ID   UBP16_XENTR             Reviewed;         864 AA.
AC   Q0VA64; F7BZB4;
DT   24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT   11-DEC-2013, sequence version 2.
DT   27-MAR-2024, entry version 109.
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   Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC   Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana.
OX   NCBI_TaxID=8364;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=20431018; DOI=10.1126/science.1183670;
RA   Hellsten U., Harland R.M., Gilchrist M.J., Hendrix D., Jurka J.,
RA   Kapitonov V., Ovcharenko I., Putnam N.H., Shu S., Taher L., Blitz I.L.,
RA   Blumberg B., Dichmann D.S., Dubchak I., Amaya E., Detter J.C., Fletcher R.,
RA   Gerhard D.S., Goodstein D., Graves T., Grigoriev I.V., Grimwood J.,
RA   Kawashima T., Lindquist E., Lucas S.M., Mead P.E., Mitros T., Ogino H.,
RA   Ohta Y., Poliakov A.V., Pollet N., Robert J., Salamov A., Sater A.K.,
RA   Schmutz J., Terry A., Vize P.D., Warren W.C., Wells D., Wills A.,
RA   Wilson R.K., Zimmerman L.B., Zorn A.M., Grainger R., Grammer T.,
RA   Khokha M.K., Richardson P.M., Rokhsar D.S.;
RT   "The genome of the Western clawed frog Xenopus tropicalis.";
RL   Science 328:633-636(2010).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Testis;
RG   NIH - Xenopus Gene Collection (XGC) project;
RL   Submitted (AUG-2006) to the EMBL/GenBank/DDBJ databases.
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. Regulates Hox gene expression via histone H2A
CC       deubiquitination. Prefers nucleosomal substrates. Does not
CC       deubiquitinate histone H2B. {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. {ECO:0000255|HAMAP-Rule:MF_03062}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03062}.
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   -!- SIMILARITY: Belongs to the peptidase C19 family. USP16 subfamily.
CC       {ECO:0000255|HAMAP-Rule:MF_03062}.
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DR   EMBL; AAMC01089338; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AAMC01089339; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; BC121230; AAI21231.1; -; mRNA.
DR   RefSeq; NP_001072158.1; NM_001078690.1.
DR   AlphaFoldDB; Q0VA64; -.
DR   STRING; 8364.ENSXETP00000034348; -.
DR   MEROPS; C19.021; -.
DR   PaxDb; 8364-ENSXETP00000043701; -.
DR   DNASU; 447956; -.
DR   Ensembl; ENSXETT00000043701; ENSXETP00000043701; ENSXETG00000020255.
DR   GeneID; 447956; -.
DR   KEGG; xtr:447956; -.
DR   AGR; Xenbase:XB-GENE-1007164; -.
DR   CTD; 10600; -.
DR   Xenbase; XB-GENE-1007164; usp16.
DR   eggNOG; KOG1873; Eukaryota.
DR   HOGENOM; CLU_007938_1_0_1; -.
DR   InParanoid; Q0VA64; -.
DR   OrthoDB; 227085at2759; -.
DR   PhylomeDB; Q0VA64; -.
DR   TreeFam; TF326075; -.
DR   Reactome; R-XTR-5689880; Ub-specific processing proteases.
DR   Proteomes; UP000008143; Chromosome 2.
DR   Bgee; ENSXETG00000020255; Expressed in 2-cell stage embryo and 11 other cell types or tissues.
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: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:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR   GO; GO:0016578; P:histone deubiquitination; IEA:UniProtKB-UniRule.
DR   GO; GO:0140014; P:mitotic nuclear division; IEA:UniProtKB-UniRule.
DR   GO; GO:0045893; P:positive regulation of DNA-templated transcription; 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   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   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   2: Evidence at transcript level;
KW   Activator; Cell cycle; Cell division; Chromatin regulator; Hydrolase;
KW   Metal-binding; Mitosis; Nucleus; Protease; Reference proteome;
KW   Thiol protease; Transcription; Transcription regulation;
KW   Ubl conjugation pathway; Zinc; Zinc-finger.
FT   CHAIN           1..864
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 16"
FT                   /id="PRO_0000367507"
FT   DOMAIN          196..863
FT                   /note="USP"
FT   ZN_FING         19..139
FT                   /note="UBP-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   REGION          162..196
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          397..497
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        162..179
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        180..196
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        402..431
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        432..450
FT                   /note="Basic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        205
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03062"
FT   ACT_SITE        798
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03062"
FT   BINDING         21
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         23
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         45
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
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         71
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         74
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         79
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         87
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         91
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         100
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         113
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         116
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   CONFLICT        106
FT                   /note="V -> M (in Ref. 2; AAI21231)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        405
FT                   /note="A -> V (in Ref. 2; AAI21231)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        452
FT                   /note="L -> Q (in Ref. 2; AAI21231)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        495
FT                   /note="I -> T (in Ref. 2; AAI21231)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        515
FT                   /note="T -> A (in Ref. 2; AAI21231)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        529
FT                   /note="L -> I (in Ref. 2; AAI21231)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        548
FT                   /note="R -> G (in Ref. 2; AAI21231)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        572
FT                   /note="V -> G (in Ref. 2; AAI21231)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        714
FT                   /note="T -> K (in Ref. 2; AAI21231)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   864 AA;  96666 MW;  8600F3A72FCAF9C7 CRC64;
     MVKKRGKNLP AQDSLDAEPV CKHLRKALDE GSVKKALVNV EWTVCQECQA DNKEKNNSDD
     ELVEDPSVWL CLKCGHRGCG RNSASQHALN HYNTPRSEPH CLVLSVDMWS AWCYLCDNEV
     PYNRSSRLGQ LVDYLQRKAK AKSKSTDSAA LDEEVKAEIV AENEVKIEDQ EEKPKGQAKW
     DKASSTQNNS TEPTVKGLSN LGNTCFFNAV MQNLSQTPAV RELLNEAKTL KKPVTVPLPD
     SSSPTNVEVH LEQQPGPLTL AMWQFLTEMQ ETKKGVVTPK EVFSQVCKKA IRFKGYQQQD
     SQELLRYLLD GMRGEEIQRV SLAMSKSLQN TLDEEEIKKI VKDSEKRRTI PNFVDHLFGG
     ELTSTIMCEE CHTVSLVHEP FLDLSLPVLD DVIVKKNSQK SSAPAPERKE EEENDDGYIK
     ERDEASPGAS KHLQKKAKKA AKKQAKNQRR QLKMQGKTVL LTDVAKQECS EDEEEIAPNN
     TESEANTRPD DEVPIADGLN TMKSDLSALE NGSETIESAM ERVTEDTDLD TSGHNTESVE
     MNAMELVRNM ENNNNNNTDV NKTLERTEGS GVDSMEATAA VDNGNADTVC VDDTEAANGL
     LDCSAASMDN ELTNSLNRLK LSSDIEPTQV EIEILPDQQQ PHTQIYEVIN EDPKTAFSTL
     SERKDLPLDG YSVLSCLYQF THKETLTGNN KLLCNVCTRK QASRLNNSNK GEKTFVYTNA
     KKQMLVSDPS PILTLHLKRF QQNGFNLRKI NRHIKFPEVL DLAPFCTSKC KNIPAGESRL
     LYSLYGVIEH SGSMRSGHYT AFVKLRRPNQ QLCEMVLKGV IPEVSGSEPG QGSWYHISDS
     HVQAVSLSRV LSSQAYLLFY ERML
//