CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-019368
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Vam6/Vps39-like protein 
Protein Synonyms/Alias
 TRAP1-like protein; hVam6p 
Gene Name
 VPS39 
Gene Synonyms/Alias
 KIAA0770; TLP; VAM6 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
204KELFPTGKQLEPLVAubiquitination[1, 2, 3]
393LLPTDYRKQLQYPNPubiquitination[2]
528VLVDQSKKANSPLKGubiquitination[2]
725MAEEYCHKHYDRNKDubiquitination[2]
781VLELHHSKLDTTKALubiquitination[2]
786HSKLDTTKALNLLPAubiquitination[2]
806DIRIFLEKVLEENAQubiquitination[2]
822KRFNQVLKNLLHAEFubiquitination[2]
843RILHQQVKCIITEEKubiquitination[2]
879VVHYFCSKEVNPADTubiquitination[2]
Reference
 [1] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [2] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [3] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302] 
Functional Description
 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. 
Sequence Annotation
 DOMAIN 15 294 CNH.
 REPEAT 573 750 CHCR.  
Keyword
 Alternative splicing; Complete proteome; Cytoplasm; Endosome; Lysosome; Membrane; Protein transport; Reference proteome; Transport. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 886 AA 
Protein Sequence
MHDAFEPVPI LEKLPLQIDC LAAWEEWLLV GTKQGHLLLY RIRKDVVPAD VASPESGSCN 60
RFEVTLEKSN KNFSKKIQQI HVVSQFKILV SLLENNIYVH DLLTFQQITT VSKAKGASLF 120
TCDLQHTETG EEVLRMCVAV KKKLQLYFWK DREFHELQGD FSVPDVPKSM AWCENSICVG 180
FKRDYYLIRV DGKGSIKELF PTGKQLEPLV APLADGKVAV GQDDLTVVLN EEGICTQKCA 240
LNWTDIPVAM EHQPPYIIAV LPRYVEIRTF EPRLLVQSIE LQRPRFITSG GSNIIYVASN 300
HFVWRLIPVP MATQIQQLLQ DKQFELALQL AEMKDDSDSE KQQQIHHIKN LYAFNLFCQK 360
RFDESMQVFA KLGTDPTHVM GLYPDLLPTD YRKQLQYPNP LPVLSGAELE KAHLALIDYL 420
TQKRSQLVKK LNDSDHQSST SPLMEGTPTI KSKKKLLQII DTTLLKCYLH TNVALVAPLL 480
RLENNHCHIE ESEHVLKKAH KYSELIILYE KKGLHEKALQ VLVDQSKKAN SPLKGHERTV 540
QYLQHLGTEN LHLIFSYSVW VLRDFPEDGL KIFTEDLPEV ESLPRDRVLG FLIENFKGLA 600
IPYLEHIIHV WEETGSRFHN CLIQLYCEKV QGLMKEYLLS FPAGKTPVPA GEEEGELGEY 660
RQKLLMFLEI SSYYDPGRLI CDFPFDGLLE ERALLLGRMG KHEQALFIYV HILKDTRMAE 720
EYCHKHYDRN KDGNKDVYLS LLRMYLSPPS IHCLGPIKLE LLEPKANLQA ALQVLELHHS 780
KLDTTKALNL LPANTQINDI RIFLEKVLEE NAQKKRFNQV LKNLLHAEFL RVQEERILHQ 840
QVKCIITEEK VCMVCKKKIG NSAFARYPNG VVVHYFCSKE VNPADT 886 
Gene Ontology
 GO:0030897; C:HOPS complex; IDA:UniProtKB.
 GO:0031902; C:late endosome membrane; IEA:UniProtKB-SubCell.
 GO:0005765; C:lysosomal membrane; IEA:UniProtKB-SubCell.
 GO:0005083; F:small GTPase regulator activity; IEA:InterPro.
 GO:0015031; P:protein transport; IEA:UniProtKB-KW. 
Interpro
 IPR001180; Citron.
 IPR019452; VPS39/TGF_beta_rcpt-assoc_1.
 IPR019453; VPS39/TGF_beta_rcpt-assoc_2. 
Pfam
 PF00780; CNH
 PF10366; Vps39_1
 PF10367; Vps39_2 
SMART
  
PROSITE
 PS50236; CHCR
 PS50219; CNH 
PRINTS