Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Vam6/Vps39-like protein

Gene

Vps39

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

May play a role in clustering and fusion of late endosomes and lysosomes (By similarity). 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 (By similarity).By similarity
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. Involved in homotypic vesicle fusions between late endosomes and in heterotypic fusions between late endosomes and lysosomes. Required for fusion of endosomes and autophagosomes with lysosomes (By similarity).By similarity

GO - Biological processi

Keywordsi

Biological processAutophagy, Protein transport, Transport

Names & Taxonomyi

Protein namesi
Recommended name:
Vam6/Vps39-like protein
Gene namesi
Name:Vps39
Synonyms:Pldn, Vam6
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:2443189 Vps39

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

Disruption phenotypei

Embryonic lethal, before E6.5.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000659021 – 886Vam6/Vps39-like proteinAdd BLAST886

Proteomic databases

PaxDbiQ8R5L3
PRIDEiQ8R5L3

PTM databases

iPTMnetiQ8R5L3
PhosphoSitePlusiQ8R5L3

Expressioni

Gene expression databases

BgeeiENSMUSG00000027291 Expressed in 257 organ(s), highest expression level in cerebellum
CleanExiMM_PLDN
MM_VPS39
ExpressionAtlasiQ8R5L3 baseline and differential
GenevisibleiQ8R5L3 MM

Interactioni

Subunit structurei

Homooligomer (By similarity). 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 (By similarity). 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. Interacts with PLEKHM2; involved in VPS39 recruitment to ARL8B-containing lysosomes (By similarity). Associates with adaptor protein complex 3 (AP-3) and clathrin:AP-3 complexes (PubMed:21411634).By similarity1 Publication

Protein-protein interaction databases

BioGridi234638, 3 interactors
IntActiQ8R5L3, 2 interactors
STRINGi10090.ENSMUSP00000099559

Structurei

3D structure databases

ProteinModelPortaliQ8R5L3
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
InParanoidiQ8R5L3
KOiK20183
OMAiRTIRYLQ
OrthoDBiEOG091G04D1
PhylomeDBiQ8R5L3
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
Isoform 1 (identifier: Q8R5L3-1) [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 RKKLQLYFWK
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
EHQPPYIVAV LPRYVEIRTL 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
LPTLSGAELE 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 ESLPRDRVLN FLIENFKALA
610 620 630 640 650
IPYLEHIIHV WEETGSQFHN CLIQLYCEKV QSLMKDYLLS LPTGKSPVPA
660 670 680 690 700
GEEGGELGEY RQKLLMFLEI SSHYDPGRLI CDFPFDGLLE ERALLLGRMG
710 720 730 740 750
KHEQALFIYV HVLKDTKMAK EYCHKHYDQN KEGNKDVYLS LLRMYLSPPS
760 770 780 790 800
IHCLGPIKLE LLEPQANLQA ALQVLELHYS KLDTTKAINL LPANTQINDI
810 820 830 840 850
RIFLEKVLEE NAQKKRFNQV LKNLLHAEFL RVQEERILHQ QVKCIITEEK
860 870 880
VCMVCKKKIG NSAFARYPNG VVVHYFCSKE VNSADT
Length:886
Mass (Da):101,693
Last modified:June 1, 2002 - v1
Checksum:iBD46EF52D404C2DA
GO
Isoform 2 (identifier: Q8R5L3-2) [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):100,653
Checksum:i71B8E8E4A2F8345D
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_00407647 – 58VPADV…PESGS → G in isoform 2. 2 PublicationsAdd BLAST12

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF281050 mRNA Translation: AAL79766.1
AF281051 mRNA Translation: AAL79767.1
BC007479 mRNA Translation: AAH07479.1
CCDSiCCDS16619.1 [Q8R5L3-2]
CCDS38210.1 [Q8R5L3-1]
RefSeqiNP_671495.1, NM_147153.3 [Q8R5L3-1]
NP_849182.1, NM_178851.3 [Q8R5L3-2]
UniGeneiMm.246131

Genome annotation databases

EnsembliENSMUST00000028752; ENSMUSP00000028752; ENSMUSG00000027291 [Q8R5L3-2]
ENSMUST00000102501; ENSMUSP00000099559; ENSMUSG00000027291 [Q8R5L3-1]
GeneIDi269338
KEGGimmu:269338
UCSCiuc008lvj.2 mouse [Q8R5L3-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF281050 mRNA Translation: AAL79766.1
AF281051 mRNA Translation: AAL79767.1
BC007479 mRNA Translation: AAH07479.1
CCDSiCCDS16619.1 [Q8R5L3-2]
CCDS38210.1 [Q8R5L3-1]
RefSeqiNP_671495.1, NM_147153.3 [Q8R5L3-1]
NP_849182.1, NM_178851.3 [Q8R5L3-2]
UniGeneiMm.246131

3D structure databases

ProteinModelPortaliQ8R5L3
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi234638, 3 interactors
IntActiQ8R5L3, 2 interactors
STRINGi10090.ENSMUSP00000099559

PTM databases

iPTMnetiQ8R5L3
PhosphoSitePlusiQ8R5L3

Proteomic databases

PaxDbiQ8R5L3
PRIDEiQ8R5L3

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000028752; ENSMUSP00000028752; ENSMUSG00000027291 [Q8R5L3-2]
ENSMUST00000102501; ENSMUSP00000099559; ENSMUSG00000027291 [Q8R5L3-1]
GeneIDi269338
KEGGimmu:269338
UCSCiuc008lvj.2 mouse [Q8R5L3-1]

Organism-specific databases

CTDi23339
MGIiMGI:2443189 Vps39

Phylogenomic databases

eggNOGiKOG2063 Eukaryota
ENOG410XNSX LUCA
GeneTreeiENSGT00530000063596
HOGENOMiHOG000046531
HOVERGENiHBG056493
InParanoidiQ8R5L3
KOiK20183
OMAiRTIRYLQ
OrthoDBiEOG091G04D1
PhylomeDBiQ8R5L3
TreeFamiTF105803

Miscellaneous databases

PROiPR:Q8R5L3
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000027291 Expressed in 257 organ(s), highest expression level in cerebellum
CleanExiMM_PLDN
MM_VPS39
ExpressionAtlasiQ8R5L3 baseline and differential
GenevisibleiQ8R5L3 MM

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_MOUSE
AccessioniPrimary (citable) accession number: Q8R5L3
Secondary accession number(s): Q922I3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: June 1, 2002
Last modified: November 7, 2018
This is version 126 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again