ID UBP16_RAT Reviewed; 826 AA.
AC Q2KJ09;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 24-MAR-2009, sequence version 2.
DT 27-MAR-2024, entry version 127.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 16 {ECO:0000255|HAMAP-Rule:MF_03062};
DE EC=3.4.19.12 {ECO:0000255|HAMAP-Rule:MF_03062};
DE AltName: Full=Deubiquitinating enzyme 16 {ECO:0000255|HAMAP-Rule:MF_03062};
DE AltName: Full=Ubiquitin thioesterase 16 {ECO:0000255|HAMAP-Rule:MF_03062};
DE AltName: Full=Ubiquitin-specific-processing protease 16 {ECO:0000255|HAMAP-Rule:MF_03062};
GN Name=Usp16;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-659 (ISOFORM 2).
RC TISSUE=Prostate;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-414, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: Specifically deubiquitinates 'Lys-120' of histone H2A
CC (H2AK119Ub), a specific tag for epigenetic transcriptional repression,
CC thereby acting as a coactivator. Deubiquitination of histone H2A is a
CC prerequisite for subsequent phosphorylation at 'Ser-11' of histone H3
CC (H3S10ph), and is required for chromosome segregation when cells enter
CC into mitosis. In resting B- and T-lymphocytes, phosphorylation by AURKB
CC leads to enhance its activity, thereby maintaining transcription in
CC resting lymphocytes. Regulates Hox gene expression via histone H2A
CC deubiquitination. Prefers nucleosomal substrates. Does not
CC deubiquitinate histone H2B. Also deubiquitinates non-histone proteins,
CC such as ribosomal protein RPS27A: deubiquitination of monoubiquitinated
CC RPS27A promotes maturation of the 40S ribosomal subunit.
CC {ECO:0000255|HAMAP-Rule:MF_03062}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC residue protein attached to proteins as an intracellular targeting
CC signal).; EC=3.4.19.12; Evidence={ECO:0000255|HAMAP-Rule:MF_03062};
CC -!- SUBUNIT: Homotetramer. Associates with late pre-40S ribosomes.
CC {ECO:0000255|HAMAP-Rule:MF_03062}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03062}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q2KJ09-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q2KJ09-2; Sequence=VSP_036725;
CC -!- DOMAIN: The UBP-type zinc finger binds 3 zinc ions that form a pair of
CC cross-braced ring fingers encapsulated within a third zinc finger in
CC the primary structure. It recognizes the C-terminal tail of free
CC ubiquitin. {ECO:0000255|HAMAP-Rule:MF_03062}.
CC -!- PTM: Phosphorylated at the onset of mitosis and dephosphorylated during
CC the metaphase/anaphase transition. Phosphorylation by AURKB enhances
CC the deubiquitinase activity. {ECO:0000255|HAMAP-Rule:MF_03062}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. USP16 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_03062}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAI12387.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
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DR EMBL; CH473989; EDM10641.1; -; Genomic_DNA.
DR EMBL; BC112386; AAI12387.1; ALT_SEQ; mRNA.
DR RefSeq; NP_001093971.1; NM_001100501.1. [Q2KJ09-2]
DR RefSeq; XP_006248077.1; XM_006248015.2. [Q2KJ09-1]
DR AlphaFoldDB; Q2KJ09; -.
DR STRING; 10116.ENSRNOP00000002173; -.
DR iPTMnet; Q2KJ09; -.
DR PhosphoSitePlus; Q2KJ09; -.
DR PaxDb; 10116-ENSRNOP00000002173; -.
DR Ensembl; ENSRNOT00000002173.7; ENSRNOP00000002173.5; ENSRNOG00000001598.7. [Q2KJ09-2]
DR GeneID; 288306; -.
DR KEGG; rno:288306; -.
DR UCSC; RGD:1307192; rat. [Q2KJ09-1]
DR AGR; RGD:1307192; -.
DR CTD; 10600; -.
DR RGD; 1307192; Usp16.
DR VEuPathDB; HostDB:ENSRNOG00000001598; -.
DR eggNOG; KOG1873; Eukaryota.
DR GeneTree; ENSGT00940000156013; -.
DR HOGENOM; CLU_007938_1_0_1; -.
DR InParanoid; Q2KJ09; -.
DR OMA; MAAGHYV; -.
DR OrthoDB; 227085at2759; -.
DR PhylomeDB; Q2KJ09; -.
DR TreeFam; TF326075; -.
DR PRO; PR:Q2KJ09; -.
DR Proteomes; UP000002494; Chromosome 11.
DR Proteomes; UP000234681; Chromosome 11.
DR Bgee; ENSRNOG00000001598; Expressed in testis and 19 other cell types or tissues.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; ISS:UniProtKB.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; ISS:UniProtKB.
DR GO; GO:0042393; F:histone binding; ISS:UniProtKB.
DR GO; GO:0140950; F:histone H2A deubiquitinase activity; ISS:UniProtKB.
DR GO; GO:0043024; F:ribosomal small subunit binding; ISS:UniProtKB.
DR GO; GO:0003713; F:transcription coactivator activity; ISS:UniProtKB.
DR GO; GO:0043130; F:ubiquitin binding; ISS:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0006974; P:DNA damage response; ISS:UniProtKB.
DR GO; GO:0016578; P:histone deubiquitination; IEA:UniProtKB-UniRule.
DR GO; GO:0140014; P:mitotic nuclear division; IEA:UniProtKB-UniRule.
DR GO; GO:0035520; P:monoubiquitinated protein deubiquitination; ISS:UniProtKB.
DR GO; GO:0045893; P:positive regulation of DNA-templated transcription; ISS:UniProtKB.
DR GO; GO:0090070; P:positive regulation of ribosome biogenesis; ISS:UniProtKB.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISS:UniProtKB.
DR GO; GO:0045901; P:positive regulation of translational elongation; ISS:UniProtKB.
DR GO; GO:0051289; P:protein homotetramerization; ISS:UniProtKB.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0051726; P:regulation of cell cycle; IEA:InterPro.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; ISS:UniProtKB.
DR CDD; cd02667; Peptidase_C19K; 1.
DR Gene3D; 3.90.70.10; Cysteine proteinases; 2.
DR Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1.
DR HAMAP; MF_03062; UBP16; 1.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR030849; UBP16.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR InterPro; IPR001607; Znf_UBP.
DR PANTHER; PTHR21646; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR PANTHER; PTHR21646:SF12; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 16; 1.
DR Pfam; PF00443; UCH; 1.
DR Pfam; PF02148; zf-UBP; 1.
DR SMART; SM00290; ZnF_UBP; 1.
DR SUPFAM; SSF54001; Cysteine proteinases; 1.
DR SUPFAM; SSF57850; RING/U-box; 1.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
DR PROSITE; PS50271; ZF_UBP; 1.
PE 1: Evidence at protein level;
KW Activator; Alternative splicing; Cell cycle; Cell division;
KW Chromatin regulator; Hydrolase; Isopeptide bond; Metal-binding; Mitosis;
KW Nucleus; Phosphoprotein; Protease; Reference proteome; Thiol protease;
KW Transcription; Transcription regulation; Ubl conjugation;
KW Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..826
FT /note="Ubiquitin carboxyl-terminal hydrolase 16"
FT /id="PRO_0000367504"
FT DOMAIN 195..825
FT /note="USP"
FT ZN_FING 22..141
FT /note="UBP-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 145..184
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 392..456
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 526..553
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 150..181
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 394..425
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 436..452
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 526..540
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 204
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03062"
FT ACT_SITE 760
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03062"
FT BINDING 24
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 26
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 48
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 51
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 73
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 76
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 81
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 89
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 93
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 102
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 115
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 118
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT MOD_RES 188
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y5T5"
FT MOD_RES 414
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT CROSSLNK 139
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q9Y5T5"
FT VAR_SEQ 149
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_036725"
SQ SEQUENCE 826 AA; 93762 MW; 2DCC40B25676BA5E CRC64;
MGKKRTKGKS VPEKASSEST EPMCRHLRKG LEQGNLKKAL VNVEWNICQD CKTDNKVKDK
SEEEAEDPSV WLCLKCGHQG CGRDSQEQHA LKHYTTPRSE PHYLVLSLDN WSVWCYKCDE
EIKYCSSNRL GQVVDYVRKQ AGRITSKPAE KNNGHIELEN KKLEKESKNE QEREKSESMA
KENIPLDSAS QITVKGLSNL GNTCFFNAVM QNLSQTPVLR ELLKEVKMSG TIVKIEPPDL
ALTEPLEVNL EPPGPLTLAM SQFLNEMQEN KKRIVTPKEL FSQVCKKATR FKGYQQQDSQ
ELLRYLLDGM RAEEHQRVSK GILKAFGNST EKLDEEVKNK VKDYEKKKAI PSFVDRIFGG
ELTSTIMCDD CRTVSLVHES FLDLSLPVLD DQSGKKNIND KNVKKTMEEE DKDSEEEKDD
SYMKTRSDVP SGTSKHTQKK AKKQAKKQAK NQRRQQKIQE RFLHFNEICT TNYTEDNDHE
AETALPGEGE VDTEFNRGSQ EELTQTELCA NQKDVNGQEE MIESAADERK CPEHPEVKSV
STESDLGSLT SAPECPRDLN GAFLEERTSG ELDITNGLKN LTLNAAVDPD EISIEILNDS
HSPALKVYEV MNEDPETAFC TLANREAFST DECSIQHCLY QFTRNEKLQD ANKLLCEVCT
RRQCNGPKAN IKGERKHVYT NAKKQMLVSL APPVLTLHLK RFQQAGFNLR KVNKHIKFPE
ILDLAPFCTL KCKNVAEEST RVLYSLYGVV EHSGTMRSGH YTAYAKERTA SCHLSNLVLH
GDIPQDCEME STKGQWFHIS DTHVQAVPIT KVLNSQAYLL FYERIL
//
