CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012018
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
84YPKDNKRKMDETDASubiquitination[1]
95TDASSAVKVKRAVQKubiquitination[1, 2]
102KVKRAVQKTSDLIVLubiquitination[1, 2, 3, 4]
114IVLGLPWKTTEQDLKubiquitination[1, 2, 3, 4]
145DLKTGHSKGFGFVRFubiquitination[1]
160TEYETQVKVMSQRHMubiquitination[1, 3, 4]
176DGRWCDCKLPNSKQSubiquitination[1, 2]
181DCKLPNSKQSQDEPLubiquitination[1, 2, 3]
192DEPLRSRKVFVGRCTubiquitination[1]
263HISNAEPKHNSNRQLubiquitination[1]
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] 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]
 [4] 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] 
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 GWGMNH 416 
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