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Q9UBQ0

- VPS29_HUMAN

UniProt

Q9UBQ0 - VPS29_HUMAN

Protein

Vacuolar protein sorting-associated protein 29

Gene

VPS29

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 130 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    Functioni

    Essential component of the retromer complex, a complex required to retrieve lysosomal enzyme receptors (IGF2R and M6PR) from endosomes to the trans-Golgi network. Also required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA). Has low protein phosphatase activity towards a serine-phosphorylated peptide derived from IGF2R (in vitro).1 Publication

    Catalytic activityi

    O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate.1 Publication

    Cofactori

    Binds 2 zinc ions per subunit.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi8 – 81Zinc 1By similarity
    Metal bindingi10 – 101Zinc 1By similarity
    Metal bindingi39 – 391Zinc 1By similarity
    Metal bindingi39 – 391Zinc 2By similarity
    Metal bindingi62 – 621Zinc 2By similarity
    Metal bindingi86 – 861Zinc 2By similarity
    Metal bindingi115 – 1151Zinc 2By similarity
    Metal bindingi117 – 1171Zinc 1By similarity

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. phosphoserine phosphatase activity Source: UniProtKB-EC

    GO - Biological processi

    1. protein transport Source: UniProtKB-KW

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Protein transport, Transport

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    ReactomeiREACT_163710. WNT ligand biogenesis and trafficking.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Vacuolar protein sorting-associated protein 29 (EC:3.1.3.3)
    Short name:
    hVPS29
    Alternative name(s):
    PEP11 homolog
    Vesicle protein sorting 29
    Gene namesi
    Name:VPS29
    ORF Names:DC15, DC7, MDS007
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 12

    Organism-specific databases

    HGNCiHGNC:14340. VPS29.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: HPA
    2. cytosol Source: Reactome
    3. endosome Source: LIFEdb
    4. endosome membrane Source: UniProtKB-SubCell
    5. extracellular vesicular exosome Source: UniProt
    6. intracellular membrane-bounded organelle Source: HPA

    Keywords - Cellular componenti

    Cytoplasm, Endosome, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi8 – 81D → A: Loss of protein phosphatase activity. 1 Publication
    Mutagenesisi39 – 391N → A: Loss of protein phosphatase activity. 1 Publication
    Mutagenesisi39 – 391N → D: No effect on protein phosphatase activity. 1 Publication
    Mutagenesisi62 – 621D → A or N: Loss of protein phosphatase activity. 1 Publication
    Mutagenesisi86 – 861H → A: Loss of protein phosphatase activity. 1 Publication
    Mutagenesisi117 – 1171H → A: Loss of protein phosphatase activity. 1 Publication

    Organism-specific databases

    PharmGKBiPA37875.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 182182Vacuolar protein sorting-associated protein 29PRO_0000065894Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei50 – 501N6-acetyllysine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiQ9UBQ0.
    PaxDbiQ9UBQ0.
    PRIDEiQ9UBQ0.

    PTM databases

    PhosphoSiteiQ9UBQ0.

    Expressioni

    Tissue specificityi

    Ubiquitous. Highly expressed in heart, lung, placenta, spleen, peripheral blood leukocytes, thymus, colon skeletal muscle, kidney and brain.

    Gene expression databases

    ArrayExpressiQ9UBQ0.
    BgeeiQ9UBQ0.
    CleanExiHS_VPS29.
    GenevestigatoriQ9UBQ0.

    Organism-specific databases

    HPAiHPA039748.

    Interactioni

    Subunit structurei

    Component of the retromer complex composed of VPS26 (VPS26A or VPS26B), VPS29, VPS35, SNX1 and SNX2. Found in a complex with XPO7, EIF4A1, ARHGAP1, VPS26A, VPS29, VPS35 and SFN.3 Publications

    Protein-protein interaction databases

    BioGridi119683. 45 interactions.
    DIPiDIP-29077N.
    IntActiQ9UBQ0. 3 interactions.
    MINTiMINT-1422473.
    STRINGi9606.ENSP00000380795.

    Structurei

    Secondary structure

    1
    182
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 65
    Turni11 – 144
    Beta strandi16 – 183
    Helixi20 – 256
    Beta strandi32 – 365
    Helixi43 – 5210
    Beta strandi54 – 585
    Beta strandi71 – 777
    Beta strandi80 – 856
    Beta strandi90 – 923
    Helixi96 – 10611
    Beta strandi109 – 1135
    Beta strandi115 – 1184
    Beta strandi120 – 1245
    Beta strandi127 – 1315
    Beta strandi149 – 1568
    Beta strandi159 – 16810
    Beta strandi171 – 18010

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1W24X-ray2.10A1-182[»]
    2R17X-ray2.80A/B1-182[»]
    ProteinModelPortaliQ9UBQ0.
    SMRiQ9UBQ0. Positions 1-181.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9UBQ0.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the VPS29 family.Curated

    Phylogenomic databases

    eggNOGiCOG0622.
    HOVERGENiHBG056165.
    KOiK07095.
    OrthoDBiEOG7JHM6S.
    PhylomeDBiQ9UBQ0.
    TreeFamiTF300880.

    Family and domain databases

    Gene3Di3.60.21.10. 1 hit.
    InterProiIPR024654. Calcineurin-like_PHP_lpxH.
    IPR029052. Metallo-depent_PP-like.
    IPR000979. Phosphodiesterase_MJ0936/Vps29.
    [Graphical view]
    PANTHERiPTHR11124. PTHR11124. 1 hit.
    PfamiPF12850. Metallophos_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF56300. SSF56300. 1 hit.
    TIGRFAMsiTIGR00040. yfcE. 1 hit.

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9UBQ0-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK    50
    TLAGDVHIVR GDFDENLNYP EQKVVTVGQF KIGLIHGHQV IPWGDMASLA 100
    LLQRQFDVDI LISGHTHKFE AFEHENKFYI NPGSATGAYN ALETNIIPSF 150
    VLMDIQASTV VTYVYQLIGD DVKVERIEYK KP 182
    Length:182
    Mass (Da):20,506
    Last modified:May 1, 2000 - v1
    Checksum:i6E0CDE6B720C9BF8
    GO
    Isoform 2 (identifier: Q9UBQ0-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-1: M → MAGHR

    Show »
    Length:186
    Mass (Da):20,927
    Checksum:i7875116A30665D6F
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti1 – 22ML → MKIVLYPV in AAF86872. 1 PublicationCurated
    Sequence conflicti119 – 1191F → S in CAB66549. (PubMed:11230166)Curated
    Sequence conflicti119 – 1191F → S in CAG38499. 1 PublicationCurated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 11M → MAGHR in isoform 2. 4 PublicationsVSP_004073

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF193795 mRNA. Translation: AAF04596.1.
    AF175264 mRNA. Translation: AAF89952.1.
    AF168716 mRNA. Translation: AAF87318.1.
    AF201936 mRNA. Translation: AAF86872.1.
    AF201946 mRNA. Translation: AAF17238.1.
    AL136614 mRNA. Translation: CAB66549.1.
    CR457182 mRNA. Translation: CAG33463.1.
    CR533468 mRNA. Translation: CAG38499.1.
    BC000880 mRNA. Translation: AAH00880.1.
    BC095446 mRNA. Translation: AAH95446.1.
    CCDSiCCDS41832.1. [Q9UBQ0-1]
    CCDS53832.1. [Q9UBQ0-2]
    PIRiJC7515.
    RefSeqiNP_057310.1. NM_016226.4. [Q9UBQ0-1]
    NP_476528.1. NM_057180.2. [Q9UBQ0-2]
    UniGeneiHs.600114.

    Genome annotation databases

    EnsembliENST00000360579; ENSP00000353786; ENSG00000111237. [Q9UBQ0-2]
    ENST00000549578; ENSP00000447058; ENSG00000111237. [Q9UBQ0-1]
    GeneIDi51699.
    KEGGihsa:51699.
    UCSCiuc001tqx.3. human. [Q9UBQ0-2]
    uc001tqy.3. human. [Q9UBQ0-1]

    Polymorphism databases

    DMDMi25453325.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF193795 mRNA. Translation: AAF04596.1 .
    AF175264 mRNA. Translation: AAF89952.1 .
    AF168716 mRNA. Translation: AAF87318.1 .
    AF201936 mRNA. Translation: AAF86872.1 .
    AF201946 mRNA. Translation: AAF17238.1 .
    AL136614 mRNA. Translation: CAB66549.1 .
    CR457182 mRNA. Translation: CAG33463.1 .
    CR533468 mRNA. Translation: CAG38499.1 .
    BC000880 mRNA. Translation: AAH00880.1 .
    BC095446 mRNA. Translation: AAH95446.1 .
    CCDSi CCDS41832.1. [Q9UBQ0-1 ]
    CCDS53832.1. [Q9UBQ0-2 ]
    PIRi JC7515.
    RefSeqi NP_057310.1. NM_016226.4. [Q9UBQ0-1 ]
    NP_476528.1. NM_057180.2. [Q9UBQ0-2 ]
    UniGenei Hs.600114.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1W24 X-ray 2.10 A 1-182 [» ]
    2R17 X-ray 2.80 A/B 1-182 [» ]
    ProteinModelPortali Q9UBQ0.
    SMRi Q9UBQ0. Positions 1-181.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 119683. 45 interactions.
    DIPi DIP-29077N.
    IntActi Q9UBQ0. 3 interactions.
    MINTi MINT-1422473.
    STRINGi 9606.ENSP00000380795.

    PTM databases

    PhosphoSitei Q9UBQ0.

    Polymorphism databases

    DMDMi 25453325.

    Proteomic databases

    MaxQBi Q9UBQ0.
    PaxDbi Q9UBQ0.
    PRIDEi Q9UBQ0.

    Protocols and materials databases

    DNASUi 51699.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000360579 ; ENSP00000353786 ; ENSG00000111237 . [Q9UBQ0-2 ]
    ENST00000549578 ; ENSP00000447058 ; ENSG00000111237 . [Q9UBQ0-1 ]
    GeneIDi 51699.
    KEGGi hsa:51699.
    UCSCi uc001tqx.3. human. [Q9UBQ0-2 ]
    uc001tqy.3. human. [Q9UBQ0-1 ]

    Organism-specific databases

    CTDi 51699.
    GeneCardsi GC12M110929.
    HGNCi HGNC:14340. VPS29.
    HPAi HPA039748.
    MIMi 606932. gene.
    neXtProti NX_Q9UBQ0.
    PharmGKBi PA37875.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG0622.
    HOVERGENi HBG056165.
    KOi K07095.
    OrthoDBi EOG7JHM6S.
    PhylomeDBi Q9UBQ0.
    TreeFami TF300880.

    Enzyme and pathway databases

    Reactomei REACT_163710. WNT ligand biogenesis and trafficking.

    Miscellaneous databases

    EvolutionaryTracei Q9UBQ0.
    GeneWikii VPS29.
    GenomeRNAii 51699.
    NextBioi 55714.
    PROi Q9UBQ0.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9UBQ0.
    Bgeei Q9UBQ0.
    CleanExi HS_VPS29.
    Genevestigatori Q9UBQ0.

    Family and domain databases

    Gene3Di 3.60.21.10. 1 hit.
    InterProi IPR024654. Calcineurin-like_PHP_lpxH.
    IPR029052. Metallo-depent_PP-like.
    IPR000979. Phosphodiesterase_MJ0936/Vps29.
    [Graphical view ]
    PANTHERi PTHR11124. PTHR11124. 1 hit.
    Pfami PF12850. Metallophos_2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56300. SSF56300. 1 hit.
    TIGRFAMsi TIGR00040. yfcE. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Human homologues of yeast vacuolar protein sorting 29 and 35."
      Edgar A.J., Polak J.M.
      Biochem. Biophys. Res. Commun. 277:622-630(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
      Tissue: Lung.
    2. "Human orthologs of yeast vacuolar protein sorting proteins Vps26, 29, and 35: assembly into multimeric complexes."
      Renfrew Haft C., de la Luz Sierra M., Bafford R., Lesniak M.A., Barr V.A., Taylor S.I.
      Mol. Biol. Cell 11:4105-4116(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH VPS26A; VPS35; SNX1 AND SNX2.
      Tissue: Parathyroid.
    3. "Novel genes expressed in hematopoietic stem/progenitor cells from myelodysplastic syndrome patients."
      Huang C., Zhang C., Tu Y., Gu W., Wang Y., Han Z., Chen Z., Zhou J., Gu J., Huang Q., Yu Y., Xu S., Ren S., Fu G., Li N.
      Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Hematopoietic stem cell.
    4. "Novel genes expressed in human dendritic cells."
      Peng Y., Li Y., Tu Y., Xu S., Han Z., Fu G., Chen Z.
      Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Dendritic cell.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Fetal brain.
    6. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
      Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
      Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    7. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
      Tissue: Brain and Cervix.
    8. "Exportin 7 defines a novel general nuclear export pathway."
      Mingot J.-M., Bohnsack M.T., Jaekle U., Goerlich D.
      EMBO J. 23:3227-3236(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN A COMPLEX WITH XPO7; ARHGAP1; EIF4A1; VPS26A; VPS35 AND SFN.
    9. "The mammalian retromer regulates transcytosis of the polymeric immunoglobulin receptor."
      Verges M., Luton F., Gruber C., Tiemann F., Reinders L.G., Huang L., Burlingame A.L., Haft C.R., Mostov K.E.
      Nat. Cell Biol. 6:763-769(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    10. "The human Vps29 retromer component is a metallo-phosphoesterase for a cation-independent mannose 6-phosphate receptor substrate peptide."
      Damen E., Krieger E., Nielsen J.E., Eygensteyn J., van Leeuwen J.E.M.
      Biochem. J. 398:399-409(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF ASP-8; ASN-39; ASP-62; HIS-86 AND HIS-117, SUBUNIT.
    11. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
      Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
      Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-50, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. "Crystal structure of human vacuolar protein sorting protein 29 reveals a phosphodiesterase/nuclease-like fold and two protein-protein interaction sites."
      Wang D., Guo M., Liang Z., Fan J., Zhu Z., Zang J., Zhu Z., Li X., Teng M., Niu L., Dong Y., Liu P.
      J. Biol. Chem. 280:22962-22967(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), METAL-BINDING.
    14. Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH VPS35, ELECTRON MICROSCOPY OF THE RETROMER COMPLEX CONTAINING VPS29; VPS35 AND VPS26.

    Entry informationi

    Entry nameiVPS29_HUMAN
    AccessioniPrimary (citable) accession number: Q9UBQ0
    Secondary accession number(s): Q502Y5
    , Q6FIF8, Q6IAH3, Q9H0W0, Q9NRP1, Q9NRU7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 25, 2002
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 130 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 12
      Human chromosome 12: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3