT MOD_RES 14
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 19
FT /note="Phosphoserine"
FT /evidence="ECO:0000305|PubMed:22889169"
FT MUTAGEN 6..8
FT /note="RRR->AAA: Loss of coatomer-binding."
FT /evidence="ECO:0000269|PubMed:22889169"
FT MUTAGEN 19
FT /note="S->A: Alters phosphorylation but has not effect on
FT Golgi enzymes localization."
FT MUTAGEN 88
FT /note="W->A: Abolishes phosphoinositide binding and Golgi
FT localization; when associated with A-97."
FT /evidence="ECO:0000269|PubMed:20026658"
FT MUTAGEN 97
FT /note="R->A: Abolishes phosphoinositide binding and Golgi
FT localization; when associated with A-88."
FT /evidence="ECO:0000269|PubMed:20026658"
FT MUTAGEN 178
FT /note="K->A: Abolishes phosphoinositide binding and Golgi
FT localization; when associated with A-181."
FT /evidence="ECO:0000269|PubMed:20026658"
FT MUTAGEN 181
FT /note="R->A: Abolishes phosphoinositide binding and Golgi
FT localization; when associated with A-178."
FT /evidence="ECO:0000269|PubMed:20026658"
FT HELIX 69..76
FT /evidence="ECO:0007829|PDB:2ZIH"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 90..106
FT /evidence="ECO:0007829|PDB:2ZIH"
FT STRAND 109..112
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 116..120
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 123..125
FT /evidence="ECO:0007829|PDB:2ZIH"
FT STRAND 126..131
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 139..149
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 156..162
FT /evidence="ECO:0007829|PDB:2ZIH"
FT TURN 163..165
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 170..175
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 180..190
FT /evidence="ECO:0007829|PDB:2ZIH"
FT STRAND 197..200
FT /evidence="ECO:0007829|PDB:2ZIH"
FT STRAND 205..208
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 214..228
FT /evidence="ECO:0007829|PDB:2ZIH"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:2ZIH"
FT STRAND 239..241
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 248..261
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 266..269
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 274..290
FT /evidence="ECO:0007829|PDB:2ZIH"
FT STRAND 292..295
FT /evidence="ECO:0007829|PDB:2ZIH"
FT STRAND 303..307
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 310..319
FT /evidence="ECO:0007829|PDB:2ZIH"
FT HELIX 325..339
FT /evidence="ECO:0007829|PDB:2ZIH"
FT TURN 340..342
FT /evidence="ECO:0007829|PDB:2ZIH"
SQ SEQUENCE 345 AA; 39287 MW; 9D111E5F894F3646 CRC64;
MSTLQRRRVN RADSGDTSSI HSSANNTKGD KIANIAVDGD DDNGTNKKIA YDPEESKLRD
NINIPTLTLM EEVLLMGLRD REGYLSFWND SISYALRGCI IIELALRGKI RILDDSARKR
FDLSERLIEV IDSSKTGEVL LDETLQLMKN DEPLSISNWI DLLSGETWNL LKINYQLKQV
RERLAKGLVD KGVLRTEMKN FFLFDMATHP IADASCKEAI KRRVLSVLVS RNMELSYNEY
FPETTSFKII RTLALICGSY GANVLENVLT TLEYEKRDKA ISRAEEIMAQ FSQYPFDLEK
ETELGVSVNL NKEVKEEIEN NPGHDLQLEV IAGVFEVFSR MDMLL
