CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-029745
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Vimentin 
Protein Synonyms/Alias
 Vimentin variant 3 
Gene Name
 VIM 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
97DAINTEFKNTRTNEKubiquitination[1, 2, 3, 4, 5, 6]
104KNTRTNEKVELQELNacetylation[7, 8]
104KNTRTNEKVELQELNubiquitination[1, 2, 3, 4, 5, 6, 9]
120RFANYIDKVRFLEQQacetylation[6, 8]
120RFANYIDKVRFLEQQubiquitination[1, 2, 3, 4, 5, 6, 9, 10]
129RFLEQQNKILLAELEubiquitination[1, 2, 3, 4, 5, 6, 9]
139LAELEQLKGQGKSRLacetylation[6, 8]
139LAELEQLKGQGKSRLubiquitination[1, 2, 3, 4, 5, 6, 9]
143EQLKGQGKSRLGDLYubiquitination[1, 2, 6, 9]
168VDQLTNDKARVEVERacetylation[6, 8]
168VDQLTNDKARVEVERubiquitination[1, 2, 4, 9]
188DIMRLREKLQEEMLQubiquitination[1, 2, 3, 4, 5, 6, 9]
223ARLDLERKVESLQEEacetylation[7]
223ARLDLERKVESLQEEubiquitination[6, 9]
235QEEIAFLKKLHEEEIacetylation[6, 8]
235QEEIAFLKKLHEEEIubiquitination[1, 2, 3, 5, 9]
236EEIAFLKKLHEEEIQubiquitination[3, 6, 9]
262QIDVDVSKPDLTAALubiquitination[3]
282QYESVAAKNLQEAEEubiquitination[1, 2, 3, 4, 5, 6, 9]
292QEAEEWYKSKFADLSacetylation[8]
292QEAEEWYKSKFADLSubiquitination[1, 4, 5, 6, 9]
294AEEWYKSKFADLSEAacetylation[8]
294AEEWYKSKFADLSEAubiquitination[1, 2, 4, 5, 6, 9]
313NDALRQAKQESTEYRacetylation[8]
313NDALRQAKQESTEYRubiquitination[1, 2, 6, 9]
334TCEVDALKGTNESLEacetylation[6]
334TCEVDALKGTNESLEubiquitination[2, 3, 4, 5, 6, 9, 11]
373QDEIQNMKEEMARHLacetylation[8]
373QDEIQNMKEEMARHLubiquitination[1, 2, 3, 4, 5, 6, 9]
402IEIATYRKLLEGEESacetylation[6, 8]
402IEIATYRKLLEGEESubiquitination[2, 3, 4, 5, 6, 9, 11, 12]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] Monoclonal antibody cocktail as an enrichment tool for acetylome analysis.
 Shaw PG, Chaerkady R, Zhang Z, Davidson NE, Pandey A.
 Anal Chem. 2011 May 15;83(10):3623-6. [PMID: 21466224]
 [8] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [9] 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]
 [10] A data set of human endogenous protein ubiquitination sites.
 Shi Y, Chan DW, Jung SY, Malovannaya A, Wang Y, Qin J.
 Mol Cell Proteomics. 2011 May;10(5):M110.002089. [PMID: 20972266]
 [11] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
 [12] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048
Functional Description
  
Sequence Annotation
  
Keyword
 Coiled coil; Complete proteome; Intermediate filament; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 431 AA 
Protein Sequence
MSTRSVSSSS YRRMFGGPGT ASRPSSSRSY VTTSTRTYSL GSALRPSTSR SLYASSPGGV 60
YATRSSAVRL RSSVPGVRLL QDSVDFSLAD AINTEFKNTR TNEKVELQEL NDRFANYIDK 120
VRFLEQQNKI LLAELEQLKG QGKSRLGDLY EEEMRELRRQ VDQLTNDKAR VEVERDNLAE 180
DIMRLREKLQ EEMLQREEAE NTLQSFRQDV DNASLARLDL ERKVESLQEE IAFLKKLHEE 240
EIQELQAQIQ EQHVQIDVDV SKPDLTAALR DVRQQYESVA AKNLQEAEEW YKSKFADLSE 300
AANRNNDALR QAKQESTEYR RQVQSLTCEV DALKGTNESL ERQMREMEEN FAVEAANYQD 360
TIGRLQDEIQ NMKEEMARHL REYQDLLNVK MALDIEIATY RKLLEGEESR ISLPLPNFSS 420
LNLRGKHFIS L 431 
Gene Ontology
 GO:0005882; C:intermediate filament; IEA:UniProtKB-KW.
 GO:0045111; C:intermediate filament cytoskeleton; IDA:HPA.
 GO:0005198; F:structural molecule activity; IEA:InterPro. 
Interpro
 IPR016044; F.
 IPR001664; IF.
 IPR006821; Intermed_filament_DNA-bd.
 IPR018039; Intermediate_filament_CS. 
Pfam
 PF00038; Filament
 PF04732; Filament_head 
SMART
  
PROSITE
 PS00226; IF 
PRINTS