ID   UBP40_MOUSE             Reviewed;        1235 AA.
AC   Q8BWR4; Q08EB7; Q148V0; Q3TLV1; Q3TMN0; Q3V1R4; Q5EBN6;
DT   10-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT   09-JAN-2007, sequence version 2.
DT   24-JAN-2024, entry version 153.
DE   RecName: Full=Ubiquitin carboxyl-terminal hydrolase 40;
DE            EC=3.4.19.12;
DE   AltName: Full=Deubiquitinating enzyme 40;
DE   AltName: Full=Ubiquitin thioesterase 40;
DE   AltName: Full=Ubiquitin-specific-processing protease 40;
GN   Name=Usp40;
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] (ISOFORMS 2 AND 4), AND NUCLEOTIDE
RP   SEQUENCE [LARGE SCALE MRNA] OF 1-1140 AND 967-1235 (ISOFORM 1).
RC   STRAIN=C57BL/6J; TISSUE=Embryo, Liver, Lung, and Mammary gland;
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] (ISOFORMS 1 AND 3).
RC   STRAIN=C57BL/6J; TISSUE=Eye;
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   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Liver;
RX   PubMed=17242355; DOI=10.1073/pnas.0609836104;
RA   Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
RT   "Large-scale phosphorylation analysis of mouse liver.";
RL   Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
RN   [4]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Brown adipose tissue, Pancreas, and Testis;
RX   PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA   Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA   Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT   "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL   Cell 143:1174-1189(2010).
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   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=4;
CC       Name=1;
CC         IsoId=Q8BWR4-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q8BWR4-2; Sequence=VSP_022174;
CC       Name=3;
CC         IsoId=Q8BWR4-3; Sequence=VSP_022171;
CC       Name=4;
CC         IsoId=Q8BWR4-4; Sequence=VSP_022172, VSP_022173;
CC   -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR   EMBL; AK050239; BAC34140.1; -; mRNA.
DR   EMBL; AK132295; BAE21086.1; -; mRNA.
DR   EMBL; AK165849; BAE38411.1; -; mRNA.
DR   EMBL; AK166303; BAE38691.1; -; mRNA.
DR   EMBL; BC089376; AAH89376.1; -; mRNA.
DR   EMBL; BC117957; AAI17958.1; -; mRNA.
DR   EMBL; BC117958; AAI17959.1; -; mRNA.
DR   CCDS; CCDS15137.1; -. [Q8BWR4-2]
DR   CCDS; CCDS78645.1; -. [Q8BWR4-1]
DR   RefSeq; NP_001028463.1; NM_001033291.2. [Q8BWR4-2]
DR   RefSeq; NP_001185502.1; NM_001198573.1. [Q8BWR4-1]
DR   AlphaFoldDB; Q8BWR4; -.
DR   BioGRID; 230617; 4.
DR   STRING; 10090.ENSMUSP00000140107; -.
DR   MEROPS; C19.069; -.
DR   iPTMnet; Q8BWR4; -.
DR   PhosphoSitePlus; Q8BWR4; -.
DR   EPD; Q8BWR4; -.
DR   MaxQB; Q8BWR4; -.
DR   PaxDb; 10090-ENSMUSP00000038533; -.
DR   PeptideAtlas; Q8BWR4; -.
DR   ProteomicsDB; 297700; -. [Q8BWR4-1]
DR   ProteomicsDB; 297701; -. [Q8BWR4-2]
DR   ProteomicsDB; 297702; -. [Q8BWR4-3]
DR   ProteomicsDB; 297703; -. [Q8BWR4-4]
DR   Pumba; Q8BWR4; -.
DR   Antibodypedia; 965; 154 antibodies from 23 providers.
DR   DNASU; 227334; -.
DR   Ensembl; ENSMUST00000040783.11; ENSMUSP00000038533.5; ENSMUSG00000005501.15. [Q8BWR4-2]
DR   Ensembl; ENSMUST00000187758.7; ENSMUSP00000140107.2; ENSMUSG00000005501.15. [Q8BWR4-1]
DR   GeneID; 227334; -.
DR   KEGG; mmu:227334; -.
DR   UCSC; uc007bxw.1; mouse. [Q8BWR4-2]
DR   UCSC; uc007bxx.1; mouse. [Q8BWR4-1]
DR   UCSC; uc007bxz.1; mouse. [Q8BWR4-4]
DR   AGR; MGI:2443184; -.
DR   CTD; 55230; -.
DR   MGI; MGI:2443184; Usp40.
DR   VEuPathDB; HostDB:ENSMUSG00000005501; -.
DR   eggNOG; KOG1863; Eukaryota.
DR   GeneTree; ENSGT00940000157267; -.
DR   HOGENOM; CLU_009719_0_0_1; -.
DR   InParanoid; Q8BWR4; -.
DR   OMA; PEGSHWF; -.
DR   OrthoDB; 51419at2759; -.
DR   PhylomeDB; Q8BWR4; -.
DR   TreeFam; TF106281; -.
DR   BioGRID-ORCS; 227334; 1 hit in 78 CRISPR screens.
DR   ChiTaRS; Usp40; mouse.
DR   PRO; PR:Q8BWR4; -.
DR   Proteomes; UP000000589; Chromosome 1.
DR   RNAct; Q8BWR4; Protein.
DR   Bgee; ENSMUSG00000005501; Expressed in humerus cartilage element and 211 other cell types or tissues.
DR   ExpressionAtlas; Q8BWR4; baseline and differential.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0004843; F:cysteine-type deubiquitinase activity; IBA:GO_Central.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   CDD; cd02659; peptidase_C19C; 1.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 2.
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   PANTHER; PTHR24006; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR   PANTHER; PTHR24006:SF842; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 40; 1.
DR   Pfam; PF00443; UCH; 1.
DR   SUPFAM; SSF54001; Cysteine proteinases; 1.
DR   PROSITE; PS00972; USP_1; 1.
DR   PROSITE; PS00973; USP_2; 1.
DR   PROSITE; PS50235; USP_3; 1.
DR   Genevisible; Q8BWR4; MM.
PE   1: Evidence at protein level;
KW   Alternative splicing; Hydrolase; Protease; Reference proteome;
KW   Thiol protease; Ubl conjugation pathway.
FT   CHAIN           1..1235
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 40"
FT                   /id="PRO_0000080671"
FT   DOMAIN          41..482
FT                   /note="USP"
FT   ACT_SITE        50
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   ACT_SITE        305
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   VAR_SEQ         1..128
FT                   /note="Missing (in isoform 3)"
FT                   /evidence="ECO:0000303|PubMed:15489334"
FT                   /id="VSP_022171"
FT   VAR_SEQ         490..501
FT                   /note="ARANPRYRVPCH -> GMENKKCSALLC (in isoform 4)"
FT                   /evidence="ECO:0000303|PubMed:16141072"
FT                   /id="VSP_022172"
FT   VAR_SEQ         502..1235
FT                   /note="Missing (in isoform 4)"
FT                   /evidence="ECO:0000303|PubMed:16141072"
FT                   /id="VSP_022173"
FT   VAR_SEQ         795..883
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:16141072"
FT                   /id="VSP_022174"
FT   CONFLICT        201
FT                   /note="E -> A (in Ref. 1; BAE38691)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        943
FT                   /note="A -> E (in Ref. 2; AAH89376)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        1134
FT                   /note="S -> N (in Ref. 1; BAE38411)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        1142
FT                   /note="R -> K (in Ref. 2; AAH89376)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1235 AA;  139952 MW;  CBAC7A6A0CACE03C CRC64;
     MFGNLFEEDY SSVSSSQYGR GKKLKTKGLE PPAPREFTNL SGIRNQGGTC YLSSLLQTLH
     FTPEFREALF SLGPEELGSL EDKDKPDAKV RIIPLQLQRL FAQLLLLDQE AASTIDLTDS
     FGWTNDEEMR QHDVQELNRI LFSALETSLV GTSGHDLIHR LYHGTIVNQI VCKECKNISE
     RQEDFLDLTV AVKNVSGLED ELCNMYVEEE IFDYDNLYHC GTCDRLVKAA KSAKLRKLPP
     FLTISLLRFN FDFVKCERYK DTSCYTFPLR INLKPFCEQS ELDDMEYMYD LFSVIIHKGG
     CYGGHYHVYI KDVDHLGNWQ CQEEISDTNV NVKAPQSEEE ANDPLVVLKT ILLQEEANQI
     PVDQLGQKLL KKTGISWNKK YRKQHGPLRK FLQLHPQIFL LSTDESTVSL LRNHLTQAPS
     DLQSCEQILH TLASESPGLN DDTSCPHWFD INDSKVHPIR EKDITQQFQG KESAYMLFYR
     KATLQRPPEA RANPRYRVPC HLLKEMDAAN ILLQMRRAEC DSANSTFELH LHLGPHYRFF
     NGALHPAVSE TESVWDLTFD KRKTLGDLRQ SIFQLLECWE GDMVLSVAKR VPAGLHVYHT
     LDGDDLTLCE AEVADGEDIF VWNGVEVGGV QIQTGFDCEP LLLNILHLEL SGEGSKCEQL
     VESPHVFPAN AEVGAVFTAL GTPAGAILMN SVESADGECW TAVPKEDMKK TFREQGLRNG
     SLILVQDSDS DNNSLLPKQG RWTNSMNELN WLQVKNFCQS ESEEKQVQIA VTMHTVVFDI
     RIKAIKELKL MKELAENSCL RPIDRNGKLL CPVPDSSTLE EAEVKMGSSV GLCLGKAPTS
     SQLFLFFALG TDIHPGAEMD IIVEETLSVR DCLKIMLEKS GQQGEIWHLR KMDWCYEAGE
     PLCEEDATLK ELMIRSGDTL LLTEGKLPPP GHLKMPIWWY QPARLSGHCE SRDHLNCAFS
     QDSTWRAAPT QGAPGPEPAE VSLLYLGDME ISEEATLVEL KSQALALPSV SKLAVQSTAL
     LRVWTVESKR PSRLLRTNWR QLKEYRLGRR AELCLELLQK EEDLGPRDVL LRTQLRIPGE
     RAYSLATDLI WDTTRGWTAG SLRQRVADFY SLPVEKIEIA KYFPEKFEWL PISSWNQQVA
     KRKKKKNQDT LQGGPYYLKD GDTIGIKNLL FDDNDDFSTI RDDIGKENQK RLALEKKKSR
     EVHRAQSSDL FSNAGVPARF RGPEASLSIH VASFR
//