CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-019372
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Deubiquitinating protein VCIP135 
Protein Synonyms/Alias
 Valosin-containing protein p97/p47 complex-interacting protein 1; Valosin-containing protein p97/p47 complex-interacting protein p135; VCP/p47 complex-interacting 135-kDa protein 
Gene Name
 VCPIP1 
Gene Synonyms/Alias
 KIAA1850; VCIP135 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
53SGSCPDPKCQARLFFubiquitination[1]
118KKNTELVKVMGLSNYubiquitination[2]
128GLSNYHCKLLSPILAubiquitination[1]
141LARYGMDKQTGRAKLubiquitination[1]
182VNTVGYGKDRSGSLLubiquitination[1, 2, 3, 4]
199HDTLEDIKRANKSQEubiquitination[1, 2]
203EDIKRANKSQECLIPubiquitination[1]
331PGLIPAEKCTGKDGHubiquitination[5]
335PAEKCTGKDGHLNKPubiquitination[1]
341GKDGHLNKPICIAWSubiquitination[1, 4]
362YIPLVGIKGAALPKLubiquitination[1, 2, 6]
368IKGAALPKLPMNLLPubiquitination[1]
376LPMNLLPKAWGVPQDubiquitination[1, 2, 7, 8]
386GVPQDLIKKYIKLEEubiquitination[2, 6]
387VPQDLIKKYIKLEEDubiquitination[1]
390DLIKKYIKLEEDGGCubiquitination[1]
408GDRSLQDKYLLRLVAacetylation[9]
408GDRSLQDKYLLRLVAubiquitination[1, 2, 6]
458EEVTAAAKKAVMDNRubiquitination[2, 3, 6]
459EVTAAAKKAVMDNRLubiquitination[1]
496GKLYNLAKSTHGQLRubiquitination[1]
506HGQLRTDKNYSFPLNubiquitination[1]
691SESQLPTKIILTGQKubiquitination[1, 2, 3]
698KIILTGQKTKTLHKEubiquitination[1]
700ILTGQKTKTLHKEELubiquitination[1]
729EQASVMQKRKTEKLKubiquitination[1, 2, 3, 7, 8, 10]
764SAPATPTKAPYSPTTubiquitination[3, 7, 8]
773PYSPTTSKEKKIRITubiquitination[4]
870AHSAHTVKQEDIAVTubiquitination[1, 8, 11]
879EDIAVTGKLSSKELQubiquitination[1, 3, 7, 8]
883VTGKLSSKELQEQAEubiquitination[3]
929GVFYSIMKKTMGMADubiquitination[2]
930VFYSIMKKTMGMADGubiquitination[2]
938TMGMADGKHCTFPHLubiquitination[1]
1015SGGVVKKKSEQLHNVubiquitination[1]
1028NVTAFQGKGHSLGTAubiquitination[7, 8, 10]
1053RETSVVRKHNTGTDFubiquitination[10]
Reference
 [1] 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]
 [2] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [3] 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]
 [4] 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]
 [5] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [6] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [7] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [8] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [9] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
 [10] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [11] Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry.
 Denis NJ, Vasilescu J, Lambert JP, Smith JC, Figeys D.
 Proteomics. 2007 Mar;7(6):868-74. [PMID: 17370265] 
Functional Description
 Acts as a deubiquitinating enzyme. Necessary for VCP- mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER). Mediates dissociation of the ternary complex containing STX5A, NSFL1C and VCP (By similarity). 
Sequence Annotation
 DOMAIN 208 361 OTU.
 MOD_RES 408 408 N6-acetyllysine.
 MOD_RES 747 747 Phosphoserine.
 MOD_RES 763 763 Phosphothreonine.
 MOD_RES 994 994 Phosphoserine.
 MOD_RES 1198 1198 Phosphoserine.
 CROSSLNK 870 870 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 Acetylation; Complete proteome; Endoplasmic reticulum; Golgi apparatus; Hydrolase; Isopeptide bond; Phosphoprotein; Protease; Reference proteome; Thiol protease; Ubl conjugation; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1222 AA 
Protein Sequence
MSQPPPPPPP LPPPPPPPEA PQTPSSLASA AASGGLLKRR DRRILSGSCP DPKCQARLFF 60
PASGSVSIEC TECGQRHEQQ QLLGVEEVTD PDVVLHNLLR NALLGVTGAP KKNTELVKVM 120
GLSNYHCKLL SPILARYGMD KQTGRAKLLR DMNQGELFDC ALLGDRAFLI EPEHVNTVGY 180
GKDRSGSLLY LHDTLEDIKR ANKSQECLIP VHVDGDGHCL VHAVSRALVG RELFWHALRE 240
NLKQHFQQHL ARYQALFHDF IDAAEWEDII NECDPLFVPP EGVPLGLRNI HIFGLANVLH 300
RPIILLDSLS GMRSSGDYSA TFLPGLIPAE KCTGKDGHLN KPICIAWSSS GRNHYIPLVG 360
IKGAALPKLP MNLLPKAWGV PQDLIKKYIK LEEDGGCVIG GDRSLQDKYL LRLVAAMEEV 420
FMDKHGIHPS LVADVHQYFY RRTGVIGVQP EEVTAAAKKA VMDNRLHKCL LCGALSELHV 480
PPEWLAPGGK LYNLAKSTHG QLRTDKNYSF PLNNLVCSYD SVKDVLVPDY GMSNLTACNW 540
CHGTSVRKVR GDGSIVYLDG DRTNSRSTGG KCGCGFKHFW DGKEYDNLPE AFPITLEWGG 600
RVVRETVYWF QYESDSSLNS NVYDVAMKLV TKHFPGEFGS EILVQKVVHT ILHQTAKKNP 660
DDYTPVNIDG AHAQRVGDVQ GQESESQLPT KIILTGQKTK TLHKEELNMS KTERTIQQNI 720
TEQASVMQKR KTEKLKQEQK GQPRTVSPST IRDGPSSAPA TPTKAPYSPT TSKEKKIRIT 780
TNDGRQSMVT LKSSTTFFEL QESIAREFNI PPYLQCIRYG FPPKELMPPQ AGMEKEPVPL 840
QHGDRITIEI LKSKAEGGQS AAAHSAHTVK QEDIAVTGKL SSKELQEQAE KEMYSLCLLA 900
TLMGEDVWSY AKGLPHMFQQ GGVFYSIMKK TMGMADGKHC TFPHLPGKTF VYNASEDRLE 960
LCVDAAGHFP IGPDVEDLVK EAVSQVRAEA TTRSRESSPS HGLLKLGSGG VVKKKSEQLH 1020
NVTAFQGKGH SLGTASGNPH LDPRARETSV VRKHNTGTDF SNSSTKTEPS VFTASSSNSE 1080
LIRIAPGVVT MRDGRQLDPD LVEAQRKKLQ EMVSSIQASM DRHLRDQSTE QSPSDLPQRK 1140
TEVVSSSAKS GSLQTGLPES FPLTGGTENL NTETTDGCVA DALGAAFATR SKAQRGNSVE 1200
ELEEMDSQDA EMTNTTEPMD HS 1222 
Gene Ontology
 GO:0005737; C:cytoplasm; IDA:LIFEdb.
 GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell.
 GO:0005795; C:Golgi stack; IEA:UniProtKB-SubCell.
 GO:0004843; F:ubiquitin-specific protease activity; ISS:UniProtKB.
 GO:0016320; P:endoplasmic reticulum membrane fusion; IEA:Compara.
 GO:0090168; P:Golgi reassembly; IEA:Compara.
 GO:0007067; P:mitosis; IEA:Compara.
 GO:0016567; P:protein ubiquitination; ISS:UniProtKB.
 GO:0006508; P:proteolysis; IEA:UniProtKB-KW. 
Interpro
 IPR003323; OTU. 
Pfam
 PF02338; OTU 
SMART
  
PROSITE
 PS50802; OTU 
PRINTS