CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-008419
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ubiquitin carboxyl-terminal hydrolase 11 
Protein Synonyms/Alias
 Deubiquitinating enzyme 11; Ubiquitin thioesterase 11; Ubiquitin-specific-processing protease 11 
Gene Name
 USP11 
Gene Synonyms/Alias
 UHX1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
107ESWFLVEKHWYKQWEubiquitination[1, 2, 3, 4, 5]
182GQPPIERKVIELPNIubiquitination[3]
191IELPNIQKVEVYPVEubiquitination[3]
245EDTRLWAKNSEGSLDacetylation[6]
245EDTRLWAKNSEGSLDubiquitination[1, 2, 3, 4, 5, 7]
355FRNPLGMKGEIAEAYubiquitination[1, 2, 3, 4, 5, 7]
367EAYADLVKQAWSGHHubiquitination[1, 3, 4, 5]
383SIVPHVFKNKVGHFAubiquitination[3]
385VPHVFKNKVGHFASQubiquitination[3]
447QEAWQNHKRRNDSVIubiquitination[3, 7]
493VPLPISHKRVLEVFFubiquitination[3]
519HRLVVPKKGKISDLCubiquitination[3]
521LVVPKKGKISDLCVAubiquitination[3]
531DLCVALSKHTGISPEubiquitination[1, 3, 5, 7]
714WPPRRRRKQLFTLQTubiquitination[1, 3, 4, 5, 8]
752IDWEPEMKKRYYDEVubiquitination[2, 3, 4]
753DWEPEMKKRYYDEVEubiquitination[3]
766VEAEGYVKHDCVGYVubiquitination[3, 7]
776CVGYVMKKAPVRLQEubiquitination[3]
806PWYCPSCKQHQLATKubiquitination[1, 5]
813KQHQLATKKLDLWMLubiquitination[2, 3]
835LKRFSYTKFSREKLDubiquitination[1, 3, 4, 5, 7, 8]
840YTKFSREKLDTLVEFubiquitination[1, 2, 3, 4, 5, 8]
896YTTFACNKDSGQWHYubiquitination[3]
920NENQIESKAAYVLFYubiquitination[2, 7]
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] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] 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] 
Functional Description
 Protease that can remove conjugated ubiquitin from target proteins and polyubiquitin chains. Inhibits the degradation of target proteins by the proteasome. Plays a role in the regulation of pathways leading to NF-kappa-B activation. Plays a role in the regulation of DNA repair after double-stranded DNA breaks. 
Sequence Annotation
 DOMAIN 76 184 DUSP.
 ACT_SITE 318 318 Nucleophile.
 ACT_SITE 888 888 Proton acceptor (By similarity).
 MOD_RES 245 245 N6-acetyllysine.
 MOD_RES 648 648 Phosphoserine.
 MOD_RES 948 948 Phosphoserine.  
Keyword
 Acetylation; Complete proteome; Cytoplasm; Hydrolase; Nucleus; Phosphoprotein; Protease; Reference proteome; Thiol protease; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 963 AA 
Protein Sequence
MAVAPRLFGG LCFRFRDQNP EVAVEGRLPI SHSCVGCRRE RTAMATVAAN PAAAAAAVAA 60
AAAVTEDREP QHEELPGLDS QWRQIENGES GRERPLRAGE SWFLVEKHWY KQWEAYVQGG 120
DQDSSTFPGC INNATLFQDE INWRLKEGLV EGEDYVLLPA AAWHYLVSWY GLEHGQPPIE 180
RKVIELPNIQ KVEVYPVELL LVRHNDLGKS HTVQFSHTDS IGLVLRTARE RFLVEPQEDT 240
RLWAKNSEGS LDRLYDTHIT VLDAALETGQ LIIMETRKKD GTWPSAQLHV MNNNMSEEDE 300
DFKGQPGICG LTNLGNTCFM NSALQCLSNV PQLTEYFLNN CYLEELNFRN PLGMKGEIAE 360
AYADLVKQAW SGHHRSIVPH VFKNKVGHFA SQFLGYQQHD SQELLSFLLD GLHEDLNRVK 420
KKEYVELCDA AGRPDQEVAQ EAWQNHKRRN DSVIVDTFHG LFKSTLVCPD CGNVSVTFDP 480
FCYLSVPLPI SHKRVLEVFF IPMDPRRKPE QHRLVVPKKG KISDLCVALS KHTGISPERM 540
MVADVFSHRF YKLYQLEEPL SSILDRDDIF VYEVSGRIEA IEGSREDIVV PVYLRERTPA 600
RDYNNSYYGL MLFGHPLLVS VPRDRFTWEG LYNVLMYRLS RYVTKPNSDD EDDGDEKEDD 660
EEDKDDVPGP STGGSLRDPE PEQAGPSSGV TNRCPFLLDN CLGTSQWPPR RRRKQLFTLQ 720
TVNSNGTSDR TTSPEEVHAQ PYIAIDWEPE MKKRYYDEVE AEGYVKHDCV GYVMKKAPVR 780
LQECIELFTT VETLEKENPW YCPSCKQHQL ATKKLDLWML PEILIIHLKR FSYTKFSREK 840
LDTLVEFPIR DLDFSEFVIQ PQNESNPELY KYDLIAVSNH YGGMRDGHYT TFACNKDSGQ 900
WHYFDDNSVS PVNENQIESK AAYVLFYQRQ DVARRLLSPA GSSGAPASPA CSSPPSSEFM 960
DVN 963 
Gene Ontology
 GO:0005737; C:cytoplasm; IDA:HPA.
 GO:0005634; C:nucleus; IDA:UniProtKB.
 GO:0004197; F:cysteine-type endopeptidase activity; TAS:ProtInc.
 GO:0004221; F:ubiquitin thiolesterase activity; IEA:InterPro.
 GO:0004843; F:ubiquitin-specific protease activity; IDA:UniProtKB.
 GO:0016579; P:protein deubiquitination; IDA:UniProtKB.
 GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro. 
Interpro
 IPR006615; Pept_C19_DUSP.
 IPR018200; Pept_C19ubi-hydrolase_C_CS.
 IPR001394; Peptidase_C19. 
Pfam
 PF06337; DUSP
 PF00443; UCH 
SMART
 SM00695; DUSP 
PROSITE
 PS51283; DUSP
 PS00972; UCH_2_1
 PS00973; UCH_2_2
 PS50235; UCH_2_3 
PRINTS