CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001461
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ubiquitin carboxyl-terminal hydrolase 1 
Protein Synonyms/Alias
 Deubiquitinating enzyme 1; hUBP; Ubiquitin thioesterase 1; Ubiquitin-specific-processing protease 1 
Gene Name
 USP1 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
48DSQENEEKASEYRASubiquitination[1]
73SSPINCEKRENLLPFubiquitination[1]
110PGFKSGVKHLFNIISubiquitination[1]
360SKFCSLGKITTNQGVubiquitination[1]
483PEPKTEMKTLRWAISubiquitination[1]
503ERIVGEDKYFCENCHubiquitination[1]
523ERSLLFDKMPEVITIubiquitination[1]
551CYGGGLSKINTPLLTubiquitination[2]
610LNSLELDKGNFVVDQubiquitination[1]
689NKASNPDKVASTAFAubiquitination[1, 2, 3, 4, 5, 6]
741SYVVQSLKEYEGKWLubiquitination[2, 3, 4, 5, 6]
746SLKEYEGKWLLFDDSubiquitination[3, 4, 5]
761EVKVTEEKDFLNSLSubiquitination[3, 5]
783TPYLLFYKKL*****ubiquitination[3, 5]
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] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [3] 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]
 [4] 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]
 [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] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302] 
Functional Description
 Negative regulator of DNA damage repair which specifically deubiquitinates monoubiquitinated FANCD2. Also involved in PCNA-mediated translesion synthesis (TLS) by deubiquitinating monoubiquitinated PCNA. Has almost no deubiquitinating activity by itself and requires the interaction with WDR48 to have a high activity. 
Sequence Annotation
 ACT_SITE 90 90 Nucleophile.
 ACT_SITE 593 593 Proton acceptor (By similarity).
 MOD_RES 42 42 Phosphoserine.
 MOD_RES 67 67 Phosphoserine.
 MOD_RES 475 475 Phosphoserine.  
Keyword
 Autocatalytic cleavage; Complete proteome; DNA damage; DNA repair; Hydrolase; Nucleus; Phosphoprotein; Protease; Reference proteome; Thiol protease; Ubl conjugation; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 785 AA 
Protein Sequence
MPGVIPSESN GLSRGSPSKK NRLSLKFFQK KETKRALDFT DSQENEEKAS EYRASEIDQV 60
VPAAQSSPIN CEKRENLLPF VGLNNLGNTC YLNSILQVLY FCPGFKSGVK HLFNIISRKK 120
EALKDEANQK DKGNCKEDSL ASYELICSLQ SLIISVEQLQ ASFLLNPEKY TDELATQPRR 180
LLNTLRELNP MYEGYLQHDA QEVLQCILGN IQETCQLLKK EEVKNVAELP TKVEEIPHPK 240
EEMNGINSIE MDSMRHSEDF KEKLPKGNGK RKSDTEFGNM KKKVKLSKEH QSLEENQRQT 300
RSKRKATSDT LESPPKIIPK YISENESPRP SQKKSRVKIN WLKSATKQPS ILSKFCSLGK 360
ITTNQGVKGQ SKENECDPEE DLGKCESDNT TNGCGLESPG NTVTPVNVNE VKPINKGEEQ 420
IGFELVEKLF QGQLVLRTRC LECESLTERR EDFQDISVPV QEDELSKVEE SSEISPEPKT 480
EMKTLRWAIS QFASVERIVG EDKYFCENCH HYTEAERSLL FDKMPEVITI HLKCFAASGL 540
EFDCYGGGLS KINTPLLTPL KLSLEEWSTK PTNDSYGLFA VVMHSGITIS SGHYTASVKV 600
TDLNSLELDK GNFVVDQMCE IGKPEPLNEE EARGVVENYN DEEVSIRVGG NTQPSKVLNK 660
KNVEAIGLLG GQKSKADYEL YNKASNPDKV ASTAFAENRN SETSDTTGTH ESDRNKESSD 720
QTGINISGFE NKISYVVQSL KEYEGKWLLF DDSEVKVTEE KDFLNSLSPS TSPTSTPYLL 780
FYKKL 785 
Gene Ontology
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0004197; F:cysteine-type endopeptidase activity; TAS:ProtInc.
 GO:0004221; F:ubiquitin thiolesterase activity; IDA:UniProtKB.
 GO:0004843; F:ubiquitin-specific protease activity; IDA:UniProtKB.
 GO:0006281; P:DNA repair; TAS:Reactome.
 GO:0035520; P:monoubiquitinated protein deubiquitination; IMP:UniProtKB.
 GO:0006282; P:regulation of DNA repair; IDA:UniProtKB.
 GO:0009411; P:response to UV; IDA:UniProtKB.
 GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro. 
Interpro
 IPR018200; Pept_C19ubi-hydrolase_C_CS.
 IPR001394; Peptidase_C19. 
Pfam
 PF00443; UCH 
SMART
  
PROSITE
 PS00972; UCH_2_1
 PS00973; UCH_2_2
 PS50235; UCH_2_3 
PRINTS