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Protein

Vacuolar protein sorting-associated protein 41

Gene

VPS41

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

  • Rab GTPase binding Source: SGD

GO - Biological processi

  • intracellular protein transport Source: InterPro
  • piecemeal microautophagy of nucleus Source: SGD
  • protein transport Source: SGD
  • regulation of SNARE complex assembly Source: SGD
  • regulation of vacuole fusion, non-autophagic Source: SGD
  • vacuolar protein processing Source: SGD
  • vacuole fusion, non-autophagic Source: SGD
  • vacuole organization Source: SGD
  • vesicle-mediated transport Source: SGD
Complete GO annotation...

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 Componenti: Chromosome IV

Organism-specific databases

CYGDiYDR080w.
EuPathDBiFungiDB:YDR080W.
SGDiS000002487. VPS41.

Subcellular locationi

GO - Cellular componenti

  • fungal-type vacuole membrane Source: SGD
  • HOPS complex Source: SGD
Complete GO annotation...

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.

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

Structurei

3D structure databases

ProteinModelPortaliP38959.
SMRiP38959. Positions 116-179.
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.
InParanoidiP38959.
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_dom.
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

        10         20         30         40         50
MTTDNHQNDS VLDQQSGERT IDESNSISDE NNVDNKREDV NVTSPTKSVS
60 70 80 90 100
CISQAENGVA SRTDESTITG SATDAETGDD DDDDDDDDDE DEDDEDEPPL
110 120 130 140 150
LKYTRISQLP KNFFQRDSIS SCLFGDTFFA FGTHSGILHL TTCAFEPIKT
160 170 180 190 200
IKCHRSSILC INTDGKYFAT GSIDGTVIIG SMDDPQNITQ YDFKRPINSV
210 220 230 240 250
ALHSNFQASR MFVSGGMAGD VVLSQRNWLG NRIDIVLNKK KKKKTRKDDL
260 270 280 290 300
SSDMKGPIMG IYTMGDLILW MDDDGITFCD VPTRSQLLNI PFPSRIFNVQ
310 320 330 340 350
DVRPDLFRPH VHFLESDRVV IGWGSNIWLF KVSFTKDSNS IKSGDSNSQS
360 370 380 390 400
NNMSHFNPTT NIGSLLSSAA SSFRGTPDKK VELECHFTVS MLITGLASFK
410 420 430 440 450
DDQLLCLGFD IDIEEEATID EDMKEGKNFS KRPENLLAKG NAPELKIVDL
460 470 480 490 500
FNGDEIYNDE VIMKNYEKLS INDYHLGKHI DKTTPEYYLI SSNDAIRVQE
510 520 530 540 550
LSLKDHFDWF MERKQYYKAW KIGKYVIGSE ERFSIGLKFL NSLVTKKDWG
560 570 580 590 600
TLVDHLNIIF EETLNSLDSN SYDVTQNVLK EWADIIEILI TSGNIVEIAP
610 620 630 640 650
LIPKKPALRK SVYDDVLHYF LANDMINKFH EYITKWDLKL FSVEDFEEEL
660 670 680 690 700
ETRIEAASEP TASSKEEGSN ITYRTELVHL YLKENKYTKA IPHLLKAKDL
710 720 730 740 750
RALTIIKIQN LLPQYLDQIV DIILLPYKGE ISHISKLSIF EIQTIFNKPI
760 770 780 790 800
DLLFENRHTI SVARIYEIFE HDCPKSFKKI LFCYLIKFLD TDDSFMISPY
810 820 830 840 850
ENQLIELYSE YDRQSLLPFL QKHNNYNVES AIEVCSSKLG LYNELIYLWG
860 870 880 890 900
KIGETKKALS LIIDELKNPQ LAIDFVKNWG DSELWEFMIN YSLDKPNFTK
910 920 930 940 950
AILTCSDETS EIYLKVIRGM SDDLQIDNLQ DIIKHIVQEN SLSLEVRDNI
960 970 980 990
LVIINDETKK FANEFLKIRS QGKLFQVDES DIEINDDLNG VL
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP38959.
SMRiP38959. Positions 116-179.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32136. 221 interactions.
DIPiDIP-834N.
IntActiP38959. 12 interactions.
MINTiMINT-615238.
STRINGi4932.YDR080W.

Proteomic databases

MaxQBiP38959.
PaxDbiP38959.
PeptideAtlasiP38959.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CYGDiYDR080w.
EuPathDBiFungiDB:YDR080W.
SGDiS000002487. VPS41.

Phylogenomic databases

eggNOGiNOG285467.
GeneTreeiENSGT00390000000481.
HOGENOMiHOG000141972.
InParanoidiP38959.
OMAiPALKYER.
OrthoDBiEOG7S2265.

Enzyme and pathway databases

BioCyciYEAST:G3O-29685-MONOMER.

Miscellaneous databases

NextBioi969245.
PROiP38959.

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_dom.
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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: June 24, 2015
This is version 146 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.