UBP12_YEAST
ID UBP12_YEAST Reviewed; 1254 AA.
AC P39538; D6VVZ5;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 165.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 12;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 12;
DE AltName: Full=Ubiquitin thioesterase 12;
DE AltName: Full=Ubiquitin-specific-processing protease 12;
GN Name=UBP12; OrderedLocusNames=YJL197W; ORFNames=J0340;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7754713; DOI=10.1002/yea.320100912;
RA Purnelle B., Coster F., Goffeau A.;
RT "The sequence of a 36 kb segment on the left arm of yeast chromosome X
RT identifies 24 open reading frames including NUC1, PRP21 (SPP91), CDC6,
RT CRY2, the gene for S24, a homologue to the aconitase gene ACO1 and two
RT homologues to chromosome III genes.";
RL Yeast 10:1235-1249(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-84, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1160, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [7]
RP FUNCTION IN DEUBIQUITINATION OF FZO1, AND INTERACTION WITH FZO1.
RX PubMed=23317502; DOI=10.1016/j.molcel.2012.12.003;
RA Anton F., Dittmar G., Langer T., Escobar-Henriques M.;
RT "Two deubiquitylases act on mitofusin and regulate mitochondrial fusion
RT along independent pathways.";
RL Mol. Cell 49:487-498(2013).
CC -!- FUNCTION: Ubiquitin carboxyl-terminal hydrolase that recognizes
CC ubiquitin chains that stabilize FZO1 and promote mitochondrial fusion.
CC UBP12 deubiquitylates FZO1 only after oligomerization.
CC {ECO:0000269|PubMed:23317502}.
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 with FZO1. {ECO:0000269|PubMed:23317502}.
CC -!- MISCELLANEOUS: Present with 7110 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR EMBL; X77688; CAA54762.1; -; Genomic_DNA.
DR EMBL; Z49472; CAA89492.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08611.1; -; Genomic_DNA.
DR PIR; S46636; S46636.
DR RefSeq; NP_012338.1; NM_001181630.1.
DR AlphaFoldDB; P39538; -.
DR BioGRID; 33567; 158.
DR DIP; DIP-6312N; -.
DR IntAct; P39538; 7.
DR MINT; P39538; -.
DR STRING; 4932.YJL197W; -.
DR MEROPS; C19.103; -.
DR iPTMnet; P39538; -.
DR MaxQB; P39538; -.
DR PaxDb; P39538; -.
DR PRIDE; P39538; -.
DR EnsemblFungi; YJL197W_mRNA; YJL197W; YJL197W.
DR GeneID; 853242; -.
DR KEGG; sce:YJL197W; -.
DR SGD; S000003733; UBP12.
DR VEuPathDB; FungiDB:YJL197W; -.
DR eggNOG; KOG1870; Eukaryota.
DR HOGENOM; CLU_001060_7_1_1; -.
DR InParanoid; P39538; -.
DR OMA; PYCEKPE; -.
DR BioCyc; YEAST:G3O-31628-MON; -.
DR Reactome; R-SCE-1358803; Downregulation of ERBB2:ERBB3 signaling.
DR Reactome; R-SCE-5656169; Termination of translesion DNA synthesis.
DR PRO; PR:P39538; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P39538; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0043596; C:nuclear replication fork; IDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IDA:SGD.
DR GO; GO:0010637; P:negative regulation of mitochondrial fusion; IMP:SGD.
DR GO; GO:0016579; P:protein deubiquitination; IMP:SGD.
DR GO; GO:2001020; P:regulation of response to DNA damage stimulus; IGI:SGD.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR Gene3D; 3.30.2230.10; -; 1.
DR InterPro; IPR035927; DUSP-like_sf.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR006615; Pept_C19_DUSP.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR Pfam; PF00443; UCH; 1.
DR SMART; SM00695; DUSP; 1.
DR SUPFAM; SSF143791; SSF143791; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS51283; DUSP; 1.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Phosphoprotein; Protease; Reference proteome; Thiol protease;
KW Ubl conjugation pathway.
FT CHAIN 1..1254
FT /note="Ubiquitin carboxyl-terminal hydrolase 12"
FT /id="PRO_0000080597"
FT DOMAIN 97..199
FT /note="DUSP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00613"
FT DOMAIN 364..1110
FT /note="USP"
FT REGION 827..893
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1188..1207
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 869..883
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 373
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 1068
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT MOD_RES 84
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 1160
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
SQ SEQUENCE 1254 AA; 143192 MW; 349AFA4C4CEE0EA5 CRC64;
MGSSDVSSRE CSLVYNEDPD FTDGTTPCDR LGVDLMNVLD DKDEIKQESV PVSDREIEDT
ESDASAVSSF ASANELIAEP HAASETNLGT NGQDGRNVLE QQRDVVARLI EENKETQKEG
DKVCIVPKVW YDKFFDPDVT DPEDIGPINT RMICRDFENF VLEDYNRCPY LSIAEPVFNF
LSEIYGMTSG SYPVVTNLVI NQTTGELETE YNKWFFRLHY LTEKQDGRKR RHGQDDSIMY
LSMSALNLVR DLVEKSMNLF FEKADHLDVN AVDFKIWFVS EGSDIATDSN VSTFLNSSYE
ITPLQFLELP IKKLLIPDMF ENRLDKITSN PSDLVIEIKP IEGNHHWPSN YFAYNKLEPA
SGTTGLVNLG NTCYMNSALQ CLVHIPQLRD YFLYDGYEDE INEENPLGYH GYVARAFSDL
VQKLFQNRMS IMQRNAAFPP SMFKSTIGHF NSMFSGYMQQ DSQEFLAFLL DSLHEDLNRI
IKKEYTEKPS LSPGDDVNDW NVVKKLADDT WEMHLKRNCS VITDLFVGMY KSTLYCPECQ
NVSITFDPYN DVTLPLPVDT VWDKTIKIFP MNSPPLLLEV ELSKSSTYMD LKNYVGKMSG
LDPNTLFGCE IFSNQIYVNY ESTESNAQFL TLQELIKPAD DVIFYELPVT NDNEVIVPVL
NTRIEKGYKN AMLFGVPFFI TLKEDELNNP GAIRMKLQNR FVHLSGGYIP FPEPVGNRTD
FADAFPLLVE KYPDVEFEQY KDILQYTSIK VTDKDKSFFS IKILSVEKEQ QFASNNRTGP
NFWTPISQLN LDKATDIDDK LEDVVKDIYN YSSLVDCAEG VLMQVDDEGD TEGSEAKNFS
KPFQSGDDEE NKETVTNNEN VNNTNDRDED MELTDDVEED ASTEPELTDK PEALDKIKDS
LTSTPFAILS MNDIIVCEWS ELGSNEAFSD DKIYNWENPA TLPNKELENA KLERSNAKER
TITLDDCLQL FSKPEILGLT DSWYCPTCKE HRQATKQIQL WNTPDILLIH LKRFESQRSF
SDKIDATVNF PITDLDLSRY VVYKDDPRGL IYDLYAVDNH YGGLGGGHYT AYVKNFADNK
WYYFDDSRVT ETAPENSIAG SAYLLFYIRR HKDGNGLGSS KLQEIIQKSR HGYDERIKKI
YDEQMKLYEF NKTDEEEDVS DDMIECNEDV QAPEYSNRSL EVGHIETQDC NDEDDNDDGE
RTNSGRRKLR LLKKVYKNNS GLGSSSTSEI SEGCPENEVA DLNLKNGVTL ESPE
