VPS5_YEAST
ID VPS5_YEAST Reviewed; 675 AA.
AC Q92331; D6W2D1; E9P8U6; Q08483;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=Vacuolar protein sorting-associated protein 5;
DE AltName: Full=Carboxypeptidase Y-deficient protein 10;
DE AltName: Full=Vacuolar protein-targeting protein 5;
GN Name=VPS5; Synonyms=GRD2, PEP10, VPT5; OrderedLocusNames=YOR069W;
GN ORFNames=YOR29-20;
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=9175702; DOI=10.1242/jcs.110.9.1063;
RA Nothwehr S.F., Hindes A.E.;
RT "The yeast VPS5/GRD2 gene encodes a sorting nexin-1-like protein required
RT for localizing membrane proteins to the late Golgi.";
RL J. Cell Sci. 110:1063-1072(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9285823; DOI=10.1091/mbc.8.8.1529;
RA Horazdovsky B.F., Davies B.A., Seaman M.N.J., McLaughlin S.A., Yoon S.,
RA Emr S.D.;
RT "A sorting nexin-1 homologue, Vps5p, forms a complex with Vps17p and is
RT required for recycling the vacuolar protein-sorting receptor.";
RL Mol. Biol. Cell 8:1529-1541(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9133743;
RX DOI=10.1002/(sici)1097-0061(19970330)13:4<379::aid-yea85>3.0.co;2-g;
RA Valens M., Bohn C., Daignan-Fornier B., Dang V.-D., Bolotin-Fukuhara M.;
RT "The sequence of a 54.7 kb fragment of yeast chromosome XV reveals the
RT presence of two tRNAs and 24 new open reading frames.";
RL Yeast 13:379-390(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 364-675.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [7]
RP IDENTIFICATION IN THE RETROMER COMPLEX.
RX PubMed=9700157; DOI=10.1083/jcb.142.3.665;
RA Seaman M.N., McCaffery J.M., Emr S.D.;
RT "A membrane coat complex essential for endosome-to-Golgi retrograde
RT transport in yeast.";
RL J. Cell Biol. 142:665-681(1998).
RN [8]
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 [9]
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: Plays a role in vesicular protein sorting. Required for
CC retention of late Golgi membrane proteins and vacuolar biogenesis.
CC Component of the membrane-associated retromer complex which is
CC essential in endosome-to-Golgi retrograde transport. The VPS5-VPS17
CC subcomplex may assemble onto the membrane to promote vesicle formation.
CC -!- SUBUNIT: Component of the retromer complex which consists of VPS29,
CC VPS26, VPS35, VPS5 and VPS17. Component of a retromer subcomplex
CC consisting of VPSD5 and VPS17. {ECO:0000269|PubMed:9700157}.
CC -!- INTERACTION:
CC Q92331; P32913: VPS17; NbExp=7; IntAct=EBI-20483, EBI-20366;
CC Q92331; P34110: VPS35; NbExp=3; IntAct=EBI-20483, EBI-20415;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Golgi apparatus membrane
CC {ECO:0000305}; Peripheral membrane protein {ECO:0000305}; Cytoplasmic
CC side {ECO:0000305}. Endosome membrane {ECO:0000305}; Peripheral
CC membrane protein {ECO:0000305}; Cytoplasmic side {ECO:0000305}.
CC -!- DOMAIN: The PX domain binds phosphatidylinositol 3-phosphate which is
CC necessary for peripheral membrane localization. {ECO:0000250}.
CC -!- PTM: Phosphorylated on serine residue(s).
CC -!- MISCELLANEOUS: Present with 6120 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the sorting nexin family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA94554.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA99262.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=Z74976; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U73512; AAB62976.1; -; Genomic_DNA.
DR EMBL; U84735; AAB41798.1; -; Genomic_DNA.
DR EMBL; Z70678; CAA94554.1; ALT_FRAME; Genomic_DNA.
DR EMBL; Z74976; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; Z74977; CAA99262.1; ALT_INIT; Genomic_DNA.
DR EMBL; AY558035; AAS56361.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10847.1; -; Genomic_DNA.
DR PIR; S66952; S66952.
DR RefSeq; NP_014712.2; NM_001183488.1.
DR AlphaFoldDB; Q92331; -.
DR BioGRID; 34468; 358.
DR ComplexPortal; CPX-1653; Retromer complex.
DR DIP; DIP-1740N; -.
DR IntAct; Q92331; 43.
DR MINT; Q92331; -.
DR STRING; 4932.YOR069W; -.
DR TCDB; 9.A.63.1.1; the retromer-dependent vacuolar protein sorting (r-vps) family.
DR CarbonylDB; Q92331; -.
DR iPTMnet; Q92331; -.
DR MaxQB; Q92331; -.
DR PaxDb; Q92331; -.
DR PRIDE; Q92331; -.
DR EnsemblFungi; YOR069W_mRNA; YOR069W; YOR069W.
DR GeneID; 854235; -.
DR KEGG; sce:YOR069W; -.
DR SGD; S000005595; VPS5.
DR VEuPathDB; FungiDB:YOR069W; -.
DR eggNOG; KOG2273; Eukaryota.
DR HOGENOM; CLU_021752_0_0_1; -.
DR InParanoid; Q92331; -.
DR OMA; SCAVREY; -.
DR BioCyc; YEAST:G3O-33608-MON; -.
DR PRO; PR:Q92331; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q92331; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0005768; C:endosome; IDA:SGD.
DR GO; GO:0010008; C:endosome membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0000139; C:Golgi membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0030904; C:retromer complex; IMP:SGD.
DR GO; GO:0030905; C:retromer, tubulation complex; IPI:SGD.
DR GO; GO:0035091; F:phosphatidylinositol binding; IBA:GO_Central.
DR GO; GO:0032266; F:phosphatidylinositol-3-phosphate binding; IDA:SGD.
DR GO; GO:0045053; P:protein retention in Golgi apparatus; IMP:SGD.
DR GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR GO; GO:0042147; P:retrograde transport, endosome to Golgi; IPI:SGD.
DR CDD; cd07627; BAR_Vps5p; 1.
DR CDD; cd06861; PX_Vps5p; 1.
DR Gene3D; 1.20.1270.60; -; 1.
DR Gene3D; 3.30.1520.10; -; 1.
DR InterPro; IPR027267; AH/BAR_dom_sf.
DR InterPro; IPR035803; BAR_Vps5.
DR InterPro; IPR001683; PX_dom.
DR InterPro; IPR036871; PX_dom_sf.
DR InterPro; IPR037868; PX_Vps5.
DR InterPro; IPR028648; Vps5-like.
DR InterPro; IPR015404; Vps5_C.
DR PANTHER; PTHR10555:SF170; PTHR10555:SF170; 1.
DR Pfam; PF00787; PX; 1.
DR Pfam; PF09325; Vps5; 1.
DR SMART; SM00312; PX; 1.
DR SUPFAM; SSF64268; SSF64268; 1.
DR PROSITE; PS50195; PX; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Endosome; Golgi apparatus; Membrane; Phosphoprotein;
KW Protein transport; Reference proteome; Transport.
FT CHAIN 1..675
FT /note="Vacuolar protein sorting-associated protein 5"
FT /id="PRO_0000213804"
FT DOMAIN 279..394
FT /note="PX"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00147"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 65..84
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 165..219
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 191..219
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 320
FT /ligand="a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-
FT inositol-3-phosphate)"
FT /ligand_id="ChEBI:CHEBI:58088"
FT /evidence="ECO:0000250"
FT BINDING 346
FT /ligand="a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-
FT inositol-3-phosphate)"
FT /ligand_id="ChEBI:CHEBI:58088"
FT /evidence="ECO:0000250"
FT BINDING 360
FT /ligand="a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-
FT inositol-3-phosphate)"
FT /ligand_id="ChEBI:CHEBI:58088"
FT /evidence="ECO:0000250"
FT CONFLICT 376
FT /note="V -> A (in Ref. 6; AAS56361)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 675 AA; 76484 MW; FBBA994EADBDC2BD CRC64;
MDYEDNLEAP VWDELNHEGD KTQSLVSNSI ESIGQISTNE ERKDNELLET TASFADKIDL
DSAPEWKDPG LSVAGNPQLE EHDNSKADDL INSLAPEQDP IADLKNSTTQ FIATRESGGA
LFTGNANSPL VFDDTIYDAN TSPNTSKSIS GRRSGKPRIL FDSARAQRNS KRNHSLKAKR
TTASDDTIKT PFTDPLKKAE KENEFVEEPL DDRNERRENN EGKFTASVEK NILEQVDRPL
YNLPQTGANI SSPAEVEENS EKFGKTKIGS KVPPTEKAVA FKVEVKDPVK VGELTSIHVE
YTVISESSLL ELKYAQVSRR YRDFRWLYRQ LQNNHWGKVI PPPPEKQSVG SFKENFIENR
RFQMESMLKK ICQDPVLQKD KDFLLFLTSD DFSSESKKRA FLTGSGAIND SNDLSEVRIS
EIQLLGAEDA AEVLKNGGID AESHKGFMSI SFSSLPKYNE ADEFFIEKKQ KIDELEDNLK
KLSKSLEMVD TSRNTLAAST EEFSSMVETL ASLNVSEPNS ELLNNFADVH KSIKSSLERS
SLQETLTMGV MLDDYIRSLA SVKAIFNQRS KLGYFLVVIE NDMNKKHSQL GKLGQNIHSE
KFREMRKEFQ TLERRYNLTK KQWQAVGDKI KDEFQGFSTD KIREFRNGME ISLEAAIESQ
KECIELWETF YQTNL
