ID   SNX3_YEAST              Reviewed;         162 AA.
AC   Q08826; D6W352;
DT   01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   27-MAR-2024, entry version 189.
DE   RecName: Full=Sorting nexin-3;
DE   AltName: Full=Golgi retention deficient protein 19;
GN   Name=SNX3; Synonyms=GRD19; OrderedLocusNames=YOR357C;
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], FUNCTION, AND SUBCELLULAR LOCATION.
RX   PubMed=9456318; DOI=10.1083/jcb.140.3.577;
RA   Voos W., Stevens T.H.;
RT   "Retrieval of resident late-Golgi membrane proteins from the prevacuolar
RT   compartment of Saccharomyces cerevisiae is dependent on the function of
RT   Grd19p.";
RL   J. Cell Biol. 140:577-590(1998).
RN   [2]
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   [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 RBD2; YIF1; YIP1 AND YIP5.
RX   PubMed=15263065; DOI=10.1074/mcp.m400081-mcp200;
RA   Vollert C.S., Uetz P.;
RT   "The phox homology (PX) domain protein interaction network in yeast.";
RL   Mol. Cell. Proteomics 3:1053-1064(2004).
RN   [5]
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   [6]
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   [7]
RP   DISRUPTION PHENOTYPE.
RX   PubMed=28404745; DOI=10.1091/mbc.e16-11-0772;
RA   Dalton L.E., Bean B.D.M., Davey M., Conibear E.;
RT   "Quantitative high-content imaging identifies novel regulators of Neo1
RT   trafficking at endosomes.";
RL   Mol. Biol. Cell 28:1539-1550(2017).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (2.03 ANGSTROMS) IN COMPLEX WITH PHOSPHATIDYLINOSITOL
RP   3-PHOSPHATE, AND SUBUNIT.
RX   PubMed=14514667; DOI=10.1074/jbc.m304392200;
RA   Zhou C.-Z., de La Sierra-Gallay I.L., Quevillon-Cheruel S., Collinet B.,
RA   Minard P., Blondeau K., Henckes G., Aufrere R., Leulliot N., Graille M.,
RA   Sorel I., Savarin P., de la Torre F., Poupon A., Janin J.,
RA   van Tilbeurgh H.;
RT   "Crystal structure of the yeast Phox homology (PX) domain protein Grd19p
RT   complexed to phosphatidylinositol-3-phosphate.";
RL   J. Biol. Chem. 278:50371-50376(2003).
CC   -!- FUNCTION: Required for retention of late Golgi membrane proteins.
CC       Component of the retrieval machinery that functions by direct
CC       interaction with the cytosolic tails of certain TGN membrane proteins
CC       during the sorting/budding process at the prevacuolar compartment.
CC       Binds phosphatidylinositol 3-phosphate (PtdIns(P3)).
CC       {ECO:0000269|PubMed:9456318}.
CC   -!- SUBUNIT: Monomer. Interacts with RBD2, YIF1, YIP1 and YIP5.
CC       {ECO:0000269|PubMed:14514667, ECO:0000269|PubMed:15263065}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:9456318}. Golgi
CC       apparatus membrane {ECO:0000305}; Peripheral membrane protein
CC       {ECO:0000305}; Cytoplasmic side {ECO:0000305}. Prevacuolar compartment
CC       membrane {ECO:0000305}; Peripheral membrane protein {ECO:0000305};
CC       Cytoplasmic side {ECO:0000305}. Note=Mainly cytoplasmic. A minor amount
CC       associates with membranes.
CC   -!- DISRUPTION PHENOTYPE: Abnormal retrograde transport to the Golgi
CC       apparatus with proteins missorted to the vacuole (PubMed:28404745).
CC       Sensitive to neomycin and trifluoperazine; sensitivity is suppressed by
CC       knockout of ANY1 (PubMed:28404745). {ECO:0000269|PubMed:28404745}.
CC   -!- SIMILARITY: Belongs to the sorting nexin family. {ECO:0000305}.
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DR   EMBL; AF016101; AAC15913.1; -; Genomic_DNA.
DR   EMBL; Z75265; CAA99686.1; -; Genomic_DNA.
DR   EMBL; BK006948; DAA11118.1; -; Genomic_DNA.
DR   PIR; S67269; S67269.
DR   RefSeq; NP_015002.3; NM_001183777.3.
DR   PDB; 1OCS; X-ray; 2.03 A; A=1-162.
DR   PDB; 1OCU; X-ray; 2.30 A; A/B=1-162.
DR   PDBsum; 1OCS; -.
DR   PDBsum; 1OCU; -.
DR   AlphaFoldDB; Q08826; -.
DR   SMR; Q08826; -.
DR   BioGRID; 34742; 103.
DR   IntAct; Q08826; 15.
DR   MINT; Q08826; -.
DR   STRING; 4932.YOR357C; -.
DR   iPTMnet; Q08826; -.
DR   MaxQB; Q08826; -.
DR   PaxDb; 4932-YOR357C; -.
DR   PeptideAtlas; Q08826; -.
DR   EnsemblFungi; YOR357C_mRNA; YOR357C; YOR357C.
DR   GeneID; 854539; -.
DR   KEGG; sce:YOR357C; -.
DR   AGR; SGD:S000005884; -.
DR   SGD; S000005884; SNX3.
DR   VEuPathDB; FungiDB:YOR357C; -.
DR   eggNOG; KOG2527; Eukaryota.
DR   HOGENOM; CLU_057172_2_1_1; -.
DR   InParanoid; Q08826; -.
DR   OMA; NMYTDYE; -.
DR   OrthoDB; 5475877at2759; -.
DR   BioCyc; YEAST:G3O-33828-MONOMER; -.
DR   Reactome; R-SCE-3238698; WNT ligand biogenesis and trafficking.
DR   BioGRID-ORCS; 854539; 5 hits in 10 CRISPR screens.
DR   EvolutionaryTrace; Q08826; -.
DR   PRO; PR:Q08826; -.
DR   Proteomes; UP000002311; Chromosome XV.
DR   RNAct; Q08826; Protein.
DR   GO; GO:0005829; C:cytosol; IDA:SGD.
DR   GO; GO:0031901; C:early endosome membrane; IBA:GO_Central.
DR   GO; GO:0005768; C:endosome; IDA:SGD.
DR   GO; GO:0000329; C:fungal-type vacuole membrane; HDA:SGD.
DR   GO; GO:0000139; C:Golgi membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0032994; C:protein-lipid complex; IMP:CAFA.
DR   GO; GO:0030904; C:retromer complex; IBA:GO_Central.
DR   GO; GO:0032266; F:phosphatidylinositol-3-phosphate binding; IDA:SGD.
DR   GO; GO:0032456; P:endocytic recycling; IBA:GO_Central.
DR   GO; GO:0034499; P:late endosome to Golgi transport; IMP:SGD.
DR   GO; GO:0008104; P:protein localization; IMP:SGD.
DR   GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR   CDD; cd07295; PX_Grd19; 1.
DR   DisProt; DP00482; -.
DR   Gene3D; 3.30.1520.10; Phox-like domain; 1.
DR   InterPro; IPR001683; PX_dom.
DR   InterPro; IPR036871; PX_dom_sf.
DR   InterPro; IPR042138; PX_Grd19_PX.
DR   PANTHER; PTHR45963; RE52028P; 1.
DR   PANTHER; PTHR45963:SF2; SORTING NEXIN-12; 1.
DR   Pfam; PF00787; PX; 1.
DR   SMART; SM00312; PX; 1.
DR   SUPFAM; SSF64268; PX domain; 1.
DR   PROSITE; PS50195; PX; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Golgi apparatus; Lipid-binding; Membrane;
KW   Protein transport; Reference proteome; Transport.
FT   CHAIN           1..162
FT                   /note="Sorting nexin-3"
FT                   /id="PRO_0000213805"
FT   DOMAIN          38..161
FT                   /note="PX"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00147"
FT   REGION          1..23
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         81
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:0000269|PubMed:14514667"
FT   BINDING         83
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:0000269|PubMed:14514667"
FT   BINDING         112
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:0000269|PubMed:14514667"
FT   BINDING         127
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:0000269|PubMed:14514667"
FT   STRAND          36..46
FT                   /evidence="ECO:0007829|PDB:1OCS"
FT   STRAND          50..53
FT                   /evidence="ECO:0007829|PDB:1OCU"
FT   STRAND          57..66
FT                   /evidence="ECO:0007829|PDB:1OCS"
FT   STRAND          74..81
FT                   /evidence="ECO:0007829|PDB:1OCS"
FT   HELIX           82..98
FT                   /evidence="ECO:0007829|PDB:1OCS"
FT   HELIX           117..119
FT                   /evidence="ECO:0007829|PDB:1OCU"
FT   HELIX           121..139
FT                   /evidence="ECO:0007829|PDB:1OCS"
FT   HELIX           142..147
FT                   /evidence="ECO:0007829|PDB:1OCS"
FT   HELIX           149..156
FT                   /evidence="ECO:0007829|PDB:1OCS"
SQ   SEQUENCE   162 AA;  18770 MW;  0633831F6CF165FC CRC64;
     MPREFKSFGS TEKSLLSKGH GEPSYSEIYA EPENFLEIEV HNPKTHIPNG MDSKGMFTDY
     EIICRTNLPS FHKRVSKVRR RYSDFEFFRK CLIKEISMLN HPKVMVPHLP GKILLSNRFS
     NEVIEERRQG LNTWMQSVAG HPLLQSGSKV LVRFIEAEKF VG
//