ID   VPS41_YEAST             Reviewed;         992 AA.
AC   P38959; D6VS67; P87334; Q12011;
DT   01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 2.
DT   27-MAR-2024, entry version 208.
DE   RecName: Full=Vacuolar protein sorting-associated protein 41;
DE   AltName: Full=Vacuolar morphogenesis protein 2;
GN   Name=VPS41; Synonyms=FET2, VAM2; OrderedLocusNames=YDR080W;
GN   ORFNames=D446, YD8554.13;
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].
RC   STRAIN=ATCC 26786 / X2180-1A;
RX   PubMed=9111041; DOI=10.1074/jbc.272.17.11344;
RA   Nakamura N., Hirata A., Ohsumi Y., Wada Y.;
RT   "Vam2/Vps41p and Vam6/Vps39p are components of a protein complex on the
RT   vacuolar membranes and involved in the vacuolar assembly in the yeast
RT   Saccharomyces cerevisiae.";
RL   J. Biol. Chem. 272:11344-11349(1997).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 96604 / S288c / FY1679;
RX   PubMed=7483840; DOI=10.1002/yea.320110708;
RA   Coster F., Jonniaux J.-L., Goffeau A.;
RT   "Analysis of a 32.8 kb segment of yeast chromosome IV reveals 21 open
RT   reading frames, including TPS2, PPH3, RAD55, SED1, PDC2, AFR1, SSS1, SLU7
RT   and a tRNA for arginine.";
RL   Yeast 11:673-679(1995).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169867;
RA   Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA   Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA   Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA   Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA   Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA   Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA   Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA   Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA   Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA   Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA   Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA   Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA   Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA   Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA   Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA   Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA   Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA   Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA   Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA   Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA   Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA   Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA   Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA   Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA   Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA   Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA   Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA   Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA   Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA   Mewes H.-W., Zollner A., Zaccaria P.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL   Nature 387:75-78(1997).
RN   [4]
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   [5]
RP   CHARACTERIZATION.
RX   PubMed=9159129; DOI=10.1073/pnas.94.11.5662;
RA   Radisky D.C., Snyder W.B., Emr S.D., Kaplan J.;
RT   "Characterization of VPS41, a gene required for vacuolar trafficking and
RT   high-affinity iron transport in yeast.";
RL   Proc. Natl. Acad. Sci. U.S.A. 94:5662-5666(1997).
RN   [6]
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   [7]
RP   IDENTIFICATION IN THE HOPS COMPLEX, FUNCTION OF THE HOPS COMPLEX, AND
RP   INTERACTION WITH VAM7.
RX   PubMed=16601699; DOI=10.1038/sj.emboj.7601051;
RA   Stroupe C., Collins K.M., Fratti R.A., Wickner W.;
RT   "Purification of active HOPS complex reveals its affinities for
RT   phosphoinositides and the SNARE Vam7p.";
RL   EMBO J. 25:1579-1589(2006).
RN   [8]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-26 AND SER-53, AND
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   [9]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19779198; DOI=10.1126/science.1172867;
RA   Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT   "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT   into evolution.";
RL   Science 325:1682-1686(2009).
CC   -!- FUNCTION: Required for vacuolar assembly and vacuolar traffic. Acts as
CC       component of the HOPS complex that acts during the docking stage of
CC       vacuole fusion. HOPS is an effector for the vacuolar Rab GTPase YPT7
CC       and is required for vacuolar SNARE complex assembly. It remains bound
CC       to SNARE complexes after vacuole fusion. {ECO:0000269|PubMed:16601699}.
CC   -!- SUBUNIT: Component of the HOPS complex which is composed of PEP5,
CC       VPS16, PEP3, VPS33, VPS39 and VPS41. HOPS associates with
CC       phosphoinositides and the PX domain of VAM7. Interacts with VAM7 and
CC       VPS39. {ECO:0000269|PubMed:16601699}.
CC   -!- INTERACTION:
CC       P38959; P20795: VPS33; NbExp=4; IntAct=EBI-20432, EBI-20395;
CC   -!- SUBCELLULAR LOCATION: Vacuole {ECO:0000305}.
CC   -!- MISCELLANEOUS: Present with 1170 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the VPS41 family. {ECO:0000305}.
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DR   EMBL; AB000223; BAA19071.1; -; Genomic_DNA.
DR   EMBL; X82086; CAA57607.1; -; Genomic_DNA.
DR   EMBL; Z74376; CAA98899.1; -; Genomic_DNA.
DR   EMBL; Z46796; CAA86802.1; -; Genomic_DNA.
DR   EMBL; BK006938; DAA11927.1; -; Genomic_DNA.
DR   PIR; S49835; S49835.
DR   RefSeq; NP_010365.3; NM_001180388.3.
DR   PDB; 7ZU0; EM; 4.40 A; F=1-992.
DR   PDBsum; 7ZU0; -.
DR   AlphaFoldDB; P38959; -.
DR   EMDB; EMD-14964; -.
DR   EMDB; EMD-2280; -.
DR   SMR; P38959; -.
DR   BioGRID; 32136; 593.
DR   ComplexPortal; CPX-1625; HOPS complex.
DR   DIP; DIP-834N; -.
DR   IntAct; P38959; 15.
DR   MINT; P38959; -.
DR   STRING; 4932.YDR080W; -.
DR   iPTMnet; P38959; -.
DR   MaxQB; P38959; -.
DR   PaxDb; 4932-YDR080W; -.
DR   PeptideAtlas; P38959; -.
DR   EnsemblFungi; YDR080W_mRNA; YDR080W; YDR080W.
DR   GeneID; 851653; -.
DR   KEGG; sce:YDR080W; -.
DR   AGR; SGD:S000002487; -.
DR   SGD; S000002487; VPS41.
DR   VEuPathDB; FungiDB:YDR080W; -.
DR   eggNOG; KOG2066; Eukaryota.
DR   GeneTree; ENSGT00390000000481; -.
DR   HOGENOM; CLU_001285_2_1_1; -.
DR   InParanoid; P38959; -.
DR   OMA; CYIRLQD; -.
DR   OrthoDB; 8838at2759; -.
DR   BioCyc; YEAST:G3O-29685-MONOMER; -.
DR   BioGRID-ORCS; 851653; 0 hits in 10 CRISPR screens.
DR   PRO; PR:P38959; -.
DR   Proteomes; UP000002311; Chromosome IV.
DR   RNAct; P38959; Protein.
DR   GO; GO:0005768; C:endosome; HDA:SGD.
DR   GO; GO:0000329; C:fungal-type vacuole membrane; IDA:SGD.
DR   GO; GO:0030897; C:HOPS complex; IPI:SGD.
DR   GO; GO:0005770; C:late endosome; IBA:GO_Central.
DR   GO; GO:0031267; F:small GTPase binding; IPI:SGD.
DR   GO; GO:0009267; P:cellular response to starvation; IBA:GO_Central.
DR   GO; GO:0032258; P:cytoplasm to vacuole transport by the Cvt pathway; IMP:SGD.
DR   GO; GO:0034058; P:endosomal vesicle fusion; IBA:GO_Central.
DR   GO; GO:0006886; P:intracellular protein transport; IEA:InterPro.
DR   GO; GO:0016236; P:macroautophagy; IMP:SGD.
DR   GO; GO:0034727; P:piecemeal microautophagy of the nucleus; IMP:SGD.
DR   GO; GO:0006623; P:protein targeting to vacuole; IBA:GO_Central.
DR   GO; GO:0015031; P:protein transport; IMP:SGD.
DR   GO; GO:0035542; P:regulation of SNARE complex assembly; IDA:SGD.
DR   GO; GO:0006624; P:vacuolar protein processing; IMP:SGD.
DR   GO; GO:0042144; P:vacuole fusion, non-autophagic; IDA:SGD.
DR   GO; GO:0007033; P:vacuole organization; IMP:SGD.
DR   GO; GO:0099022; P:vesicle tethering; IDA:SGD.
DR   GO; GO:0016192; P:vesicle-mediated transport; IMP:SGD.
DR   Gene3D; 1.25.40.10; Tetratricopeptide repeat domain; 1.
DR   Gene3D; 2.130.10.10; YVTN repeat-like/Quinoprotein amine dehydrogenase; 1.
DR   InterPro; IPR000547; Clathrin_H-chain/VPS_repeat.
DR   InterPro; IPR011990; TPR-like_helical_dom_sf.
DR   InterPro; IPR016902; VPS41.
DR   InterPro; IPR045111; Vps41/Vps8.
DR   InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR   InterPro; IPR036322; WD40_repeat_dom_sf.
DR   InterPro; IPR001680; WD40_rpt.
DR   PANTHER; PTHR12616; VACUOLAR PROTEIN SORTING VPS41; 1.
DR   PANTHER; PTHR12616:SF1; VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 41 HOMOLOG; 1.
DR   Pfam; PF00637; Clathrin; 1.
DR   Pfam; PF00400; WD40; 1.
DR   PIRSF; PIRSF028921; VPS41; 1.
DR   SMART; SM00299; CLH; 1.
DR   SMART; SM00320; WD40; 2.
DR   SUPFAM; SSF50978; WD40 repeat-like; 1.
DR   PROSITE; PS50236; CHCR; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Phosphoprotein; Protein transport; Reference proteome;
KW   Repeat; Transport; Vacuole; WD repeat.
FT   CHAIN           1..992
FT                   /note="Vacuolar protein sorting-associated protein 41"
FT                   /id="PRO_0000212827"
FT   REPEAT          114..152
FT                   /note="WD 1"
FT   REPEAT          153..192
FT                   /note="WD 2"
FT   REPEAT          194..234
FT                   /note="WD 3"
FT   REPEAT          240..280
FT                   /note="WD 4"
FT   REPEAT          324..366
FT                   /note="WD 5"
FT   REPEAT          753..901
FT                   /note="CHCR"
FT   REGION          1..100
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..22
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        23..41
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        42..74
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        75..97
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         26
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956"
FT   MOD_RES         53
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956"
FT   CONFLICT        424
FT                   /note="K -> M (in Ref. 2; CAA57607)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   992 AA;  113412 MW;  E1E48B4D5A1A4005 CRC64;
     MTTDNHQNDS VLDQQSGERT IDESNSISDE NNVDNKREDV NVTSPTKSVS CISQAENGVA
     SRTDESTITG SATDAETGDD DDDDDDDDDE DEDDEDEPPL LKYTRISQLP KNFFQRDSIS
     SCLFGDTFFA FGTHSGILHL TTCAFEPIKT IKCHRSSILC INTDGKYFAT GSIDGTVIIG
     SMDDPQNITQ YDFKRPINSV ALHSNFQASR MFVSGGMAGD VVLSQRNWLG NRIDIVLNKK
     KKKKTRKDDL SSDMKGPIMG IYTMGDLILW MDDDGITFCD VPTRSQLLNI PFPSRIFNVQ
     DVRPDLFRPH VHFLESDRVV IGWGSNIWLF KVSFTKDSNS IKSGDSNSQS NNMSHFNPTT
     NIGSLLSSAA SSFRGTPDKK VELECHFTVS MLITGLASFK DDQLLCLGFD IDIEEEATID
     EDMKEGKNFS KRPENLLAKG NAPELKIVDL FNGDEIYNDE VIMKNYEKLS INDYHLGKHI
     DKTTPEYYLI SSNDAIRVQE LSLKDHFDWF MERKQYYKAW KIGKYVIGSE ERFSIGLKFL
     NSLVTKKDWG TLVDHLNIIF EETLNSLDSN SYDVTQNVLK EWADIIEILI TSGNIVEIAP
     LIPKKPALRK SVYDDVLHYF LANDMINKFH EYITKWDLKL FSVEDFEEEL ETRIEAASEP
     TASSKEEGSN ITYRTELVHL YLKENKYTKA IPHLLKAKDL RALTIIKIQN LLPQYLDQIV
     DIILLPYKGE ISHISKLSIF EIQTIFNKPI DLLFENRHTI SVARIYEIFE HDCPKSFKKI
     LFCYLIKFLD TDDSFMISPY ENQLIELYSE YDRQSLLPFL QKHNNYNVES AIEVCSSKLG
     LYNELIYLWG KIGETKKALS LIIDELKNPQ LAIDFVKNWG DSELWEFMIN YSLDKPNFTK
     AILTCSDETS EIYLKVIRGM SDDLQIDNLQ DIIKHIVQEN SLSLEVRDNI LVIINDETKK
     FANEFLKIRS QGKLFQVDES DIEINDDLNG VL
//