CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-011999
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ubiquitin carboxyl-terminal hydrolase 4 
Protein Synonyms/Alias
 Deubiquitinating enzyme 4; Ubiquitin thioesterase 4; Ubiquitin-specific-processing protease 4; Ubiquitous nuclear protein homolog 
Gene Name
 USP4 
Gene Synonyms/Alias
 UNP; UNPH 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
43LIDSRWFKQWKKYVGubiquitination[1]
120GQQPIVRKVVEHGLFubiquitination[1]
132GLFVKHCKVEVYLLEubiquitination[1]
158VLSCHFSKADTIATIubiquitination[1]
167DTIATIEKEMRKLFNubiquitination[1]
186RETRLWNKYMSNTYEubiquitination[1, 2]
232PRQTLQSKSSTAPSRubiquitination[1]
348RDNPLGMKGEIAEAYubiquitination[3]
376HVAPRMFKTQVGRFAubiquitination[1]
414EDLNRVKKKPYLELKubiquitination[1]
415DLNRVKKKPYLELKDubiquitination[1]
433RPDAVVAKEAWENHRubiquitination[1]
545VYNHRFHKIFQMDEGubiquitination[1]
588PVYFRERKSRPSSTSubiquitination[1]
613LLSVPKHKLTLESLYubiquitination[1]
632DRISRYVKQPLPDEFubiquitination[1]
731AADGKLLKLNSRSTLubiquitination[1]
811KHQQATKKFDLWSLPubiquitination[2]
837YNRYWRDKLDTVVEFubiquitination[1, 3]
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] 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] 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] 
Functional Description
 Hydrolase that deubiquitinates target proteins such as the receptor ADORA2A, PDPK1 and TRIM21. Deubiquitination of ADORA2A increases the amount of functional receptor at the cell surface. Plays a role in the regulation of quality control in the ER. 
Sequence Annotation
 DOMAIN 11 122 DUSP.
 DOMAIN 142 226 Ubiquitin-like 1.
 DOMAIN 483 571 Ubiquitin-like 2.
 REGION 405 407 Necessary for interaction with RBL2 (By
 REGION 459 463 Necessary for interaction with RB1 and
 MOTIF 133 141 Nuclear export signal (By similarity).
 MOTIF 767 772 Nuclear localization signal (By
 ACT_SITE 311 311 Nucleophile.
 ACT_SITE 881 881 Proton acceptor (By similarity).
 METAL 461 461 Zinc.
 METAL 464 464 Zinc.
 METAL 799 799 Zinc.
 METAL 802 802 Zinc.
 MOD_RES 680 680 Phosphoserine (By similarity).  
Keyword
 3D-structure; Alternative splicing; Complete proteome; Cytoplasm; Hydrolase; Metal-binding; Nucleus; Phosphoprotein; Polymorphism; Protease; Proto-oncogene; Reference proteome; Repeat; Thiol protease; Ubl conjugation; Ubl conjugation pathway; Zinc. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 963 AA 
Protein Sequence
MAEGGGCRER PDAETQKSEL GPLMRTTLQR GAQWYLIDSR WFKQWKKYVG FDSWDMYNVG 60
EHNLFPGPID NSGLFSDPES QTLKEHLIDE LDYVLVPTEA WNKLLNWYGC VEGQQPIVRK 120
VVEHGLFVKH CKVEVYLLEL KLCENSDPTN VLSCHFSKAD TIATIEKEMR KLFNIPAERE 180
TRLWNKYMSN TYEQLSKLDN TVQDAGLYQG QVLVIEPQNE DGTWPRQTLQ SKSSTAPSRN 240
FTTSPKSSAS PYSSVSASLI ANGDSTSTCG MHSSGVSRGG SGFSASYNCQ EPPSSHIQPG 300
LCGLGNLGNT CFMNSALQCL SNTAPLTDYF LKDEYEAEIN RDNPLGMKGE IAEAYAELIK 360
QMWSGRDAHV APRMFKTQVG RFAPQFSGYQ QQDSQELLAF LLDGLHEDLN RVKKKPYLEL 420
KDANGRPDAV VAKEAWENHR LRNDSVIVDT FHGLFKSTLV CPECAKVSVT FDPFCYLTLP 480
LPLKKDRVME VFLVPADPHC RPTQYRVTVP LMGAVSDLCE ALSRLSGIAA ENMVVADVYN 540
HRFHKIFQMD EGLNHIMPRD DIFVYEVCST SVDGSECVTL PVYFRERKSR PSSTSSASAL 600
YGQPLLLSVP KHKLTLESLY QAVCDRISRY VKQPLPDEFG SSPLEPGACN GSRNSCEGED 660
EEEMEHQEEG KEQLSETEGS GEDEPGNDPS ETTQKKIKGQ PCPKRLFTFS LVNSYGTADI 720
NSLAADGKLL KLNSRSTLAM DWDSETRRLY YDEQESEAYE KHVSMLQPQK KKKTTVALRD 780
CIELFTTMET LGEHDPWYCP NCKKHQQATK KFDLWSLPKI LVVHLKRFSY NRYWRDKLDT 840
VVEFPIRGLN MSEFVCNLSA RPYVYDLIAV SNHYGAMGVG HYTAYAKNKL NGKWYYFDDS 900
NVSLASEDQI VTKAAYVLFY QRRDDEFYKT PSLSSSGSSD GGTRPSSSQQ GFGDDEACSM 960
DTN 963 
Gene Ontology
 GO:0005764; C:lysosome; TAS:ProtInc.
 GO:0005634; C:nucleus; IDA:UniProtKB.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0004221; F:ubiquitin thiolesterase activity; IMP:UniProtKB.
 GO:0004843; F:ubiquitin-specific protease activity; IDA:UniProtKB.
 GO:0031397; P:negative regulation of protein ubiquitination; IMP:UniProtKB.
 GO:0016579; P:protein deubiquitination; IDA:UniProtKB.
 GO:0034394; P:protein localization to cell surface; IDA:UniProtKB.
 GO:0031647; P:regulation of protein stability; 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
 PS00299; UBIQUITIN_1
 PS50053; UBIQUITIN_2
 PS00972; UCH_2_1
 PS00973; UCH_2_2
 PS50235; UCH_2_3 
PRINTS