VPS38_YEAST
ID VPS38_YEAST Reviewed; 439 AA.
AC Q05919; D6VYZ7; Q6B1J7;
DT 26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Vacuolar protein sorting-associated protein 38;
GN Name=VPS38; Synonyms=VPL17; OrderedLocusNames=YLR360W; ORFNames=L8039.11;
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=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(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 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 [4]
RP FUNCTION.
RX PubMed=9265642; DOI=10.1083/jcb.138.4.731;
RA Luo W.-J., Chang A.;
RT "Novel genes involved in endosomal traffic in yeast revealed by suppression
RT of a targeting-defective plasma membrane ATPase mutant.";
RL J. Cell Biol. 138:731-746(1997).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH VPS15; VPS30 AND
RP VPS34.
RX PubMed=11157979; DOI=10.1083/jcb.152.3.519;
RA Kihara A., Noda T., Ishihara N., Ohsumi Y.;
RT "Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in
RT autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae.";
RL J. Cell Biol. 152:519-530(2001).
RN [6]
RP FUNCTION.
RX PubMed=12244127; DOI=10.1242/jcs.00090;
RA Burda P., Padilla S.M., Sarkar S., Emr S.D.;
RT "Retromer function in endosome-to-Golgi retrograde transport is regulated
RT by the yeast Vps34 PtdIns 3-kinase.";
RL J. Cell Sci. 115:3889-3900(2002).
RN [7]
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 [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 DISRUPTION PHENOTYPE.
RX PubMed=32690699; DOI=10.1073/pnas.2008923117;
RA Chen S., Mari M., Parashar S., Liu D., Cui Y., Reggiori F., Novick P.J.,
RA Ferro-Novick S.;
RT "Vps13 is required for the packaging of the ER into autophagosomes during
RT ER-phagy.";
RL Proc. Natl. Acad. Sci. U.S.A. 117:18530-18539(2020).
CC -!- FUNCTION: Involved in endosome-to-Golgi retrograde transport as part of
CC the VPS34 PI3-kinase complex II. This complex is required for the
CC endosome-to-Golgi retrieval of PEP1 and KEX2, and the recruitment of
CC VPS5 and VPS7, two components of the retromer complex, to endosomal
CC membranes (probably through generating a specific pool of
CC phosphatidylinositol 3-phosphate allowing the recruitment of the
CC retromer complex proteins to the endosome). Mediates the interaction
CC between VPS30 and the VPS34-VPS15 core complex, leading to the
CC recruitment of VPS30 to the membrane. {ECO:0000269|PubMed:11157979,
CC ECO:0000269|PubMed:12244127, ECO:0000269|PubMed:9265642}.
CC -!- SUBUNIT: Component of the VPS34 PI3-kinase complex II composed of
CC VPS15, VPS30, VPS34 and VPS38.
CC -!- INTERACTION:
CC Q05919; Q02948: VPS30; NbExp=15; IntAct=EBI-29972, EBI-2670;
CC -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane
CC {ECO:0000269|PubMed:11157979}; Peripheral membrane protein
CC {ECO:0000305}. Endosome membrane {ECO:0000269|PubMed:11157979,
CC ECO:0000269|PubMed:14562095}; Peripheral membrane protein
CC {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Abnormal reticulophagy.
CC {ECO:0000269|PubMed:32690699}.
CC -!- MISCELLANEOUS: Present with 1070 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; U19103; AAB67572.1; -; Genomic_DNA.
DR EMBL; AY693083; AAT93102.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09663.1; -; Genomic_DNA.
DR PIR; S51378; S51378.
DR RefSeq; NP_013464.3; NM_001182249.3.
DR PDB; 5DFZ; X-ray; 4.40 A; A=1-439.
DR PDBsum; 5DFZ; -.
DR AlphaFoldDB; Q05919; -.
DR SMR; Q05919; -.
DR BioGRID; 31621; 379.
DR ComplexPortal; CPX-1677; Phosphatidylinositol 3-kinase complex II.
DR DIP; DIP-8809N; -.
DR IntAct; Q05919; 6.
DR MINT; Q05919; -.
DR STRING; 4932.YLR360W; -.
DR MaxQB; Q05919; -.
DR PaxDb; Q05919; -.
DR PRIDE; Q05919; -.
DR EnsemblFungi; YLR360W_mRNA; YLR360W; YLR360W.
DR GeneID; 851074; -.
DR KEGG; sce:YLR360W; -.
DR SGD; S000004352; VPS38.
DR VEuPathDB; FungiDB:YLR360W; -.
DR eggNOG; ENOG502RY42; Eukaryota.
DR HOGENOM; CLU_050916_0_0_1; -.
DR InParanoid; Q05919; -.
DR OMA; AFNENIM; -.
DR BioCyc; YEAST:G3O-32431-MON; -.
DR Reactome; R-SCE-1632852; Macroautophagy.
DR PRO; PR:Q05919; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q05919; protein.
DR GO; GO:0005768; C:endosome; IBA:GO_Central.
DR GO; GO:0010008; C:endosome membrane; IC:ComplexPortal.
DR GO; GO:0000329; C:fungal-type vacuole membrane; HDA:SGD.
DR GO; GO:0000139; C:Golgi membrane; IC:ComplexPortal.
DR GO; GO:0000323; C:lytic vacuole; IBA:GO_Central.
DR GO; GO:0034272; C:phosphatidylinositol 3-kinase complex, class III, type II; IDA:SGD.
DR GO; GO:0000149; F:SNARE binding; IBA:GO_Central.
DR GO; GO:0045324; P:late endosome to vacuole transport; IMP:SGD.
DR GO; GO:0016236; P:macroautophagy; IMP:SGD.
DR GO; GO:0046854; P:phosphatidylinositol phosphate biosynthetic process; IDA:ComplexPortal.
DR GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR GO; GO:0035493; P:SNARE complex assembly; IBA:GO_Central.
DR InterPro; IPR040939; Vps38.
DR Pfam; PF17649; VPS38; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; Endosome; Golgi apparatus; Membrane;
KW Protein transport; Reference proteome; Transport.
FT CHAIN 1..439
FT /note="Vacuolar protein sorting-associated protein 38"
FT /id="PRO_0000065900"
FT COILED 223..255
FT /evidence="ECO:0000255"
FT CONFLICT 55
FT /note="L -> P (in Ref. 3; AAT93102)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 439 AA; 50860 MW; 70141E084D185015 CRC64;
MKRFLLSRRQ RHLRMICFHN ISLFRANGDS KLIKEYGDGF IPCFFILESI RGELLYVSEV
QSGSLRKLSF QELPKLTGAS TMIVLKLVGL VPSDILCTIS SDKNGIIDDK WCVLCTYTID
LNKLQPINED TVLITGTNAP VLDLIDGSYT LAAEKIKPLK GLVSSHKRNI SQVKIKFSLA
YSSLLKLNKL LEYSSQVHEE INEISSKIED DFLSLKNQNH WYMRTVQKSI ETLEKEVLQR
KKSKKNIEMA QLESNDTINH SKTELSLMSQ DESINDDYGS IYSRFVQIKD RLDQLRFKKL
YQLIGIFHST DLFNSDRGYI YFEKPSSVND VINRLKLKPL NIEILLRQAG ESTKHREYVN
SQLGYYLLFL HLTAIQIFKA PLPYRLMYYG STSVIDSQYP LYFTDQMISK HQAKLIKAIH
YFNADILQFK QILENYRPT
