CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-008842
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ataxin-3 
Protein Synonyms/Alias
 Machado-Joseph disease protein 1; Spinocerebellar ataxia type 3 protein 
Gene Name
 ATXN3 
Gene Synonyms/Alias
 ATX3; MJD; MJD1; SCA3 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
117RSFICNYKEHWFTVRubiquitination[1, 2, 3, 4, 5, 6]
190VQQMHRPKLIGEELAubiquitination[2, 4, 5]
200GEELAQLKEQRVHKTubiquitination[1, 2, 3, 4, 5]
206LKEQRVHKTDLERVLubiquitination[2, 3, 4, 5, 7]
291RREAYFEKQQQKQQQubiquitination[2, 4, 5]
Reference
 [1] Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling.
 Xu G, Paige JS, Jaffrey SR.
 Nat Biotechnol. 2010 Aug;28(8):868-73. [PMID: 20639865]
 [2] 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]
 [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] 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] 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]
 [6] 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]
 [7] 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
Functional Description
 Deubiquitinating enzyme involved in protein homeostasis maintenance, transcription, cytoskeleton regulation, myogenesis and degradation of misfolded chaperone substrates. Binds long polyubiquitin chains and trims them, while it has weak or no activity against chains of 4 or less ubiquitins. Involved in degradation of misfolded chaperone substrates via its interaction with STUB1/CHIP: recruited to monoubiquitinated STUB1/CHIP, and restricts the length of ubiquitin chain attached to STUB1/CHIP substrates and preventing further chain extension. In response to misfolded substrate ubiquitination, mediates deubiquitination of monoubiquitinated STUB1/CHIP. Interacts with key regulators of transcription and represses transcription: acts as a histone- binding protein that regulates transcription. 
Sequence Annotation
 DOMAIN 1 180 Josephin.
 REPEAT 224 243 UIM 1.
 REPEAT 244 263 UIM 2.
 REPEAT 331 348 UIM 3.
 ACT_SITE 14 14 Nucleophile.
 ACT_SITE 119 119 Proton acceptor (Probable).
 ACT_SITE 134 134 Probable.
 MOD_RES 219 219 Phosphoserine (By similarity).  
Keyword
 3D-structure; Alternative splicing; Complete proteome; Hydrolase; Neurodegeneration; Nucleus; Phosphoprotein; Polymorphism; Protease; Reference proteome; Repeat; Spinocerebellar ataxia; Thiol protease; Transcription; Transcription regulation; Triplet repeat expansion; Ubl conjugation; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 364 AA 
Protein Sequence
MESIFHEKQE GSLCAQHCLN NLLQGEYFSP VELSSIAHQL DEEERMRMAE GGVTSEDYRT 60
FLQQPSGNMD DSGFFSIQVI SNALKVWGLE LILFNSPEYQ RLRIDPINER SFICNYKEHW 120
FTVRKLGKQW FNLNSLLTGP ELISDTYLAL FLAQLQQEGY SIFVVKGDLP DCEADQLLQM 180
IRVQQMHRPK LIGEELAQLK EQRVHKTDLE RVLEANDGSG MLDEDEEDLQ RALALSRQEI 240
DMEDEEADLR RAIQLSMQGS SRNISQDMTQ TSGTNLTSEE LRKRREAYFE KQQQKQQQQQ 300
QQQQQGDLSG QSSHPCERPA TSSGALGSDL GKACSPFIMF ATFTLYLTYE LHVIFALHYS 360
SFPL 364 
Gene Ontology
 GO:0005737; C:cytoplasm; TAS:ProtInc.
 GO:0005759; C:mitochondrial matrix; IEA:Compara.
 GO:0031966; C:mitochondrial membrane; IEA:Compara.
 GO:0042405; C:nuclear inclusion body; IEA:Compara.
 GO:0016363; C:nuclear matrix; IEA:UniProtKB-SubCell.
 GO:0005654; C:nucleoplasm; TAS:ProtInc.
 GO:0008242; F:omega peptidase activity; IEA:InterPro.
 GO:0001012; F:RNA polymerase II regulatory region DNA binding; IEA:Compara.
 GO:0031625; F:ubiquitin protein ligase binding; ISS:UniProtKB.
 GO:0004221; F:ubiquitin thiolesterase activity; ISS:UniProtKB.
 GO:0004843; F:ubiquitin-specific protease activity; ISS:UniProtKB.
 GO:0030036; P:actin cytoskeleton organization; IMP:MGI.
 GO:0008219; P:cell death; IEA:UniProtKB-KW.
 GO:0034605; P:cellular response to heat; IEA:Compara.
 GO:0071218; P:cellular response to misfolded protein; ISS:UniProtKB.
 GO:0035640; P:exploration behavior; IEA:Compara.
 GO:0070932; P:histone H3 deacetylation; IEA:Compara.
 GO:0045104; P:intermediate filament cytoskeleton organization; IMP:MGI.
 GO:0000226; P:microtubule cytoskeleton organization; IMP:MGI.
 GO:0006515; P:misfolded or incompletely synthesized protein catabolic process; ISS:UniProtKB.
 GO:0035520; P:monoubiquitinated protein deubiquitination; ISS:UniProtKB.
 GO:0007399; P:nervous system development; TAS:ProtInc.
 GO:0006289; P:nucleotide-excision repair; TAS:ProtInc.
 GO:0043161; P:proteasomal ubiquitin-dependent protein catabolic process; ISS:UniProtKB.
 GO:0010810; P:regulation of cell-substrate adhesion; IMP:MGI.
 GO:0006355; P:regulation of transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0007268; P:synaptic transmission; TAS:ProtInc.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR006155; Josephin.
 IPR003903; Ubiquitin-int_motif. 
Pfam
 PF02099; Josephin
 PF02809; UIM 
SMART
 SM00726; UIM 
PROSITE
 PS50957; JOSEPHIN
 PS50330; UIM 
PRINTS
 PR01233; JOSEPHIN.