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
//
