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P38959

- VPS41_YEAST

UniProt

P38959 - VPS41_YEAST

Protein

Vacuolar protein sorting-associated protein 41

Gene

VPS41

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 140 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    Required for vacuolar assembly and vacuolar traffic. Acts as component of the HOPS complex that acts during the docking stage of vacuole fusion. HOPS is an effector for the vacuolar Rab GTPase YPT7 and is required for vacuolar SNARE complex assembly. It remains bound to SNARE complexes after vacuole fusion.1 Publication

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. Rab guanyl-nucleotide exchange factor activity Source: SGD

    GO - Biological processi

    1. intracellular protein transport Source: InterPro
    2. piecemeal microautophagy of nucleus Source: SGD
    3. positive regulation of Rab GTPase activity Source: GOC
    4. protein transport Source: SGD
    5. regulation of SNARE complex assembly Source: SGD
    6. regulation of vacuole fusion, non-autophagic Source: SGD
    7. vacuolar protein processing Source: SGD
    8. vacuole fusion, non-autophagic Source: SGD
    9. vacuole organization Source: SGD
    10. vesicle-mediated transport Source: SGD

    Keywords - Biological processi

    Protein transport, Transport

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29685-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Vacuolar protein sorting-associated protein 41
    Alternative name(s):
    Vacuolar morphogenesis protein 2
    Gene namesi
    Name:VPS41
    Synonyms:FET2, VAM2
    Ordered Locus Names:YDR080W
    ORF Names:D446, YD8554.13
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDR080w.
    SGDiS000002487. VPS41.

    Subcellular locationi

    Vacuole Curated

    GO - Cellular componenti

    1. fungal-type vacuole membrane Source: SGD
    2. HOPS complex Source: SGD

    Keywords - Cellular componenti

    Vacuole

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 992992Vacuolar protein sorting-associated protein 41PRO_0000212827Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei26 – 261Phosphoserine1 Publication
    Modified residuei53 – 531Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP38959.
    PaxDbiP38959.
    PeptideAtlasiP38959.

    Expressioni

    Gene expression databases

    GenevestigatoriP38959.

    Interactioni

    Subunit structurei

    Component of the HOPS complex which is composed of PEP5, VPS16, PEP3, VPS33, VPS39 and VPS41. HOPS associates with phosphoinositides and the PX domain of VAM7. Interacts with VAM7 and VPS39.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    VPS33P207955EBI-20432,EBI-20395

    Protein-protein interaction databases

    BioGridi32136. 220 interactions.
    DIPiDIP-834N.
    IntActiP38959. 12 interactions.
    MINTiMINT-615238.
    STRINGi4932.YDR080W.

    Structurei

    3D structure databases

    ProteinModelPortaliP38959.
    SMRiP38959. Positions 117-185.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati114 – 15239WD 1Add
    BLAST
    Repeati153 – 19240WD 2Add
    BLAST
    Repeati194 – 23441WD 3Add
    BLAST
    Repeati240 – 28041WD 4Add
    BLAST
    Repeati324 – 36643WD 5Add
    BLAST
    Repeati753 – 901149CHCRAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi79 – 9416Poly-AspAdd
    BLAST
    Compositional biasi239 – 2446Poly-Lys

    Sequence similaritiesi

    Belongs to the VPS41 family.Curated
    Contains 1 CHCR (clathrin heavy-chain) repeat.PROSITE-ProRule annotation
    Contains 5 WD repeats.Curated

    Keywords - Domaini

    Repeat, WD repeat

    Phylogenomic databases

    eggNOGiNOG285467.
    GeneTreeiENSGT00390000000481.
    HOGENOMiHOG000141972.
    OMAiPALKYER.
    OrthoDBiEOG7S2265.

    Family and domain databases

    Gene3Di1.25.40.10. 1 hit.
    2.130.10.10. 1 hit.
    InterProiIPR000547. Clathrin_H-chain/VPS_repeat.
    IPR011990. TPR-like_helical.
    IPR016902. VPS41.
    IPR015943. WD40/YVTN_repeat-like_dom.
    IPR001680. WD40_repeat.
    IPR017986. WD40_repeat_dom.
    [Graphical view]
    PfamiPF00637. Clathrin. 1 hit.
    PF00400. WD40. 1 hit.
    [Graphical view]
    PIRSFiPIRSF028921. VPS41. 1 hit.
    SMARTiSM00299. CLH. 1 hit.
    SM00320. WD40. 2 hits.
    [Graphical view]
    SUPFAMiSSF50978. SSF50978. 1 hit.
    PROSITEiPS50236. CHCR. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P38959-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTTDNHQNDS VLDQQSGERT IDESNSISDE NNVDNKREDV NVTSPTKSVS    50
    CISQAENGVA SRTDESTITG SATDAETGDD DDDDDDDDDE DEDDEDEPPL 100
    LKYTRISQLP KNFFQRDSIS SCLFGDTFFA FGTHSGILHL TTCAFEPIKT 150
    IKCHRSSILC INTDGKYFAT GSIDGTVIIG SMDDPQNITQ YDFKRPINSV 200
    ALHSNFQASR MFVSGGMAGD VVLSQRNWLG NRIDIVLNKK KKKKTRKDDL 250
    SSDMKGPIMG IYTMGDLILW MDDDGITFCD VPTRSQLLNI PFPSRIFNVQ 300
    DVRPDLFRPH VHFLESDRVV IGWGSNIWLF KVSFTKDSNS IKSGDSNSQS 350
    NNMSHFNPTT NIGSLLSSAA SSFRGTPDKK VELECHFTVS MLITGLASFK 400
    DDQLLCLGFD IDIEEEATID EDMKEGKNFS KRPENLLAKG NAPELKIVDL 450
    FNGDEIYNDE VIMKNYEKLS INDYHLGKHI DKTTPEYYLI SSNDAIRVQE 500
    LSLKDHFDWF MERKQYYKAW KIGKYVIGSE ERFSIGLKFL NSLVTKKDWG 550
    TLVDHLNIIF EETLNSLDSN SYDVTQNVLK EWADIIEILI TSGNIVEIAP 600
    LIPKKPALRK SVYDDVLHYF LANDMINKFH EYITKWDLKL FSVEDFEEEL 650
    ETRIEAASEP TASSKEEGSN ITYRTELVHL YLKENKYTKA IPHLLKAKDL 700
    RALTIIKIQN LLPQYLDQIV DIILLPYKGE ISHISKLSIF EIQTIFNKPI 750
    DLLFENRHTI SVARIYEIFE HDCPKSFKKI LFCYLIKFLD TDDSFMISPY 800
    ENQLIELYSE YDRQSLLPFL QKHNNYNVES AIEVCSSKLG LYNELIYLWG 850
    KIGETKKALS LIIDELKNPQ LAIDFVKNWG DSELWEFMIN YSLDKPNFTK 900
    AILTCSDETS EIYLKVIRGM SDDLQIDNLQ DIIKHIVQEN SLSLEVRDNI 950
    LVIINDETKK FANEFLKIRS QGKLFQVDES DIEINDDLNG VL 992
    Length:992
    Mass (Da):113,412
    Last modified:November 1, 1997 - v2
    Checksum:iE1E48B4D5A1A4005
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti424 – 4241K → M in CAA57607. (PubMed:7483840)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB000223 Genomic DNA. Translation: BAA19071.1.
    X82086 Genomic DNA. Translation: CAA57607.1.
    Z74376 Genomic DNA. Translation: CAA98899.1.
    Z46796 Genomic DNA. Translation: CAA86802.1.
    BK006938 Genomic DNA. Translation: DAA11927.1.
    PIRiS49835.
    RefSeqiNP_010365.3. NM_001180388.3.

    Genome annotation databases

    EnsemblFungiiYDR080W; YDR080W; YDR080W.
    GeneIDi851653.
    KEGGisce:YDR080W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB000223 Genomic DNA. Translation: BAA19071.1 .
    X82086 Genomic DNA. Translation: CAA57607.1 .
    Z74376 Genomic DNA. Translation: CAA98899.1 .
    Z46796 Genomic DNA. Translation: CAA86802.1 .
    BK006938 Genomic DNA. Translation: DAA11927.1 .
    PIRi S49835.
    RefSeqi NP_010365.3. NM_001180388.3.

    3D structure databases

    ProteinModelPortali P38959.
    SMRi P38959. Positions 117-185.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32136. 220 interactions.
    DIPi DIP-834N.
    IntActi P38959. 12 interactions.
    MINTi MINT-615238.
    STRINGi 4932.YDR080W.

    Proteomic databases

    MaxQBi P38959.
    PaxDbi P38959.
    PeptideAtlasi P38959.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDR080W ; YDR080W ; YDR080W .
    GeneIDi 851653.
    KEGGi sce:YDR080W.

    Organism-specific databases

    CYGDi YDR080w.
    SGDi S000002487. VPS41.

    Phylogenomic databases

    eggNOGi NOG285467.
    GeneTreei ENSGT00390000000481.
    HOGENOMi HOG000141972.
    OMAi PALKYER.
    OrthoDBi EOG7S2265.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29685-MONOMER.

    Miscellaneous databases

    NextBioi 969245.
    PROi P38959.

    Gene expression databases

    Genevestigatori P38959.

    Family and domain databases

    Gene3Di 1.25.40.10. 1 hit.
    2.130.10.10. 1 hit.
    InterProi IPR000547. Clathrin_H-chain/VPS_repeat.
    IPR011990. TPR-like_helical.
    IPR016902. VPS41.
    IPR015943. WD40/YVTN_repeat-like_dom.
    IPR001680. WD40_repeat.
    IPR017986. WD40_repeat_dom.
    [Graphical view ]
    Pfami PF00637. Clathrin. 1 hit.
    PF00400. WD40. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF028921. VPS41. 1 hit.
    SMARTi SM00299. CLH. 1 hit.
    SM00320. WD40. 2 hits.
    [Graphical view ]
    SUPFAMi SSF50978. SSF50978. 1 hit.
    PROSITEi PS50236. CHCR. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Vam2/Vps41p and Vam6/Vps39p are components of a protein complex on the vacuolar membranes and involved in the vacuolar assembly in the yeast Saccharomyces cerevisiae."
      Nakamura N., Hirata A., Ohsumi Y., Wada Y.
      J. Biol. Chem. 272:11344-11349(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 26786 / X2180-1A.
    2. "Analysis of a 32.8 kb segment of yeast chromosome IV reveals 21 open reading frames, including TPS2, PPH3, RAD55, SED1, PDC2, AFR1, SSS1, SLU7 and a tRNA for arginine."
      Coster F., Jonniaux J.-L., Goffeau A.
      Yeast 11:673-679(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 96604 / S288c / FY1679.
    3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. "Characterization of VPS41, a gene required for vacuolar trafficking and high-affinity iron transport in yeast."
      Radisky D.C., Snyder W.B., Emr S.D., Kaplan J.
      Proc. Natl. Acad. Sci. U.S.A. 94:5662-5666(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    7. "Purification of active HOPS complex reveals its affinities for phosphoinositides and the SNARE Vam7p."
      Stroupe C., Collins K.M., Fratti R.A., Wickner W.
      EMBO J. 25:1579-1589(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE HOPS COMPLEX, FUNCTION OF THE HOPS COMPLEX, INTERACTION WITH VAM7.
    8. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-26 AND SER-53, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiVPS41_YEAST
    AccessioniPrimary (citable) accession number: P38959
    Secondary accession number(s): D6VS67, P87334, Q12011
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 140 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 1170 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3