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Protein

Vam6/Vps39-like protein

Gene

VPS39

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

Functioni

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.1 Publication
Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act in part as a component of the putative HOPS endosomal tethering complex which is proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes (PubMed:23351085). Involved in homotypic vesicle fusions between late endosomes and in heterotypic fusions between late endosomes and lysosomes (PubMed:11448994, PubMed:23351085, PubMed:23167963). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:25783203).1 Publication3 Publications

GO - Biological processi

  • autophagy Source: UniProtKB
  • endosomal vesicle fusion Source: UniProtKB
  • endosome to lysosome transport Source: UniProtKB
  • intracellular protein transport Source: InterPro
  • late endosome to lysosome transport Source: UniProtKB
  • retrograde transport, endosome to plasma membrane Source: UniProtKB
  • vesicle-mediated transport Source: GO_Central

Keywordsi

Biological processAutophagy, 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
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

EuPathDBiHostDB:ENSG00000166887.15
HGNCiHGNC:20593 VPS39
MIMi612188 gene
neXtProtiNX_Q96JC1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Endosome, Lysosome, Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi23339
OpenTargetsiENSG00000166887
PharmGKBiPA134945163

Polymorphism and mutation databases

BioMutaiVPS39
DMDMi66774218

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000659011 – 886Vam6/Vps39-like proteinAdd BLAST886

Proteomic databases

EPDiQ96JC1
MaxQBiQ96JC1
PaxDbiQ96JC1
PeptideAtlasiQ96JC1
PRIDEiQ96JC1
ProteomicsDBi76939
76940 [Q96JC1-2]

PTM databases

iPTMnetiQ96JC1
PhosphoSitePlusiQ96JC1

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiENSG00000166887 Expressed in 228 organ(s), highest expression level in corpus callosum
CleanExiHS_VPS39
ExpressionAtlasiQ96JC1 baseline and differential
GenevisibleiQ96JC1 HS

Interactioni

Subunit structurei

Homooligomer (PubMed:11448994). 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 (PubMed:12941698). Component of the putative homotypic fusion and vacuole protein sorting (HOPS) complex; the core of which composed of the class C Vps proteins VPS11, VPS16, VPS18 and VPS33A, is associated with VPS39 and VPS41 (PubMed:23351085, PubMed:23901104, PubMed:25908847). Interacts with PLEKHM2; involved in VPS39 recruitment to ARL8B-containing lysosomes (PubMed:25908847). Associates with adaptor protein complex 3 (AP-3) and clathrin:AP-3 complexes (By similarity).By similarity2 Publications4 Publications

Protein-protein interaction databases

BioGridi116925, 26 interactors
CORUMiQ96JC1
IntActiQ96JC1, 17 interactors
MINTiQ96JC1
STRINGi9606.ENSP00000326534

Structurei

3D structure databases

ProteinModelPortaliQ96JC1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini15 – 294CNHPROSITE-ProRule annotationAdd BLAST280
Repeati573 – 750CHCRAdd BLAST178

Sequence similaritiesi

Belongs to the VAM6/VPS39 family.Curated

Phylogenomic databases

eggNOGiKOG2063 Eukaryota
ENOG410XNSX LUCA
GeneTreeiENSGT00530000063596
HOGENOMiHOG000046531
HOVERGENiHBG056493
InParanoidiQ96JC1
KOiK20183
OMAiRTIRYLQ
OrthoDBiEOG091G04D1
PhylomeDBiQ96JC1
TreeFamiTF105803

Family and domain databases

InterProiView protein in InterPro
IPR000547 Clathrin_H-chain/VPS_repeat
IPR001180 CNH_dom
IPR032914 Vam6/VPS39/TRAP1
IPR019452 VPS39/TGF_beta_rcpt-assoc_1
IPR019453 VPS39/TGF_beta_rcpt-assoc_2
PANTHERiPTHR12894 PTHR12894, 1 hit
PfamiView protein in Pfam
PF00780 CNH, 1 hit
PF10366 Vps39_1, 1 hit
PF10367 Vps39_2, 1 hit
SMARTiView protein in SMART
SM00036 CNH, 1 hit
PROSITEiView protein in PROSITE
PS50236 CHCR, 1 hit
PS50219 CNH, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H3BTU0H3BTU0_HUMAN
Vam6/Vps39-like protein
VPS39
47Annotation score:

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti135R → Q in AAK72222 (PubMed:11448994).Curated1
Sequence conflicti191D → G in CAD97646 (PubMed:17974005).Curated1
Sequence conflicti846I → T in CAD97646 (PubMed:17974005).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_00407547 – 58VPADV…PESGS → G in isoform 2. 4 PublicationsAdd BLAST12

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.4 human [Q96JC1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

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
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116925, 26 interactors
CORUMiQ96JC1
IntActiQ96JC1, 17 interactors
MINTiQ96JC1
STRINGi9606.ENSP00000326534

PTM databases

iPTMnetiQ96JC1
PhosphoSitePlusiQ96JC1

Polymorphism and mutation databases

BioMutaiVPS39
DMDMi66774218

Proteomic databases

EPDiQ96JC1
MaxQBiQ96JC1
PaxDbiQ96JC1
PeptideAtlasiQ96JC1
PRIDEiQ96JC1
ProteomicsDBi76939
76940 [Q96JC1-2]

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.4 human [Q96JC1-1]

Organism-specific databases

CTDi23339
DisGeNETi23339
EuPathDBiHostDB:ENSG00000166887.15
GeneCardsiVPS39
H-InvDBiHIX0038106
HGNCiHGNC:20593 VPS39
MIMi612188 gene
neXtProtiNX_Q96JC1
OpenTargetsiENSG00000166887
PharmGKBiPA134945163
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2063 Eukaryota
ENOG410XNSX LUCA
GeneTreeiENSGT00530000063596
HOGENOMiHOG000046531
HOVERGENiHBG056493
InParanoidiQ96JC1
KOiK20183
OMAiRTIRYLQ
OrthoDBiEOG091G04D1
PhylomeDBiQ96JC1
TreeFamiTF105803

Miscellaneous databases

ChiTaRSiVPS39 human
GeneWikiiVPS39
GenomeRNAii23339
PROiPR:Q96JC1
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000166887 Expressed in 228 organ(s), highest expression level in corpus callosum
CleanExiHS_VPS39
ExpressionAtlasiQ96JC1 baseline and differential
GenevisibleiQ96JC1 HS

Family and domain databases

InterProiView protein in InterPro
IPR000547 Clathrin_H-chain/VPS_repeat
IPR001180 CNH_dom
IPR032914 Vam6/VPS39/TRAP1
IPR019452 VPS39/TGF_beta_rcpt-assoc_1
IPR019453 VPS39/TGF_beta_rcpt-assoc_2
PANTHERiPTHR12894 PTHR12894, 1 hit
PfamiView protein in Pfam
PF00780 CNH, 1 hit
PF10366 Vps39_1, 1 hit
PF10367 Vps39_2, 1 hit
SMARTiView protein in SMART
SM00036 CNH, 1 hit
PROSITEiView protein in PROSITE
PS50236 CHCR, 1 hit
PS50219 CNH, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiVPS39_HUMAN
AccessioniPrimary (citable) accession number: Q96JC1
Secondary accession number(s): O94869
, Q71SQ6, Q7Z3V3, Q96B93, Q96RM0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: May 24, 2005
Last modified: November 7, 2018
This is version 146 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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