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Q96JC1

- VPS39_HUMAN

UniProt

Q96JC1 - VPS39_HUMAN

Protein

Vam6/Vps39-like protein

Gene

VPS39

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 108 (01 Oct 2014)
      Sequence version 2 (24 May 2005)
      Previous versions | rss
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    Functioni

    May play a role in clustering and fusion of late endosomes and lysosomes. Regulator of TGF-beta/activin signaling, inhibiting SMAD3- and activating SMAD2-dependent transcription. Acts by interfering with SMAD3/SMAD4 complex formation, this would lead to inhibition of SMAD3-dependent transcription and relieve SMAD3 inhibition of SMAD2-dependent promoters, thus increasing SMAD2-dependent transcription. Does not affect TGF-beta-induced SMAD2 or SMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation.2 Publications

    GO - Molecular functioni

    1. small GTPase regulator activity Source: InterPro

    GO - Biological processi

    1. intracellular protein transport Source: InterPro
    2. vesicle-mediated transport Source: InterPro

    Keywords - Biological processi

    Protein transport, Transport

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Vam6/Vps39-like protein
    Alternative name(s):
    TRAP1-like protein
    Short name:
    hVam6p
    Gene namesi
    Name:VPS39
    Synonyms:KIAA0770, TLP, VAM6
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 15

    Organism-specific databases

    HGNCiHGNC:20593. VPS39.

    Subcellular locationi

    Cytoplasm. Lysosome membrane; Peripheral membrane protein. Late endosome membrane; Peripheral membrane protein
    Note: Colocalizes with TGFBR1 and TGFBR2 in cytoplasmic vesicular structures and most prominently in cortical vesicles.

    GO - Cellular componenti

    1. HOPS complex Source: UniProtKB
    2. late endosome membrane Source: UniProtKB-SubCell
    3. lysosomal membrane Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm, Endosome, Lysosome, Membrane

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA134945163.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 886886Vam6/Vps39-like proteinPRO_0000065901Add
    BLAST

    Proteomic databases

    MaxQBiQ96JC1.
    PaxDbiQ96JC1.
    PRIDEiQ96JC1.

    PTM databases

    PhosphoSiteiQ96JC1.

    Expressioni

    Tissue specificityi

    Widely expressed, with highest levels in heart, skeletal muscle, kidney, pancreas, brain, placenta and spleen.2 Publications

    Gene expression databases

    ArrayExpressiQ96JC1.
    BgeeiQ96JC1.
    CleanExiHS_VPS39.
    GenevestigatoriQ96JC1.

    Organism-specific databases

    HPAiHPA047620.

    Interactioni

    Subunit structurei

    Homooligomer. Interacts with TGFBR2 and, less efficiently, with TGFBR1; interaction with TGFBR2 is independent of the receptor kinase activity and of the presence of TGF-beta. Also interacts with ACVR2B, but not with BMPR2. Interacts with SMAD4, preferentially following TGF-beta treatment. Does not interact with SAMD2 or SMAD3.1 Publication

    Protein-protein interaction databases

    BioGridi116925. 11 interactions.
    IntActiQ96JC1. 1 interaction.
    MINTiMINT-3054492.
    STRINGi9606.ENSP00000326534.

    Structurei

    3D structure databases

    ProteinModelPortaliQ96JC1.
    SMRiQ96JC1. Positions 76-105.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini15 – 294280CNHPROSITE-ProRule annotationAdd
    BLAST
    Repeati573 – 750178CHCRAdd
    BLAST

    Sequence similaritiesi

    Belongs to the VAM6/VPS39 family.Curated
    Contains 1 CHCR (clathrin heavy-chain) repeat.PROSITE-ProRule annotation
    Contains 1 CNH domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG241434.
    HOGENOMiHOG000046531.
    HOVERGENiHBG056493.
    InParanoidiQ96JC1.
    OMAiCLGPIKM.
    OrthoDBiEOG715Q3C.
    PhylomeDBiQ96JC1.
    TreeFamiTF105803.

    Family and domain databases

    InterProiIPR001180. Citron.
    IPR000547. Clathrin_H-chain/VPS_repeat.
    IPR019452. VPS39/TGF_beta_rcpt-assoc_1.
    IPR019453. VPS39/TGF_beta_rcpt-assoc_2.
    [Graphical view]
    PfamiPF00780. CNH. 1 hit.
    PF10366. Vps39_1. 1 hit.
    PF10367. Vps39_2. 1 hit.
    [Graphical view]
    PROSITEiPS50236. CHCR. 1 hit.
    PS50219. CNH. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q96JC1-1) [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

    MHDAFEPVPI LEKLPLQIDC LAAWEEWLLV GTKQGHLLLY RIRKDVVPAD    50
    VASPESGSCN RFEVTLEKSN KNFSKKIQQI HVVSQFKILV SLLENNIYVH 100
    DLLTFQQITT VSKAKGASLF TCDLQHTETG EEVLRMCVAV KKKLQLYFWK 150
    DREFHELQGD FSVPDVPKSM AWCENSICVG FKRDYYLIRV DGKGSIKELF 200
    PTGKQLEPLV APLADGKVAV GQDDLTVVLN EEGICTQKCA LNWTDIPVAM 250
    EHQPPYIIAV LPRYVEIRTF EPRLLVQSIE LQRPRFITSG GSNIIYVASN 300
    HFVWRLIPVP MATQIQQLLQ DKQFELALQL AEMKDDSDSE KQQQIHHIKN 350
    LYAFNLFCQK RFDESMQVFA KLGTDPTHVM GLYPDLLPTD YRKQLQYPNP 400
    LPVLSGAELE KAHLALIDYL TQKRSQLVKK LNDSDHQSST SPLMEGTPTI 450
    KSKKKLLQII DTTLLKCYLH TNVALVAPLL RLENNHCHIE ESEHVLKKAH 500
    KYSELIILYE KKGLHEKALQ VLVDQSKKAN SPLKGHERTV QYLQHLGTEN 550
    LHLIFSYSVW VLRDFPEDGL KIFTEDLPEV ESLPRDRVLG FLIENFKGLA 600
    IPYLEHIIHV WEETGSRFHN CLIQLYCEKV QGLMKEYLLS FPAGKTPVPA 650
    GEEEGELGEY RQKLLMFLEI SSYYDPGRLI CDFPFDGLLE ERALLLGRMG 700
    KHEQALFIYV HILKDTRMAE EYCHKHYDRN KDGNKDVYLS LLRMYLSPPS 750
    IHCLGPIKLE LLEPKANLQA ALQVLELHHS KLDTTKALNL LPANTQINDI 800
    RIFLEKVLEE NAQKKRFNQV LKNLLHAEFL RVQEERILHQ QVKCIITEEK 850
    VCMVCKKKIG NSAFARYPNG VVVHYFCSKE VNPADT 886
    Length:886
    Mass (Da):101,809
    Last modified:May 24, 2005 - v2
    Checksum:iE5A40A3C787EB112
    GO
    Isoform 2 (identifier: Q96JC1-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         47-58: VPADVASPESGS → G

    Show »
    Length:875
    Mass (Da):100,769
    Checksum:i295A0D8A0E824795
    GO

    Sequence cautioni

    The sequence BAA34490.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti135 – 1351R → Q in AAK72222. (PubMed:11448994)Curated
    Sequence conflicti191 – 1911D → G in CAD97646. (PubMed:17974005)Curated
    Sequence conflicti846 – 8461I → T in CAD97646. (PubMed:17974005)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei47 – 5812VPADV…PESGS → G in isoform 2. 4 PublicationsVSP_004075Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF280814 mRNA. Translation: AAK72222.1.
    AF334400 Genomic DNA. Translation: AAK58862.1.
    AF281052 mRNA. Translation: AAQ05978.1.
    AB018313 mRNA. Translation: BAA34490.2. Different initiation.
    BX537404 mRNA. Translation: CAD97646.1.
    AC036103 Genomic DNA. No translation available.
    CH471125 Genomic DNA. Translation: EAW92536.1.
    BC015817 mRNA. Translation: AAH15817.2.
    BC068559 mRNA. Translation: AAH68559.1.
    CCDSiCCDS10083.1. [Q96JC1-2]
    RefSeqiNP_056104.2. NM_015289.2. [Q96JC1-2]
    XP_005254316.1. XM_005254259.2. [Q96JC1-1]
    UniGeneiHs.88025.

    Genome annotation databases

    EnsembliENST00000318006; ENSP00000326534; ENSG00000166887. [Q96JC1-2]
    ENST00000348544; ENSP00000335193; ENSG00000166887. [Q96JC1-1]
    GeneIDi23339.
    KEGGihsa:23339.
    UCSCiuc001zpc.3. human. [Q96JC1-2]
    uc001zpd.3. human. [Q96JC1-1]

    Polymorphism databases

    DMDMi66774218.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF280814 mRNA. Translation: AAK72222.1 .
    AF334400 Genomic DNA. Translation: AAK58862.1 .
    AF281052 mRNA. Translation: AAQ05978.1 .
    AB018313 mRNA. Translation: BAA34490.2 . Different initiation.
    BX537404 mRNA. Translation: CAD97646.1 .
    AC036103 Genomic DNA. No translation available.
    CH471125 Genomic DNA. Translation: EAW92536.1 .
    BC015817 mRNA. Translation: AAH15817.2 .
    BC068559 mRNA. Translation: AAH68559.1 .
    CCDSi CCDS10083.1. [Q96JC1-2 ]
    RefSeqi NP_056104.2. NM_015289.2. [Q96JC1-2 ]
    XP_005254316.1. XM_005254259.2. [Q96JC1-1 ]
    UniGenei Hs.88025.

    3D structure databases

    ProteinModelPortali Q96JC1.
    SMRi Q96JC1. Positions 76-105.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 116925. 11 interactions.
    IntActi Q96JC1. 1 interaction.
    MINTi MINT-3054492.
    STRINGi 9606.ENSP00000326534.

    PTM databases

    PhosphoSitei Q96JC1.

    Polymorphism databases

    DMDMi 66774218.

    Proteomic databases

    MaxQBi Q96JC1.
    PaxDbi Q96JC1.
    PRIDEi Q96JC1.

    Protocols and materials databases

    DNASUi 23339.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000318006 ; ENSP00000326534 ; ENSG00000166887 . [Q96JC1-2 ]
    ENST00000348544 ; ENSP00000335193 ; ENSG00000166887 . [Q96JC1-1 ]
    GeneIDi 23339.
    KEGGi hsa:23339.
    UCSCi uc001zpc.3. human. [Q96JC1-2 ]
    uc001zpd.3. human. [Q96JC1-1 ]

    Organism-specific databases

    CTDi 23339.
    GeneCardsi GC15M042450.
    H-InvDB HIX0038106.
    HGNCi HGNC:20593. VPS39.
    HPAi HPA047620.
    MIMi 612188. gene.
    neXtProti NX_Q96JC1.
    PharmGKBi PA134945163.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG241434.
    HOGENOMi HOG000046531.
    HOVERGENi HBG056493.
    InParanoidi Q96JC1.
    OMAi CLGPIKM.
    OrthoDBi EOG715Q3C.
    PhylomeDBi Q96JC1.
    TreeFami TF105803.

    Miscellaneous databases

    ChiTaRSi VPS39. human.
    GeneWikii VPS39.
    GenomeRNAii 23339.
    NextBioi 45293.
    PROi Q96JC1.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q96JC1.
    Bgeei Q96JC1.
    CleanExi HS_VPS39.
    Genevestigatori Q96JC1.

    Family and domain databases

    InterProi IPR001180. Citron.
    IPR000547. Clathrin_H-chain/VPS_repeat.
    IPR019452. VPS39/TGF_beta_rcpt-assoc_1.
    IPR019453. VPS39/TGF_beta_rcpt-assoc_2.
    [Graphical view ]
    Pfami PF00780. CNH. 1 hit.
    PF10366. Vps39_1. 1 hit.
    PF10367. Vps39_2. 1 hit.
    [Graphical view ]
    PROSITEi PS50236. CHCR. 1 hit.
    PS50219. CNH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Human Vam6p promotes lysosome clustering and fusion in vivo."
      Caplan S., Hartnell L.M., Aguilar R.C., Naslavsky N., Bonifacino J.S.
      J. Cell Biol. 154:109-122(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1), FUNCTION, HOMOOLIGOMERIZATION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
      Tissue: Brain.
    2. "A human homolog of yeast Vps39."
      Dell'Angelica E.C.
      Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
    3. "Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
      Nagase T., Ishikawa K., Suyama M., Kikuno R., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
      DNA Res. 5:277-286(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Brain.
    4. "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones."
      Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.
      DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: SEQUENCE REVISION.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Endometrial tumor.
    6. "Analysis of the DNA sequence and duplication history of human chromosome 15."
      Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K., Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N., Abouelleil A.
      , Arachchi H.M., Baradarani L., Birditt B., Bloom S., Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K., DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J., Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E., Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B., Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R., O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B., Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S., Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C.
      Nature 440:671-675(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    7. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    8. "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] (ISOFORM 2), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 101-886 (ISOFORMS 1/2).
      Tissue: Lung and Testis.
    9. "TLP, a novel modulator of TGF-beta signaling, has opposite effects on Smad2- and Smad3-dependent signaling."
      Felici A., Wurthner J.U., Parks W.T., Giam L.R., Reiss M., Karpova T.S., McNally J.G., Roberts A.B.
      EMBO J. 22:4465-4477(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH ACVR2B; SMAD4; TGFBR1 AND TGFBR2, TISSUE SPECIFICITY.
    10. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
      Tissue: Placenta.

    Entry informationi

    Entry nameiVPS39_HUMAN
    AccessioniPrimary (citable) accession number: Q96JC1
    Secondary accession number(s): O94869
    , Q71SQ6, Q7Z3V3, Q96B93, Q96RM0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 25, 2002
    Last sequence update: May 24, 2005
    Last modified: October 1, 2014
    This is version 108 of the entry and version 2 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

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 15
      Human chromosome 15: 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3