Human Gene VPS39 (ENST00000318006.10) from GENCODE V44
Description: Homo sapiens VPS39 subunit of HOPS complex (VPS39), transcript variant 2, mRNA. (from RefSeq NM_015289) RefSeq Summary (NM_015289): This gene encodes a protein that may promote clustering and fusion of late endosomes and lysosomes. The protein may also act as an adaptor protein that modulates the transforming growth factor-beta response by coupling the transforming growth factor-beta receptor complex to the Smad pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]. Gencode Transcript: ENST00000318006.10 Gencode Gene: ENSG00000166887.16 Transcript (Including UTRs) Position: hg38 chr15:42,158,701-42,208,304 Size: 49,604 Total Exon Count: 25 Strand: - Coding Region Position: hg38 chr15:42,160,754-42,208,153 Size: 47,400 Coding Exon Count: 25
ID:VPS39_HUMAN DESCRIPTION: RecName: Full=Vam6/Vps39-like protein; AltName: Full=TRAP1-like protein;; Short=hVam6p; 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. SUBUNIT: 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. 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. TISSUE SPECIFICITY: Widely expressed, with highest levels in heart, skeletal muscle, kidney, pancreas, brain, placenta and spleen. SIMILARITY: Belongs to the VAM6/VPS39 family. SIMILARITY: Contains 1 CNH domain. SEQUENCE CAUTION: Sequence=BAA34490.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on Q96JC1
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
Gene Ontology (GO) Annotations with Structured Vocabulary
Biological Process: GO:0006886 intracellular protein transport GO:0006914 autophagy GO:0008333 endosome to lysosome transport GO:0015031 protein transport GO:0016192 vesicle-mediated transport GO:0034058 endosomal vesicle fusion GO:1902774 late endosome to lysosome transport GO:1990126 retrograde transport, endosome to plasma membrane