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Protein

Vacuolar protein sorting-associated protein 30

Gene

VPS30

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 cytoplasm to vacuole transport (Cvt), autophagy, nucleophagy, and mitophagy, as a part of the autophagy-specific VPS34 PI3-kinase complex I. This complex is essential to recruit the ATG8-phosphatidylinositol conjugate and the ATG12-ATG5 conjugate to the pre-autophagosomal structure. Also involved in endosome-to-Golgi retrograde transport as part of the VPS34 PI3-kinase complex II. This second complex is required for the endosome-to-Golgi retrieval of PEP1 and KEX2, and the recruitment of VPS5 and VPS7, two components of the retromer complex, to endosomal membranes (probably through the synthesis of a specific pool of phosphatidylinositol 3-phosphate recruiting the retromer to the endosomes). Plays also a role in regulation of filamentous growth.14 Publications

GO - Biological processi

  • autophagosome assembly Source: ParkinsonsUK-UCL
  • autophagy Source: SGD
  • CVT pathway Source: ParkinsonsUK-UCL
  • late endosome to vacuole transport Source: SGD
  • macroautophagy Source: SGD
  • pexophagy Source: SGD
  • phosphatidylinositol biosynthetic process Source: SGD
  • piecemeal microautophagy of nucleus Source: SGD
  • protein targeting to vacuole Source: UniProtKB
  • retrograde transport, endosome to Golgi Source: SGD
Complete GO annotation...

Keywords - Biological processi

Autophagy, Protein transport, Transport

Enzyme and pathway databases

BioCyciYEAST:G3O-34019-MONOMER.
ReactomeiR-SCE-1632852. Macroautophagy.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 30
Alternative name(s):
Autophagy-related protein 6
Gene namesi
Name:VPS30
Synonyms:APG6, ATG6, VPT30
Ordered Locus Names:YPL120W
ORF Names:LPH7
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL120W.
SGDiS000006041. VPS30.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytosol Source: GOC
  • endosome membrane Source: UniProtKB-SubCell
  • extrinsic component of membrane Source: SGD
  • phosphatidylinositol 3-kinase complex, class III, type I Source: SGD
  • phosphatidylinositol 3-kinase complex, class III, type II Source: SGD
  • pre-autophagosomal structure membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Endosome, Membrane, Vacuole

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 557557Vacuolar protein sorting-associated protein 30PRO_0000218559Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei142 – 1421PhosphothreonineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ02948.
PRIDEiQ02948.

PTM databases

iPTMnetiQ02948.

Interactioni

Subunit structurei

Component of the autophagy-specific VPS34 PI3-kinase complex I composed of VPS15, VPS30, VPS34, ATG14 and ATG38; and of the VPS34 PI3-kinase complex II composed of VPS15, VPS30, VPS34 and VPS38.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
ATG14P382707EBI-2670,EBI-2699
VPS38Q059198EBI-2670,EBI-29972

Protein-protein interaction databases

BioGridi36061. 244 interactions.
DIPiDIP-2961N.
IntActiQ02948. 10 interactions.
MINTiMINT-533816.

Structurei

Secondary structure

1
557
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni322 – 3265Combined sources
Beta strandi329 – 3324Combined sources
Beta strandi335 – 3384Combined sources
Beta strandi341 – 3433Combined sources
Helixi353 – 37321Combined sources
Beta strandi379 – 3846Combined sources
Helixi387 – 3893Combined sources
Beta strandi391 – 3955Combined sources
Beta strandi413 – 4197Combined sources
Helixi435 – 45925Combined sources
Beta strandi502 – 5043Combined sources
Helixi513 – 53725Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3VP7X-ray2.30A320-539[»]
5DFZX-ray4.40D1-557[»]
ProteinModelPortaliQ02948.
SMRiQ02948. Positions 320-538.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni320 – 539220BARAAdd
BLAST
Regioni515 – 54026Required for membrane-association, autophagic function during starvation and normal autophagosome morphology1 PublicationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili189 – 322134Sequence analysisAdd
BLAST

Domaini

The C-terminal domain called the BARA domain is dispensable for the construction of both VPS34 PI3-kinase complexes, but is specifically required for autophagy through the targeting of complex I to the pre-autophagosomal structure.1 Publication

Sequence similaritiesi

Belongs to the beclin family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

GeneTreeiENSGT00390000008164.
HOGENOMiHOG000158093.
InParanoidiQ02948.
KOiK08334.
OMAiNINWILT.
OrthoDBiEOG77DJHZ.

Family and domain databases

InterProiIPR007243. Atg6/Beclin.
[Graphical view]
PANTHERiPTHR12768. PTHR12768. 2 hits.
PfamiPF04111. APG6. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q02948-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKCQTCHLPL QLDPSLEGLS LTQRNLLLSN NSIITATNEN VISNKGIEAA
60 70 80 90 100
DNCGPQIPKE RLRRLGEIQN IKDLNLKDDK LITDSFVFLN HDDDDNANIT
110 120 130 140 150
SNSREDQRYG NANGNDNKKA NSDTSDGTST FRDHDEEEQE ATDEDENQQI
160 170 180 190 200
QLNSKTLSTQ VNAMTNVFNI LSSQTNIDFP ICQDCCNILI NRLKSEYDDA
210 220 230 240 250
IKERDTYAQF LSKLESQNKE ISESNKEKQY SHNLSEKENL KKEEERLLDQ
260 270 280 290 300
LLRLEMTDDD LDGELVRLQE KKVQLENEKL QKLSDQNLMD LNNIQFNKNL
310 320 330 340 350
QSLKLQYELS LNQLDKLRKI NIFNATFKIS HSGPFATING LRLGSIPESV
360 370 380 390 400
VPWKEINAAL GQLILLLATI NKNLKINLVD YELQPMGSFS KIKKRMVNSV
410 420 430 440 450
EYNNSTTNAP GDWLILPVYY DENFNLGRIF RKETKFDKSL ETTLEIISEI
460 470 480 490 500
TRQLSTIASS YSSQTLTTSQ DESSMNNAND VENSTSILEL PYIMNKDKIN
510 520 530 540 550
GLSVKLHGSS PNLEWTTAMK FLLTNVKWLL AFSSNLLSKS ITLSPTVNYN

DKTISGN
Length:557
Mass (Da):63,261
Last modified:November 1, 1996 - v1
Checksum:i4BA74B614CABE1C0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB011072 Genomic DNA. Translation: BAA32104.1.
U43503 Genomic DNA. Translation: AAB68242.1.
BK006949 Genomic DNA. Translation: DAA11313.1.
PIRiS62002.
RefSeqiNP_015205.1. NM_001183934.1.

Genome annotation databases

EnsemblFungiiYPL120W; YPL120W; YPL120W.
GeneIDi855983.
KEGGisce:YPL120W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB011072 Genomic DNA. Translation: BAA32104.1.
U43503 Genomic DNA. Translation: AAB68242.1.
BK006949 Genomic DNA. Translation: DAA11313.1.
PIRiS62002.
RefSeqiNP_015205.1. NM_001183934.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3VP7X-ray2.30A320-539[»]
5DFZX-ray4.40D1-557[»]
ProteinModelPortaliQ02948.
SMRiQ02948. Positions 320-538.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36061. 244 interactions.
DIPiDIP-2961N.
IntActiQ02948. 10 interactions.
MINTiMINT-533816.

PTM databases

iPTMnetiQ02948.

Proteomic databases

MaxQBiQ02948.
PRIDEiQ02948.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL120W; YPL120W; YPL120W.
GeneIDi855983.
KEGGisce:YPL120W.

Organism-specific databases

EuPathDBiFungiDB:YPL120W.
SGDiS000006041. VPS30.

Phylogenomic databases

GeneTreeiENSGT00390000008164.
HOGENOMiHOG000158093.
InParanoidiQ02948.
KOiK08334.
OMAiNINWILT.
OrthoDBiEOG77DJHZ.

Enzyme and pathway databases

BioCyciYEAST:G3O-34019-MONOMER.
ReactomeiR-SCE-1632852. Macroautophagy.

Miscellaneous databases

PROiQ02948.

Family and domain databases

InterProiIPR007243. Atg6/Beclin.
[Graphical view]
PANTHERiPTHR12768. PTHR12768. 2 hits.
PfamiPF04111. APG6. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Apg14p and Apg6/Vps30p form a protein complex essential for autophagy in the yeast, Saccharomyces cerevisiae."
    Kametaka S., Okano T., Ohsumi M., Ohsumi Y.
    J. Biol. Chem. 273:22284-22291(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH ATG14.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae."
    Tsukada M., Ohsumi Y.
    FEBS Lett. 333:169-174(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Endosome to Golgi retrieval of the vacuolar protein sorting receptor, Vps10p, requires the function of the VPS29, VPS30, and VPS35 gene products."
    Seaman M.N.J., Marcusson E.G., Cereghino J.L., Emr S.D.
    J. Cell Biol. 137:79-92(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  6. "The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation."
    Suzuki K., Kirisako T., Kamada Y., Mizushima N., Noda T., Ohsumi Y.
    EMBO J. 20:5971-5981(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae."
    Kihara A., Noda T., Ishihara N., Ohsumi Y.
    J. Cell Biol. 152:519-530(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH VPS15; VPS34; VPS38 AND ATG14.
  8. "Retromer function in endosome-to-Golgi retrograde transport is regulated by the yeast Vps34 PtdIns 3-kinase."
    Burda P., Padilla S.M., Sarkar S., Emr S.D.
    J. Cell Sci. 115:3889-3900(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "Characterization of an ERAD gene as VPS30/ATG6 reveals two alternative and functionally distinct protein quality control pathways: one for soluble Z variant of human alpha-1 proteinase inhibitor (A1PiZ) and another for aggregates of A1PiZ."
    Kruse K.B., Brodsky J.L., McCracken A.A.
    Mol. Biol. Cell 17:203-212(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. "Overexpression of autophagy-related genes inhibits yeast filamentous growth."
    Ma J., Jin R., Dobry C.J., Lawson S.K., Kumar A.
    Autophagy 3:604-609(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  13. "Hierarchy of Atg proteins in pre-autophagosomal structure organization."
    Suzuki K., Kubota Y., Sekito T., Ohsumi Y.
    Genes Cells 12:209-218(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  14. "Assortment of phosphatidylinositol 3-kinase complexes--Atg14p directs association of complex I to the pre-autophagosomal structure in Saccharomyces cerevisiae."
    Obara K., Sekito T., Ohsumi Y.
    Mol. Biol. Cell 17:1527-1539(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ATG14, SUBCELLULAR LOCATION.
  15. "The role of autophagy in mitochondria maintenance: characterization of mitochondrial functions in autophagy-deficient S. cerevisiae strains."
    Zhang Y., Qi H., Taylor R., Xu W., Liu L.F., Jin S.
    Autophagy 3:337-346(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  16. "O-mannosylation is required for degradation of the endoplasmic reticulum-associated degradation substrate Gas1*p via the ubiquitin/proteasome pathway in Saccharomyces cerevisiae."
    Hirayama H., Fujita M., Yoko-o T., Jigami Y.
    J. Biochem. 143:555-567(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE VPS34 PI3-KINASE COMPLEX II.
  17. "Piecemeal microautophagy of the nucleus requires the core macroautophagy genes."
    Krick R., Muehe Y., Prick T., Bremer S., Schlotterhose P., Eskelinen E.L., Millen J., Goldfarb D.S., Thumm M.
    Mol. Biol. Cell 19:4492-4505(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  18. "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 THR-142, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  19. "ER-associated complexes (ERACs) containing aggregated cystic fibrosis transmembrane conductance regulator (CFTR) are degraded by autophagy."
    Fu L., Sztul E.
    Eur. J. Cell Biol. 88:215-226(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  20. Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION.
  21. "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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-142, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  22. "Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity."
    Araki Y., Ku W.C., Akioka M., May A.I., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y.
    J. Cell Biol. 203:299-313(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE AUTOPHAGY-SPECIFIC VPS34 PI3-KINASE COMPLEX I.
  23. "Fine mapping of autophagy-related proteins during autophagosome formation in Saccharomyces cerevisiae."
    Suzuki K., Akioka M., Kondo-Kakuta C., Yamamoto H., Ohsumi Y.
    J. Cell Sci. 126:2534-2544(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  24. "Role of membrane association and Atg14-dependent phosphorylation in beclin-1-mediated autophagy."
    Fogel A.I., Dlouhy B.J., Wang C., Ryu S.W., Neutzner A., Hasson S.A., Sideris D.P., Abeliovich H., Youle R.J.
    Mol. Cell. Biol. 33:3675-3688(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, MEMBRANE-SPANNING REGION.
  25. "Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 6 and its specific role in autophagy."
    Noda N.N., Kobayashi T., Adachi W., Fujioka Y., Ohsumi Y., Inagaki F.
    J. Biol. Chem. 287:16256-16266(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 320-539, DOMAIN, FUNCTION.

Entry informationi

Entry nameiBECN1_YEAST
AccessioniPrimary (citable) accession number: Q02948
Secondary accession number(s): D6W3P7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 140 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2490 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

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 one 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.