CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-023930
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ubiquitin carboxyl-terminal hydrolase 16 
Protein Synonyms/Alias
 Deubiquitinating enzyme 16; Ubiquitin thioesterase 16; Ubiquitin-processing protease UBP-M; Ubiquitin-specific-processing protease 16 
Gene Name
 USP16 
Gene Synonyms/Alias
 MSTP039 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
37GLEQGNLKKALVNVEubiquitination[1]
293CKKAVRFKGYQQQDSubiquitination[1, 2, 3, 4, 5]
426KDNDSYIKERSDIPSubiquitination[1]
764GHYTAYAKARTANSHubiquitination[6]
Reference
 [1] 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]
 [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] 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]
 [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] 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] 
Functional Description
 Specifically deubiquitinates histone H2A, a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Deubiquitination of histone H2A is a prerequisite for subsequent phosphorylation at 'Ser-10' of histone H3, and is required for chromosome segregation when cells enter into mitosis. Regulates Hox gene expression via histone H2A deubiquitination. Prefers nucleosomal substrates. Does not deubiquitinate histone H2B. 
Sequence Annotation
 ZN_FING 60 125 UBP-type.
 ACT_SITE 205 205 Nucleophile.
 ACT_SITE 758 758 Proton acceptor (By similarity).
 METAL 24 24 Zinc 1.
 METAL 26 26 Zinc 1.
 METAL 48 48 Zinc 2.
 METAL 51 51 Zinc 2.
 METAL 74 74 Zinc 3.
 METAL 77 77 Zinc 3.
 METAL 82 82 Zinc 2.
 METAL 88 88 Zinc 2.
 METAL 90 90 Zinc 2.
 METAL 94 94 Zinc 3.
 METAL 103 103 Zinc 3.
 METAL 116 116 Zinc 1.
 METAL 119 119 Zinc 1.
 MOD_RES 415 415 Phosphoserine.
 MOD_RES 552 552 Phosphoserine.
 MOD_RES 554 554 Phosphothreonine.  
Keyword
 3D-structure; Activator; Alternative splicing; Cell cycle; Cell division; Chromatin regulator; Chromosomal rearrangement; Complete proteome; Hydrolase; Metal-binding; Mitosis; Nucleus; Phosphoprotein; Polymorphism; Protease; Reference proteome; Thiol protease; Transcription; Transcription regulation; Ubl conjugation pathway; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 823 AA 
Protein Sequence
MGKKRTKGKT VPIDDSSETL EPVCRHIRKG LEQGNLKKAL VNVEWNICQD CKTDNKVKDK 60
AEEETEEKPS VWLCLKCGHQ GCGRNSQEQH ALKHYLTPRS EPHCLVLSLD NWSVWCYVCD 120
NEVQYCSSNQ LGQVVDYVRK QASITTPKPA EKDNGNIELE NKKLEKESKN EQEREKKENM 180
AKENPPMNSP CQITVKGLSN LGNTCFFNAV MQNLSQTPVL RELLKEVKMS GTIVKIEPPD 240
LALTEPLEIN LEPPGPLTLA MSQFLNEMQE TKKGVVTPKE LFSQVCKKAV RFKGYQQQDS 300
QELLRYLLDG MRAEEHQRVS KGILKAFGNS TEKLDEELKN KVKDYEKKKS MPSFVDRIFG 360
GELTSMIMCD QCRTVSLVHE SFLDLSLPVL DDQSGKKSVN DKNLKKTVED EDQDSEEEKD 420
NDSYIKERSD IPSGTSKHLQ KKAKKQAKKQ AKNQRRQQKI QGKVLHLNDI CTIDHPEDSE 480
YEAEMSLQGE VNIKSNHISQ EGVMHKEYCV NQKDLNGQAK MIESVTDNQK STEEVDMKNI 540
NMDNDLEVLT SSPTRNLNGA YLTEGSNGEV DISNGFKNLN LNAALHPDEI NIEILNDSHT 600
PGTKVYEVVN EDPETAFCTL ANREVFNTDE CSIQHCLYQF TRNEKLRDAN KLLCEVCTRR 660
QCNGPKANIK GERKHVYTNA KKQMLISLAP PVLTLHLKRF QQAGFNLRKV NKHIKFPEIL 720
DLAPFCTLKC KNVAEENTRV LYSLYGVVEH SGTMRSGHYT AYAKARTANS HLSNLVLHGD 780
IPQDFEMESK GQWFHISDTH VQAVPTTKVL NSQAYLLFYE RIL 823 
Gene Ontology
 GO:0005737; C:cytoplasm; TAS:ProtInc.
 GO:0005634; C:nucleus; IDA:UniProtKB.
 GO:0004197; F:cysteine-type endopeptidase activity; IMP:UniProtKB.
 GO:0042393; F:histone binding; IDA:UniProtKB.
 GO:0003713; F:transcription coactivator activity; IDA:UniProtKB.
 GO:0043130; F:ubiquitin binding; IDA:UniProtKB.
 GO:0004221; F:ubiquitin thiolesterase activity; IDA:UniProtKB.
 GO:0004843; F:ubiquitin-specific protease activity; IDA:UniProtKB.
 GO:0008270; F:zinc ion binding; IDA:UniProtKB.
 GO:0051301; P:cell division; IEA:UniProtKB-KW.
 GO:0070537; P:histone H2A K63-linked deubiquitination; IMP:UniProtKB.
 GO:0007067; P:mitosis; IDA:UniProtKB.
 GO:0045893; P:positive regulation of transcription, DNA-dependent; IMP:UniProtKB.
 GO:0045901; P:positive regulation of translational elongation; IMP:UniProtKB.
 GO:0051289; P:protein homotetramerization; IPI:UniProtKB.
 GO:0006974; P:response to DNA damage stimulus; IDA:UniProtKB.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW.
 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