SNX3_YEAST
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 03-AUG-2022, entry version 182.
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 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 -!- 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; 100.
DR IntAct; Q08826; 15.
DR MINT; Q08826; -.
DR STRING; 4932.YOR357C; -.
DR iPTMnet; Q08826; -.
DR MaxQB; Q08826; -.
DR PaxDb; Q08826; -.
DR PRIDE; Q08826; -.
DR EnsemblFungi; YOR357C_mRNA; YOR357C; YOR357C.
DR GeneID; 854539; -.
DR KEGG; sce:YOR357C; -.
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 BioCyc; YEAST:G3O-33828-MON; -.
DR Reactome; R-SCE-3238698; WNT ligand biogenesis and trafficking.
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; -; 1.
DR InterPro; IPR001683; PX_dom.
DR InterPro; IPR036871; PX_dom_sf.
DR InterPro; IPR042138; PX_Grd19_PX.
DR Pfam; PF00787; PX; 1.
DR SMART; SM00312; PX; 1.
DR SUPFAM; SSF64268; SSF64268; 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
