ID   UBP3_MOUSE              Reviewed;         520 AA.
AC   Q91W36;
DT   09-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-DEC-2001, sequence version 1.
DT   27-MAR-2024, entry version 164.
DE   RecName: Full=Ubiquitin carboxyl-terminal hydrolase 3;
DE            EC=3.4.19.12;
DE   AltName: Full=Deubiquitinating enzyme 3;
DE   AltName: Full=Ubiquitin thioesterase 3;
DE   AltName: Full=Ubiquitin-specific-processing protease 3;
GN   Name=Usp3;
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC   Murinae; Mus; Mus.
OX   NCBI_TaxID=10090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=C57BL/6J; TISSUE=Forelimb;
RX   PubMed=16141072; DOI=10.1126/science.1112014;
RA   Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA   Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA   Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA   Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA   Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA   Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA   Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA   Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA   Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA   Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA   Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA   Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA   Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA   Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA   Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA   Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA   Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA   Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA   Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA   Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA   Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA   Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA   Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA   Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA   Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA   van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA   Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA   Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA   Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA   Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA   Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA   Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA   Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA   Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT   "The transcriptional landscape of the mammalian genome.";
RL   Science 309:1559-1563(2005).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Salivary gland;
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).
CC   -!- FUNCTION: Hydrolase that deubiquitinates monoubiquitinated target
CC       proteins such as histone H2A and H2B. Required for proper progression
CC       through S phase and subsequent mitotic entry. May regulate the DNA
CC       damage response (DDR) checkpoint through deubiquitination of H2A at DNA
CC       damage sites. Associates with the chromatin (By similarity).
CC       {ECO:0000250}.
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;
CC   -!- SUBUNIT: Interacts (via UBP-type domain) with H2A; the interaction is
CC       less efficient than with monoubiquitinated H2A. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus. Note=Localizes preferentially with
CC       monoubiquitinated H2A to chromatin.
CC   -!- DOMAIN: Both protease activity and an intact zinc finger are required
CC       for H2A monodeubiquitination.
CC   -!- SIMILARITY: Belongs to the peptidase C19 family. USP3 subfamily.
CC       {ECO:0000305}.
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DR   EMBL; AK031141; BAC27276.1; -; mRNA.
DR   EMBL; BC017156; AAH17156.1; -; mRNA.
DR   CCDS; CCDS23305.1; -.
DR   RefSeq; NP_659186.1; NM_144937.4.
DR   AlphaFoldDB; Q91W36; -.
DR   SMR; Q91W36; -.
DR   BioGRID; 231662; 1.
DR   STRING; 10090.ENSMUSP00000122199; -.
DR   MEROPS; C19.026; -.
DR   iPTMnet; Q91W36; -.
DR   PhosphoSitePlus; Q91W36; -.
DR   SwissPalm; Q91W36; -.
DR   EPD; Q91W36; -.
DR   MaxQB; Q91W36; -.
DR   PaxDb; 10090-ENSMUSP00000122199; -.
DR   PeptideAtlas; Q91W36; -.
DR   ProteomicsDB; 298462; -.
DR   Pumba; Q91W36; -.
DR   Antibodypedia; 13304; 342 antibodies from 33 providers.
DR   DNASU; 235441; -.
DR   Ensembl; ENSMUST00000127569.8; ENSMUSP00000122199.2; ENSMUSG00000032376.13.
DR   GeneID; 235441; -.
DR   KEGG; mmu:235441; -.
DR   UCSC; uc009qey.2; mouse.
DR   AGR; MGI:2152450; -.
DR   CTD; 9960; -.
DR   MGI; MGI:2152450; Usp3.
DR   VEuPathDB; HostDB:ENSMUSG00000032376; -.
DR   eggNOG; KOG1867; Eukaryota.
DR   GeneTree; ENSGT00940000157850; -.
DR   InParanoid; Q91W36; -.
DR   OMA; AGKRIYN; -.
DR   OrthoDB; 227085at2759; -.
DR   PhylomeDB; Q91W36; -.
DR   TreeFam; TF315281; -.
DR   Reactome; R-MMU-5689880; Ub-specific processing proteases.
DR   BioGRID-ORCS; 235441; 3 hits in 117 CRISPR screens.
DR   ChiTaRS; Usp3; mouse.
DR   PRO; PR:Q91W36; -.
DR   Proteomes; UP000000589; Chromosome 9.
DR   RNAct; Q91W36; Protein.
DR   Bgee; ENSMUSG00000032376; Expressed in undifferentiated genital tubercle and 253 other cell types or tissues.
DR   ExpressionAtlas; Q91W36; baseline and differential.
DR   GO; GO:0000785; C:chromatin; ISO:MGI.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0036464; C:cytoplasmic ribonucleoprotein granule; ISO:MGI.
DR   GO; GO:0090543; C:Flemming body; ISO:MGI.
DR   GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0004843; F:cysteine-type deubiquitinase activity; ISO:MGI.
DR   GO; GO:0042393; F:histone binding; ISO:MGI.
DR   GO; GO:0140950; F:histone H2A deubiquitinase activity; ISO:MGI.
DR   GO; GO:0140936; F:histone H2B deubiquitinase activity; ISO:MGI.
DR   GO; GO:1990841; F:promoter-specific chromatin binding; ISO:MGI.
DR   GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; ISO:MGI.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR   GO; GO:0006281; P:DNA repair; ISO:MGI.
DR   GO; GO:0140861; P:DNA repair-dependent chromatin remodeling; ISO:MGI.
DR   GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; ISO:MGI.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 1.
DR   Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1.
DR   InterPro; IPR038765; Papain-like_cys_pep_sf.
DR   InterPro; IPR001394; Peptidase_C19_UCH.
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:SF19; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 3; 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.
DR   Genevisible; Q91W36; MM.
PE   2: Evidence at transcript level;
KW   Acetylation; Cell cycle; Chromatin regulator; DNA damage; Hydrolase;
KW   Metal-binding; Nucleus; Protease; Reference proteome; Thiol protease;
KW   Ubl conjugation pathway; Zinc; Zinc-finger.
FT   CHAIN           1..520
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 3"
FT                   /id="PRO_0000080620"
FT   DOMAIN          159..511
FT                   /note="USP"
FT   ZN_FING         1..121
FT                   /note="UBP-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   ACT_SITE        168
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   ACT_SITE        471
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   BINDING         3
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         5
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         29
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         32
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         41
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         44
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         49
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         56
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         60
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         82
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         95
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         98
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   MOD_RES         1
FT                   /note="N-acetylmethionine"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y6I4"
SQ   SEQUENCE   520 AA;  58868 MW;  E160B48ECA47483D CRC64;
     MECPHLSSSV CIAPDSAKFP NGSPSSWCCS VCRSNKSPWV CLTCSSVHCG RYVNGHAKKH
     YEDAQIPLLN HKRSEKQEKA QHTVCMDCSS YSTYCYRCDD FVVNDTKLGL VQKVREHLQN
     LENSAFTADR HRKRKLLENS SLNSKLLKVN GSTTAICATG LRNLGNTCFM NAILQSLSNI
     EQFCCYFKEL PAVELRNGKT AGRRTYHTRS QGDSNVSLVE EFRKTLCALW QGSQTAFSPE
     SLFYVVWKIM PNFRGYQQQD AHEFMRYLLD HLHLELQGGF NGVSRSAILQ ENSTLSASNK
     CCINGASTVV TAIFGGILQN EVNCLICGTE SRKFDPFLDL SLDIPSQFRS KRSKNQENGP
     VCSLRDCLRS FTDLEELDET ELYMCHKCKK KQKSTKKFWI QKLPKALCLH LKRFHWTAYL
     RNKVDTYVQF PLRGLDMKCY LLEPENSGPD SCLYDLAAVV VHHGSGVGSG HYTAYAVHEG
     RWFHFNDSTV TVTDEETVGK AKAYILFYVE RQARAGAEKL
//