UBP16_DANRE
ID UBP16_DANRE Reviewed; 815 AA.
AC A8HAL1;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 13-NOV-2007, sequence version 1.
DT 03-AUG-2022, entry version 108.
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; ORFNames=si:dkey-121n8.2;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
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; CR854897; CAP09451.1; -; Genomic_DNA.
DR RefSeq; NP_001139569.1; NM_001146097.1.
DR RefSeq; XP_009290187.1; XM_009291912.2.
DR AlphaFoldDB; A8HAL1; -.
DR STRING; 7955.ENSDARP00000080080; -.
DR PaxDb; A8HAL1; -.
DR PeptideAtlas; A8HAL1; -.
DR Ensembl; ENSDART00000085645; ENSDARP00000080080; ENSDARG00000060633.
DR Ensembl; ENSDART00000192112; ENSDARP00000144791; ENSDARG00000090935.
DR GeneID; 569700; -.
DR KEGG; dre:569700; -.
DR CTD; 10600; -.
DR ZFIN; ZDB-GENE-030131-4153; usp16.
DR eggNOG; KOG1873; Eukaryota.
DR GeneTree; ENSGT00390000005285; -.
DR GeneTree; ENSGT00940000156013; -.
DR HOGENOM; CLU_007938_1_0_1; -.
DR InParanoid; A8HAL1; -.
DR OMA; DGMRTEE; -.
DR OrthoDB; 278083at2759; -.
DR PhylomeDB; A8HAL1; -.
DR TreeFam; TF326075; -.
DR Reactome; R-DRE-5689880; Ub-specific processing proteases.
DR Reactome; R-DRE-5696395; Formation of Incision Complex in GG-NER.
DR PRO; PR:A8HAL1; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 15.
DR Bgee; ENSDARG00000060633; Expressed in blastula and 22 other tissues.
DR ExpressionAtlas; A8HAL1; baseline.
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:0006974; P:cellular response to DNA damage stimulus; ISS:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0016578; P:histone deubiquitination; ISS:UniProtKB.
DR GO; GO:0070537; P:histone H2A K63-linked 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:0045901; P:positive regulation of translational elongation; 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 SMART; SM00290; ZnF_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 3: Inferred from homology;
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..815
FT /note="Ubiquitin carboxyl-terminal hydrolase 16"
FT /id="PRO_0000367505"
FT DOMAIN 208..814
FT /note="USP"
FT ZN_FING 22..143
FT /note="UBP-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT REGION 1..27
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 148..200
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 411..510
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 13..27
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 170..189
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 411..426
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 427..450
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 451..466
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 467..510
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 217
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03062"
FT ACT_SITE 752
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 76
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="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 84
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="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 95
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 104
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 117
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 120
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
SQ SEQUENCE 815 AA; 90450 MW; 50CF71DC500EE191 CRC64;
MGKKKVKDRS AGTDSSSETA GPSCTHIRKG TENSVLKKAC LNEHWSSCQD CEQDKPEEKQ
ILEDQTDGES PAVWMCLKCG HRGCGRSGNQ HAIKHYETPR SEPHCLVLSL DVWSVWCYIC
DDEVQYSSTG QLAQLITNIR KQVLTAPDKR NASKKSWKED ISVMNSAEQT QDEEKGKKGK
QKSSSKQEDS PKSHQSAAAG SSAVVSVRGL SNLGNTCFFN AVVQSLSQTQ YLRELLKQIA
EEKSSFSITP ALSSELDPLQ IQLERPGSLT LAMCQLMNEI QETKKGVVTP KELFTQVCKK
APRFKGFQQQ DSQELLRYLL DGMRAEEAKR VNSGILEALK SSGKNFEAEQ TKKIVKEYEK
DGAPKNFVDR VFGGAMSSTV MCKECKTVSL VTEMFLDLSL PVADEAYRKK NQKKAVQHRH
SVSDDGDQDT SSLANGNEDM PTGTGSKYQQ KKAKKQAKKQ AKNQRRQQKQ GGKVTLDAIT
NQSSTDPADS SMQTQTVSVN GSADAQPADT NQEDLSLEKH NEDQDDEEPE QEQAASVNNR
FTALSEDQTT EDIAEQVNED EDEIEQNCAE EEELVEELNT MSLTTPSEGD VENGEDTLED
VKEYTVVNRD PELAFRALAS RTAPVKQECS VESCLYQFTE VEHLTENNRL MCVTCTKQQP
GYKDGCKKAV YRDALKQMLI SDPPVVLTLH LKRFQQVAYS VCKVNRHVQF PQILDLAPFC
SLNCTGVKEG ETQVLYSLYG IVEHSGTMRS GHYTAYVKSR PSTHNCVQNG TAAASGDAEA
SKGSWFHISD SSVHPVPEAK VQSSQAYLLF YEKIS
