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Protein

Vam6/Vps39-like protein

Gene

VPS39

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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: GO_Central
Complete GO annotation...

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
Complete GO annotation...

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

BgeeiQ96JC1.
CleanExiHS_VPS39.
ExpressionAtlasiQ96JC1. baseline and differential.
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. 12 interactions.
IntActiQ96JC1. 1 interaction.
MINTiMINT-3054492.
STRINGi9606.ENSP00000326534.

Structurei

3D structure databases

ProteinModelPortaliQ96JC1.
SMRiQ96JC1. Positions 255-280.
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.
GeneTreeiENSGT00530000063596.
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

        10         20         30         40         50
MHDAFEPVPI LEKLPLQIDC LAAWEEWLLV GTKQGHLLLY RIRKDVVPAD
60 70 80 90 100
VASPESGSCN RFEVTLEKSN KNFSKKIQQI HVVSQFKILV SLLENNIYVH
110 120 130 140 150
DLLTFQQITT VSKAKGASLF TCDLQHTETG EEVLRMCVAV KKKLQLYFWK
160 170 180 190 200
DREFHELQGD FSVPDVPKSM AWCENSICVG FKRDYYLIRV DGKGSIKELF
210 220 230 240 250
PTGKQLEPLV APLADGKVAV GQDDLTVVLN EEGICTQKCA LNWTDIPVAM
260 270 280 290 300
EHQPPYIIAV LPRYVEIRTF EPRLLVQSIE LQRPRFITSG GSNIIYVASN
310 320 330 340 350
HFVWRLIPVP MATQIQQLLQ DKQFELALQL AEMKDDSDSE KQQQIHHIKN
360 370 380 390 400
LYAFNLFCQK RFDESMQVFA KLGTDPTHVM GLYPDLLPTD YRKQLQYPNP
410 420 430 440 450
LPVLSGAELE KAHLALIDYL TQKRSQLVKK LNDSDHQSST SPLMEGTPTI
460 470 480 490 500
KSKKKLLQII DTTLLKCYLH TNVALVAPLL RLENNHCHIE ESEHVLKKAH
510 520 530 540 550
KYSELIILYE KKGLHEKALQ VLVDQSKKAN SPLKGHERTV QYLQHLGTEN
560 570 580 590 600
LHLIFSYSVW VLRDFPEDGL KIFTEDLPEV ESLPRDRVLG FLIENFKGLA
610 620 630 640 650
IPYLEHIIHV WEETGSRFHN CLIQLYCEKV QGLMKEYLLS FPAGKTPVPA
660 670 680 690 700
GEEEGELGEY RQKLLMFLEI SSYYDPGRLI CDFPFDGLLE ERALLLGRMG
710 720 730 740 750
KHEQALFIYV HILKDTRMAE EYCHKHYDRN KDGNKDVYLS LLRMYLSPPS
760 770 780 790 800
IHCLGPIKLE LLEPKANLQA ALQVLELHHS KLDTTKALNL LPANTQINDI
810 820 830 840 850
RIFLEKVLEE NAQKKRFNQV LKNLLHAEFL RVQEERILHQ QVKCIITEEK
860 870 880
VCMVCKKKIG NSAFARYPNG VVVHYFCSKE VNPADT
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.Curated

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:
EMBLi
GenBanki
DDBJi
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]
CCDS73710.1. [Q96JC1-1]
RefSeqiNP_001288067.1. NM_001301138.1. [Q96JC1-1]
NP_056104.2. NM_015289.3. [Q96JC1-2]
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:
EMBLi
GenBanki
DDBJi
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]
CCDS73710.1. [Q96JC1-1]
RefSeqiNP_001288067.1. NM_001301138.1. [Q96JC1-1]
NP_056104.2. NM_015289.3. [Q96JC1-2]
UniGeneiHs.88025.

3D structure databases

ProteinModelPortaliQ96JC1.
SMRiQ96JC1. Positions 255-280.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116925. 12 interactions.
IntActiQ96JC1. 1 interaction.
MINTiMINT-3054492.
STRINGi9606.ENSP00000326534.

PTM databases

PhosphoSiteiQ96JC1.

Polymorphism databases

DMDMi66774218.

Proteomic databases

MaxQBiQ96JC1.
PaxDbiQ96JC1.
PRIDEiQ96JC1.

Protocols and materials databases

DNASUi23339.
Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi23339.
GeneCardsiGC15M042450.
H-InvDBHIX0038106.
HGNCiHGNC:20593. VPS39.
HPAiHPA047620.
MIMi612188. gene.
neXtProtiNX_Q96JC1.
PharmGKBiPA134945163.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG241434.
GeneTreeiENSGT00530000063596.
HOGENOMiHOG000046531.
HOVERGENiHBG056493.
InParanoidiQ96JC1.
OMAiCLGPIKM.
OrthoDBiEOG715Q3C.
PhylomeDBiQ96JC1.
TreeFamiTF105803.

Miscellaneous databases

ChiTaRSiVPS39. human.
GeneWikiiVPS39.
GenomeRNAii23339.
NextBioi45293.
PROiQ96JC1.
SOURCEiSearch...

Gene expression databases

BgeeiQ96JC1.
CleanExiHS_VPS39.
ExpressionAtlasiQ96JC1. baseline and differential.
GenevestigatoriQ96JC1.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: February 4, 2015
This is version 112 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

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.