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Q96JC1 (VPS39_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 107. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Vam6/Vps39-like protein
Alternative name(s):
TRAP1-like protein
Short name=hVam6p
Gene names
Name:VPS39
Synonyms:KIAA0770, TLP, VAM6
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length886 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.9

Subunit structure

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. Ref.1 Ref.9

Subcellular location

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. Ref.1 Ref.10

Tissue specificity

Widely expressed, with highest levels in heart, skeletal muscle, kidney, pancreas, brain, placenta and spleen. Ref.1 Ref.9

Sequence similarities

Belongs to the VAM6/VPS39 family.

Contains 1 CHCR (clathrin heavy-chain) repeat.

Contains 1 CNH domain.

Sequence caution

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

Ontologies

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q96JC1-1)

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.
Isoform 2 (identifier: Q96JC1-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 886886Vam6/Vps39-like protein
PRO_0000065901

Regions

Domain15 – 294280CNH
Repeat573 – 750178CHCR

Natural variations

Alternative sequence47 – 5812VPADV…PESGS → G in isoform 2.
VSP_004075

Experimental info

Sequence conflict1351R → Q in AAK72222. Ref.1
Sequence conflict1911D → G in CAD97646. Ref.5
Sequence conflict8461I → T in CAD97646. Ref.5

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 24, 2005. Version 2.
Checksum: E5A40A3C787EB112

FASTA886101,809
        10         20         30         40         50         60 
MHDAFEPVPI LEKLPLQIDC LAAWEEWLLV GTKQGHLLLY RIRKDVVPAD VASPESGSCN 

        70         80         90        100        110        120 
RFEVTLEKSN KNFSKKIQQI HVVSQFKILV SLLENNIYVH DLLTFQQITT VSKAKGASLF 

       130        140        150        160        170        180 
TCDLQHTETG EEVLRMCVAV KKKLQLYFWK DREFHELQGD FSVPDVPKSM AWCENSICVG 

       190        200        210        220        230        240 
FKRDYYLIRV DGKGSIKELF PTGKQLEPLV APLADGKVAV GQDDLTVVLN EEGICTQKCA 

       250        260        270        280        290        300 
LNWTDIPVAM EHQPPYIIAV LPRYVEIRTF EPRLLVQSIE LQRPRFITSG GSNIIYVASN 

       310        320        330        340        350        360 
HFVWRLIPVP MATQIQQLLQ DKQFELALQL AEMKDDSDSE KQQQIHHIKN LYAFNLFCQK 

       370        380        390        400        410        420 
RFDESMQVFA KLGTDPTHVM GLYPDLLPTD YRKQLQYPNP LPVLSGAELE KAHLALIDYL 

       430        440        450        460        470        480 
TQKRSQLVKK LNDSDHQSST SPLMEGTPTI KSKKKLLQII DTTLLKCYLH TNVALVAPLL 

       490        500        510        520        530        540 
RLENNHCHIE ESEHVLKKAH KYSELIILYE KKGLHEKALQ VLVDQSKKAN SPLKGHERTV 

       550        560        570        580        590        600 
QYLQHLGTEN LHLIFSYSVW VLRDFPEDGL KIFTEDLPEV ESLPRDRVLG FLIENFKGLA 

       610        620        630        640        650        660 
IPYLEHIIHV WEETGSRFHN CLIQLYCEKV QGLMKEYLLS FPAGKTPVPA GEEEGELGEY 

       670        680        690        700        710        720 
RQKLLMFLEI SSYYDPGRLI CDFPFDGLLE ERALLLGRMG KHEQALFIYV HILKDTRMAE 

       730        740        750        760        770        780 
EYCHKHYDRN KDGNKDVYLS LLRMYLSPPS IHCLGPIKLE LLEPKANLQA ALQVLELHHS 

       790        800        810        820        830        840 
KLDTTKALNL LPANTQINDI RIFLEKVLEE NAQKKRFNQV LKNLLHAEFL RVQEERILHQ 

       850        860        870        880 
QVKCIITEEK VCMVCKKKIG NSAFARYPNG VVVHYFCSKE VNPADT 

« Hide

Isoform 2 [UniParc].

Checksum: 295A0D8A0E824795
Show »

FASTA875100,769

References

« Hide 'large scale' references
[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]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
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]"Integral and associated lysosomal membrane proteins."
Schroeder B., Wrocklage C., Pan C., Jaeger R., Koesters B., Schaefer H., Elsaesser H.-P., Mann M., Hasilik A.
Traffic 8:1676-1686(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
Tissue: Placenta.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS10083.1. [Q96JC1-2]
RefSeqNP_056104.2. NM_015289.2. [Q96JC1-2]
XP_005254316.1. XM_005254259.2. [Q96JC1-1]
UniGeneHs.88025.

3D structure databases

ProteinModelPortalQ96JC1.
SMRQ96JC1. Positions 76-105.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116925. 11 interactions.
IntActQ96JC1. 1 interaction.
MINTMINT-3054492.
STRING9606.ENSP00000326534.

PTM databases

PhosphoSiteQ96JC1.

Polymorphism databases

DMDM66774218.

Proteomic databases

MaxQBQ96JC1.
PaxDbQ96JC1.
PRIDEQ96JC1.

Protocols and materials databases

DNASU23339.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000318006; ENSP00000326534; ENSG00000166887. [Q96JC1-2]
ENST00000348544; ENSP00000335193; ENSG00000166887. [Q96JC1-1]
GeneID23339.
KEGGhsa:23339.
UCSCuc001zpc.3. human. [Q96JC1-2]
uc001zpd.3. human. [Q96JC1-1]

Organism-specific databases

CTD23339.
GeneCardsGC15M042450.
H-InvDBHIX0038106.
HGNCHGNC:20593. VPS39.
HPAHPA047620.
MIM612188. gene.
neXtProtNX_Q96JC1.
PharmGKBPA134945163.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG241434.
HOGENOMHOG000046531.
HOVERGENHBG056493.
InParanoidQ96JC1.
OMACLGPIKM.
OrthoDBEOG715Q3C.
PhylomeDBQ96JC1.
TreeFamTF105803.

Gene expression databases

ArrayExpressQ96JC1.
BgeeQ96JC1.
CleanExHS_VPS39.
GenevestigatorQ96JC1.

Family and domain databases

InterProIPR001180. Citron.
IPR000547. Clathrin_H-chain/VPS_repeat.
IPR019452. VPS39/TGF_beta_rcpt-assoc_1.
IPR019453. VPS39/TGF_beta_rcpt-assoc_2.
[Graphical view]
PfamPF00780. CNH. 1 hit.
PF10366. Vps39_1. 1 hit.
PF10367. Vps39_2. 1 hit.
[Graphical view]
PROSITEPS50236. CHCR. 1 hit.
PS50219. CNH. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSVPS39. human.
GeneWikiVPS39.
GenomeRNAi23339.
NextBio45293.
PROQ96JC1.
SOURCESearch...

Entry information

Entry nameVPS39_HUMAN
AccessionPrimary (citable) accession number: Q96JC1
Secondary accession number(s): O94869 expand/collapse secondary AC list , Q71SQ6, Q7Z3V3, Q96B93, Q96RM0
Entry history
Integrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: May 24, 2005
Last modified: July 9, 2014
This is version 107 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 15

Human chromosome 15: entries, gene names and cross-references to MIM