UBP16_XENTR
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 03-AUG-2022, entry version 101.
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
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.ENSXETP00000043701; -.
DR MEROPS; C19.021; -.
DR PaxDb; Q0VA64; -.
DR DNASU; 447956; -.
DR GeneID; 447956; -.
DR KEGG; xtr:447956; -.
DR CTD; 10600; -.
DR Xenbase; XB-GENE-1007164; usp16.
DR eggNOG; KOG1873; Eukaryota.
DR HOGENOM; CLU_007938_1_0_1; -.
DR InParanoid; Q0VA64; -.
DR OMA; DGMRTEE; -.
DR OrthoDB; 278083at2759; -.
DR PhylomeDB; Q0VA64; -.
DR TreeFam; TF326075; -.
DR Reactome; R-XTR-5689880; Ub-specific processing proteases.
DR Proteomes; UP000008143; Chromosome 2.
DR Proteomes; UP000790000; Unplaced.
DR Bgee; ENSXETG00000020255; Expressed in 2-cell stage embryo and 11 other 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; ISS:UniProtKB.
DR GO; GO:0000278; P:mitotic cell cycle; ISS:UniProtKB.
DR GO; GO:0140014; P:mitotic nuclear division; IEA:UniProtKB-UniRule.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0051289; P:protein homotetramerization; ISS:UniProtKB.
DR GO; GO:0051726; P:regulation of cell cycle; IEA:InterPro.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR Gene3D; 3.30.40.10; -; 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 Pfam; PF00443; UCH; 1.
DR Pfam; PF02148; zf-UBP; 1.
DR SUPFAM; SSF54001; SSF54001; 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
