CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-024002
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ubiquitin carboxyl-terminal hydrolase 3 
Protein Synonyms/Alias
 Deubiquitinating enzyme 3; Ubiquitin thioesterase 3; Ubiquitin-specific-processing protease 3 
Gene Name
 USP3 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
107DFVVNDTKLGLVQKVubiquitination[1, 2]
113TKLGLVQKVREHLQNubiquitination[2]
135ADRHKKRKLLENSTLubiquitination[2]
145ENSTLNSKLLKVNGSubiquitination[1, 2, 3, 4]
148TLNSKLLKVNGSTTAubiquitination[2]
333ICGTESRKFDPFLDLubiquitination[3]
354QFRSKRSKNQENGPVubiquitination[1, 2]
387TELYMCHKCKKKQKSubiquitination[1]
389LYMCHKCKKKQKSTKubiquitination[2]
423WTAYLRNKVDTYVEFubiquitination[1, 2, 3, 4, 5, 6]
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] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [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] 
Functional Description
 Hydrolase that deubiquitinates monoubiquitinated target proteins such as histone H2A and H2B. Required for proper progression through S phase and subsequent mitotic entry. May regulate the DNA damage response (DDR) checkpoint through deubiquitination of H2A at DNA damage sites. Associates with the chromatin. 
Sequence Annotation
 ZN_FING 27 104 UBP-type.
 ACT_SITE 168 168 Nucleophile (By similarity).
 ACT_SITE 471 471 Proton acceptor (By similarity).
 MOD_RES 1 1 N-acetylmethionine.  
Keyword
 Acetylation; Alternative splicing; Cell cycle; Chromatin regulator; Complete proteome; DNA damage; Hydrolase; Metal-binding; Nucleus; Polymorphism; Protease; Reference proteome; Thiol protease; Ubl conjugation pathway; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 520 AA 
Protein Sequence
MECPHLSSSV CIAPDSAKFP NGSPSSWCCS VCRSNKSPWV CLTCSSVHCG RYVNGHAKKH 60
YEDAQVPLTN HKKSEKQDKV QHTVCMDCSS YSTYCYRCDD FVVNDTKLGL VQKVREHLQN 120
LENSAFTADR HKKRKLLENS TLNSKLLKVN GSTTAICATG LRNLGNTCFM NAILQSLSNI 180
EQFCCYFKEL PAVELRNGKT AGRRTYHTRS QGDNNVSLVE EFRKTLCALW QGSQTAFSPE 240
SLFYVVWKIM PNFRGYQQQD AHEFMRYLLD HLHLELQGGF NGVSRSAILQ ENSTLSASNK 300
CCINGASTVV TAIFGGILQN EVNCLICGTE SRKFDPFLDL SLDIPSQFRS KRSKNQENGP 360
VCSLRDCLRS FTDLEELDET ELYMCHKCKK KQKSTKKFWI QKLPKVLCLH LKRFHWTAYL 420
RNKVDTYVEF PLRGLDMKCY LLEPENSGPE SCLYDLAAVV VHHGSGVGSG HYTAYATHEG 480
RWFHFNDSTV TLTDEETVVK AKAYILFYVE HQAKAGSDKL 520 
Gene Ontology
 GO:0000790; C:nuclear chromatin; IDA:UniProtKB.
 GO:0004221; F:ubiquitin thiolesterase activity; IMP:UniProtKB.
 GO:0004843; F:ubiquitin-specific protease activity; TAS:ProtInc.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0006281; P:DNA repair; IMP:UniProtKB.
 GO:0016578; P:histone deubiquitination; IDA:UniProtKB.
 GO:0000278; P:mitotic cell cycle; IMP:UniProtKB.
 GO:0031647; P:regulation of protein stability; IDA:UniProtKB.
 GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro. 
Interpro
 IPR018200; Pept_C19ubi-hydrolase_C_CS.
 IPR001394; Peptidase_C19.
 IPR013083; Znf_RING/FYVE/PHD.
 IPR001607; Znf_UBP. 
Pfam
 PF00443; UCH
 PF02148; zf-UBP 
SMART
  
PROSITE
 PS00972; UCH_2_1
 PS00973; UCH_2_2
 PS50235; UCH_2_3
 PS50271; ZF_UBP 
PRINTS