SNX4_YEAST
ID SNX4_YEAST Reviewed; 423 AA.
AC P47057; D6VWE7; Q06794;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1996, sequence version 1.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=Sorting nexin-4 {ECO:0000303|PubMed:12554655};
DE AltName: Full=Autophagy-related protein 24 {ECO:0000303|PubMed:14536056};
DE AltName: Full=Cytoplasm to vacuole targeting protein 13 {ECO:0000303|PubMed:8663607};
GN Name=SNX4 {ECO:0000303|PubMed:12554655, ECO:0000312|SGD:S000003573};
GN Synonyms=ATG24 {ECO:0000303|PubMed:14536056},
GN CVT13 {ECO:0000303|PubMed:8663607}; OrderedLocusNames=YJL036W;
GN ORFNames=J1244;
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].
RA Sora S., Tiboni O., Sanangelantoni A.M.;
RL Submitted (FEB-1995) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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 [5]
RP FUNCTION.
RX PubMed=8663607; DOI=10.1074/jbc.271.30.17621;
RA Harding T.M., Hefner-Gravink A., Thumm M., Klionsky D.J.;
RT "Genetic and phenotypic overlap between autophagy and the cytoplasm to
RT vacuole protein targeting pathway.";
RL J. Biol. Chem. 271:17621-17624(1996).
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH ATG17 AND ATG20, AND
RP MUTAGENESIS OF TYR-79.
RX PubMed=12048214; DOI=10.1074/jbc.m204736200;
RA Nice D.C. III, Sato T.K., Stromhaug P.E., Emr S.D., Klionsky D.J.;
RT "Cooperative binding of the cytoplasm to vacuole targeting pathway
RT proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-
RT autophagosomal structure is required for selective autophagy.";
RL J. Biol. Chem. 277:30198-30207(2002).
RN [7]
RP NOMENCLATURE.
RX PubMed=14536056; DOI=10.1016/s1534-5807(03)00296-x;
RA Klionsky D.J., Cregg J.M., Dunn W.A. Jr., Emr S.D., Sakai Y.,
RA Sandoval I.V., Sibirny A., Subramani S., Thumm M., Veenhuis M., Ohsumi Y.;
RT "A unified nomenclature for yeast autophagy-related genes.";
RL Dev. Cell 5:539-545(2003).
RN [8]
RP FUNCTION, AND INTERACTION WITH SNX41 AND SNC1.
RX PubMed=12554655; DOI=10.1093/emboj/cdg062;
RA Hettema E.H., Lewis M.J., Black M.W., Pelham H.R.B.;
RT "Retromer and the sorting nexins Snx4/41/42 mediate distinct retrieval
RT pathways from yeast endosomes.";
RL EMBO J. 22:548-557(2003).
RN [9]
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 [10]
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 [11]
RP FUNCTION.
RX PubMed=15800066; DOI=10.1091/mbc.e04-10-0941;
RA Krsmanovic T., Pawelec A., Sydor T., Kolling R.;
RT "Control of Ste6 recycling by ubiquitination in the early endocytic pathway
RT in yeast.";
RL Mol. Biol. Cell 16:2809-2821(2005).
RN [12]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=17420293; DOI=10.1083/jcb.200609161;
RA Strochlic T.I., Setty T.G., Sitaram A., Burd C.G.;
RT "Grd19/Snx3p functions as a cargo-specific adapter for retromer-dependent
RT endocytic recycling.";
RL J. Cell Biol. 177:115-125(2007).
RN [13]
RP FUNCTION.
RX PubMed=18818209; DOI=10.1074/jbc.m802403200;
RA Kanki T., Klionsky D.J.;
RT "Mitophagy in yeast occurs through a selective mechanism.";
RL J. Biol. Chem. 283:32386-32393(2008).
RN [14]
RP FUNCTION.
RX PubMed=19793921; DOI=10.1091/mbc.e09-03-0225;
RA Kanki T., Wang K., Baba M., Bartholomew C.R., Lynch-Day M.A., Du Z.,
RA Geng J., Mao K., Yang Z., Yen W.L., Klionsky D.J.;
RT "A genomic screen for yeast mutants defective in selective mitochondria
RT autophagy.";
RL Mol. Biol. Cell 20:4730-4738(2009).
RN [15]
RP FUNCTION.
RX PubMed=20861302; DOI=10.1091/mbc.e10-05-0457;
RA Ohashi Y., Munro S.;
RT "Membrane delivery to the yeast autophagosome from the Golgi-endosomal
RT system.";
RL Mol. Biol. Cell 21:3998-4008(2010).
RN [16]
RP FUNCTION.
RX PubMed=20729555; DOI=10.1074/jbc.m110.147264;
RA LeBlanc M.A., McMaster C.R.;
RT "Lipid binding requirements for oxysterol-binding protein Kes1 inhibition
RT of autophagy and endosome-trans-Golgi trafficking pathways.";
RL J. Biol. Chem. 285:33875-33884(2010).
RN [17]
RP FUNCTION.
RX PubMed=21429936; DOI=10.1242/jcs.076406;
RA Mendl N., Occhipinti A., Muller M., Wild P., Dikic I., Reichert A.S.;
RT "Mitophagy in yeast is independent of mitochondrial fission and requires
RT the stress response gene WHI2.";
RL J. Cell Sci. 124:1339-1350(2011).
CC -!- FUNCTION: Sorting nexin, involved in the separation or division of
CC vacuoles throughout the entire life cycle of the cells
CC (PubMed:12048214, PubMed:12554655, PubMed:15800066, PubMed:17420293,
CC PubMed:18818209, PubMed:19793921, PubMed:20729555, PubMed:20861302,
CC PubMed:21429936, PubMed:8663607). Involved in retrieval of late-Golgi
CC SNAREs from post-Golgi endosomes to the trans-Golgi network, for
CC cytoplasm to vacuole transport (Cvt), autophagy, mitophagy, and
CC pexophagy (PubMed:12048214, PubMed:12554655, PubMed:15800066,
CC PubMed:17420293, PubMed:18818209, PubMed:19793921, PubMed:20729555,
CC PubMed:20861302, PubMed:21429936, PubMed:8663607). Involved in proper
CC sorting of the v-SNARE protein SNC1 (PubMed:12554655).
CC {ECO:0000269|PubMed:12048214, ECO:0000269|PubMed:12554655,
CC ECO:0000269|PubMed:15800066, ECO:0000269|PubMed:17420293,
CC ECO:0000269|PubMed:18818209, ECO:0000269|PubMed:19793921,
CC ECO:0000269|PubMed:20729555, ECO:0000269|PubMed:20861302,
CC ECO:0000269|PubMed:21429936, ECO:0000269|PubMed:8663607}.
CC -!- SUBUNIT: Forms a complex with ATG20 and ATG17 (PubMed:12048214). Binds
CC also to SNC1 and SNX41 (PubMed:12554655). {ECO:0000269|PubMed:12048214,
CC ECO:0000269|PubMed:12554655}.
CC -!- INTERACTION:
CC P47057; Q06410: ATG17; NbExp=2; IntAct=EBI-17610, EBI-30856;
CC P47057; Q07528: ATG20; NbExp=7; IntAct=EBI-17610, EBI-36894;
CC P47057; Q04053: SNX41; NbExp=7; IntAct=EBI-17610, EBI-30464;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:12048214}.
CC Preautophagosomal structure membrane {ECO:0000269|PubMed:12048214};
CC Peripheral membrane protein {ECO:0000269|PubMed:12048214}. Endosome
CC membrane {ECO:0000269|PubMed:17420293}; Peripheral membrane protein
CC {ECO:0000269|PubMed:12048214}. Note=Endosome and other perivacuolar
CC punctate structures (PubMed:17420293). Associates to
CC phosphatidylinositol 3-phosphate, necessary for peripheral membrane
CC localization to the perivacuolar punctate structures (PubMed:12048214).
CC {ECO:0000269|PubMed:12048214, ECO:0000269|PubMed:17420293}.
CC -!- DOMAIN: The PX domain binds phosphatidylinositol 3-phosphate which is
CC necessary for peripheral membrane localization to the perivacuolar
CC punctate structures. {ECO:0000250|UniProtKB:Q96L94}.
CC -!- MISCELLANEOUS: Present with 358 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=CAA88260.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; Z48229; CAA88260.1; ALT_FRAME; Genomic_DNA.
DR EMBL; Z49311; CAA89327.1; -; Genomic_DNA.
DR EMBL; AY693177; AAT93196.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08763.1; -; Genomic_DNA.
DR PIR; S56808; S56808.
DR RefSeq; NP_012498.1; NM_001181470.1.
DR AlphaFoldDB; P47057; -.
DR SMR; P47057; -.
DR BioGRID; 33724; 340.
DR ComplexPortal; CPX-1377; SNX4-ATG20 sorting nexin complex.
DR ComplexPortal; CPX-1378; SNX4-SNX41 sorting nexin complex.
DR DIP; DIP-2707N; -.
DR IntAct; P47057; 24.
DR MINT; P47057; -.
DR STRING; 4932.YJL036W; -.
DR iPTMnet; P47057; -.
DR MaxQB; P47057; -.
DR PaxDb; P47057; -.
DR PRIDE; P47057; -.
DR EnsemblFungi; YJL036W_mRNA; YJL036W; YJL036W.
DR GeneID; 853416; -.
DR KEGG; sce:YJL036W; -.
DR SGD; S000003573; SNX4.
DR VEuPathDB; FungiDB:YJL036W; -.
DR eggNOG; KOG2273; Eukaryota.
DR HOGENOM; CLU_027221_0_0_1; -.
DR InParanoid; P47057; -.
DR OMA; QKSGHYL; -.
DR BioCyc; YEAST:G3O-31502-MON; -.
DR PRO; PR:P47057; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P47057; protein.
DR GO; GO:0010009; C:cytoplasmic side of endosome membrane; IDA:ComplexPortal.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0005769; C:early endosome; IDA:SGD.
DR GO; GO:0019898; C:extrinsic component of membrane; IDA:SGD.
DR GO; GO:0000407; C:phagophore assembly site; IDA:SGD.
DR GO; GO:0034045; C:phagophore assembly site membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0032266; F:phosphatidylinositol-3-phosphate binding; IDA:SGD.
DR GO; GO:0000422; P:autophagy of mitochondrion; IMP:SGD.
DR GO; GO:0032258; P:cytoplasm to vacuole transport by the Cvt pathway; IMP:SGD.
DR GO; GO:0034498; P:early endosome to Golgi transport; IMP:SGD.
DR GO; GO:0032456; P:endocytic recycling; IMP:SGD.
DR GO; GO:0006886; P:intracellular protein transport; IDA:ComplexPortal.
DR GO; GO:0034727; P:piecemeal microautophagy of the nucleus; IMP:SGD.
DR GO; GO:2000786; P:positive regulation of autophagosome assembly; IBA:GO_Central.
DR GO; GO:0036010; P:protein localization to endosome; IGI:SGD.
DR GO; GO:0006623; P:protein targeting to vacuole; IMP:SGD.
DR GO; GO:0015031; P:protein transport; IBA:GO_Central.
DR GO; GO:0061709; P:reticulophagy; IBA:GO_Central.
DR GO; GO:0042147; P:retrograde transport, endosome to Golgi; IDA:ComplexPortal.
DR GO; GO:0061912; P:selective autophagy; IDA:ComplexPortal.
DR Gene3D; 1.20.1270.60; -; 1.
DR Gene3D; 3.30.1520.10; -; 1.
DR InterPro; IPR027267; AH/BAR_dom_sf.
DR InterPro; IPR001683; PX_dom.
DR InterPro; IPR036871; PX_dom_sf.
DR Pfam; PF00787; PX; 1.
DR SMART; SM00312; PX; 1.
DR SUPFAM; SSF103657; SSF103657; 1.
DR SUPFAM; SSF64268; SSF64268; 1.
DR PROSITE; PS50195; PX; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Cytoplasm; Endosome; Lipid-binding; Membrane;
KW Protein transport; Reference proteome; Transport.
FT CHAIN 1..423
FT /note="Sorting nexin-4"
FT /id="PRO_0000213818"
FT DOMAIN 29..157
FT /note="PX"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00147"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 217..252
FT /evidence="ECO:0000255"
FT COILED 346..381
FT /evidence="ECO:0000255"
FT COMPBIAS 1..22
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 78
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|UniProtKB:Q3UR97"
FT BINDING 80
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|UniProtKB:Q96L94"
FT BINDING 104
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|UniProtKB:Q96L94"
FT BINDING 123
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|UniProtKB:Q6P4T1"
FT MUTAGEN 79
FT /note="Y->A: Abolishes the intracellular punctate
FT localization and decreases the cytoplasm to vacuole
FT transport."
FT /evidence="ECO:0000269|PubMed:12048214"
FT CONFLICT 292..304
FT /note="QLIKLKDQKQIDY -> PDQIERPETDRL (in Ref. 1; CAA88260)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 423 AA; 49002 MW; 10964322A1A22F16 CRC64;
MTDKGKNDLT SKAKDKARGN PEKPPYWFEI IVSDPQKRTG DPGSSSGYVS YQISTKTNNT
SFYDNRGDPE SIIVVHRRYS DLLLLHDILL NRFPTCIIPP LPDKKVFQYI AGDRFSQRFT
QKRCHSLQNF LRRVSLHPDL SQSKVFKTFL VSKDWESHRK VLQDSLQPNK DEVTDAFMNA
FKTVHKQNEE FTEIREKSDK LDRTVTKIDK LFHKVVKKND SMSEDYTKLG SNLQELQELV
TGENEELAAK LKIFNEGVTQ LSYGLQDLTK YLDYEYIVDL KDLEHYIDSM RQLIKLKDQK
QIDYEELSDY LTRSIKEKNN LISGYGGSNF FANKLEELAG INQEASRREK INKLEGKITS
LTGELENAKK VADGFEQECL KEIDHFESVK TAEIKKSLGS LADHHIEFYE RILEAWEKVD
DSL
