CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012017
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 TAR DNA-binding protein 43 
Protein Synonyms/Alias
 TDP-43 
Gene Name
 TARDBP 
Gene Synonyms/Alias
 TDP43 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
79VYVVNYPKDNKRKMDubiquitination[1]
82VNYPKDNKRKMDETDubiquitination[1]
95TDASSAVKVKRAVQKubiquitination[1, 2, 3]
97ASSAVKVKRAVQKTSubiquitination[1]
102KVKRAVQKTSDLIVLubiquitination[1, 2, 4]
114IVLGLPWKTTEQDLKubiquitination[2, 4]
121KTTEQDLKEYFSTFGubiquitination[2]
140VQVKKDLKTGHSKGFubiquitination[2]
145DLKTGHSKGFGFVRFubiquitination[1, 2]
160TEYETQVKVMSQRHMubiquitination[1, 2, 4]
176DGRWCDCKLPNSKQSubiquitination[1, 2, 3]
181DCKLPNSKQSQDEPLubiquitination[1, 2, 3]
192DEPLRSRKVFVGRCTubiquitination[1]
263HISNAEPKHNSNRQLubiquitination[2]
Reference
 [1] 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]
 [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] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [4] 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] 
Functional Description
 DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3'-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeat. Stabilizes the low molecular weight neurofilament (NFL) mRNA through a direct interaction with the 3' UTR. 
Sequence Annotation
 DOMAIN 104 200 RRM 1.
 DOMAIN 191 262 RRM 2.
 MOD_RES 292 292 Phosphoserine.  
Keyword
 3D-structure; Alternative splicing; Amyotrophic lateral sclerosis; Complete proteome; Direct protein sequencing; Disease mutation; DNA-binding; mRNA processing; mRNA splicing; Neurodegeneration; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; Repressor; RNA-binding; Transcription; Transcription regulation; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 414 AA 
Protein Sequence
MSEYIRVTED ENDEPIEIPS EDDGTVLLST VTAQFPGACG LRYRNPVSQC MRGVRLVEGI 60
LHAPDAGWGN LVYVVNYPKD NKRKMDETDA SSAVKVKRAV QKTSDLIVLG LPWKTTEQDL 120
KEYFSTFGEV LMVQVKKDLK TGHSKGFGFV RFTEYETQVK VMSQRHMIDG RWCDCKLPNS 180
KQSQDEPLRS RKVFVGRCTE DMTEDELREF FSQYGDVMDV FIPKPFRAFA FVTFADDQIA 240
QSLCGEDLII KGISVHISNA EPKHNSNRQL ERSGRFGGNP GGFGNQGGFG NSRGGGAGLG 300
NNQGSNMGGG MNFGAFSINP AMMAAAQAAL QSSWGMMGML ASQQNQSGPS GNNQNQGNMQ 360
REPNQAFGSG NNSYSGSNSG AAIGWGSASN AGSGSGFNGG FGSSMDSKSS GWGM 414 
Gene Ontology
 GO:0005634; C:nucleus; IDA:BHF-UCL.
 GO:0003690; F:double-stranded DNA binding; IDA:BHF-UCL.
 GO:0003730; F:mRNA 3'-UTR binding; IDA:BHF-UCL.
 GO:0000166; F:nucleotide binding; IEA:InterPro.
 GO:0003700; F:sequence-specific DNA binding transcription factor activity; TAS:ProtInc.
 GO:0070935; P:3'-UTR-mediated mRNA stabilization; IDA:BHF-UCL.
 GO:0008219; P:cell death; IEA:UniProtKB-KW.
 GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
 GO:0043922; P:negative regulation by host of viral transcription; IDA:BHF-UCL.
 GO:0008380; P:RNA splicing; IDA:BHF-UCL.
 GO:0006366; P:transcription from RNA polymerase II promoter; TAS:ProtInc. 
Interpro
 IPR012677; Nucleotide-bd_a/b_plait.
 IPR000504; RRM_dom. 
Pfam
 PF00076; RRM_1 
SMART
 SM00360; RRM 
PROSITE
 PS50102; RRM 
PRINTS