UBP13_YEAST
ID UBP13_YEAST Reviewed; 747 AA.
AC P38187; D6VPT4;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 3.
DT 03-AUG-2022, entry version 174.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 13;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 13;
DE AltName: Full=Ubiquitin thioesterase 13;
DE AltName: Full=Ubiquitin-specific-processing protease 13;
GN Name=UBP13; OrderedLocusNames=YBL067C; ORFNames=YBL0621;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA Mewes H.-W., Kleine K.;
RT "Complete DNA sequence of yeast chromosome II.";
RL EMBO J. 13:5795-5809(1994).
RN [2]
RP GENOME REANNOTATION, AND SEQUENCE REVISION TO 180.
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 [3]
RP IDENTIFICATION OF FRAMESHIFT.
RX PubMed=12748633; DOI=10.1038/nature01644;
RA Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.;
RT "Sequencing and comparison of yeast species to identify genes and
RT regulatory elements.";
RL Nature 423:241-254(2003).
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-198, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [6]
RP IDENTIFICATION BY 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 [7]
RP IDENTIFICATION BY 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).
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 -!- MISCELLANEOUS: Present with 125 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA84887.1; Type=Frameshift; Evidence={ECO:0000305};
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; Z35828; CAA84887.1; ALT_FRAME; Genomic_DNA.
DR EMBL; BK006936; DAA07054.2; -; Genomic_DNA.
DR PIR; S45803; S45803.
DR RefSeq; NP_009486.3; NM_001178307.2.
DR AlphaFoldDB; P38187; -.
DR SMR; P38187; -.
DR BioGRID; 32633; 246.
DR DIP; DIP-795N; -.
DR IntAct; P38187; 2.
DR MINT; P38187; -.
DR STRING; 4932.YBL067C; -.
DR MEROPS; C19.100; -.
DR iPTMnet; P38187; -.
DR MaxQB; P38187; -.
DR PaxDb; P38187; -.
DR PRIDE; P38187; -.
DR EnsemblFungi; YBL067C_mRNA; YBL067C; YBL067C.
DR GeneID; 852212; -.
DR KEGG; sce:YBL067C; -.
DR SGD; S000000163; UBP13.
DR VEuPathDB; FungiDB:YBL067C; -.
DR eggNOG; KOG1864; Eukaryota.
DR GeneTree; ENSGT00940000176606; -.
DR HOGENOM; CLU_008279_12_1_1; -.
DR InParanoid; P38187; -.
DR OMA; DINDELC; -.
DR BioCyc; YEAST:G3O-28963-MON; -.
DR Reactome; R-SCE-110314; Recognition of DNA damage by PCNA-containing replication complex.
DR Reactome; R-SCE-5689880; Ub-specific processing proteases.
DR PRO; PR:P38187; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P38187; protein.
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; IDA:SGD.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IBA:GO_Central.
DR GO; GO:0010995; P:free ubiquitin chain depolymerization; IMP:SGD.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
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 Pfam; PF00443; UCH; 1.
DR SUPFAM; SSF54001; SSF54001; 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..747
FT /note="Ubiquitin carboxyl-terminal hydrolase 13"
FT /id="PRO_0000080598"
FT DOMAIN 140..668
FT /note="USP"
FT REGION 172..305
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 318..367
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 172..196
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 221..239
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 243..257
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 259..273
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 319..344
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 149
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 619
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT MOD_RES 198
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358"
FT CONFLICT 180
FT /note="Q -> H (in Ref. 1; CAA84887)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 747 AA; 83856 MW; 817DE2F89ED8EEA4 CRC64;
MIRRWLTISK SGKKKKAVND TITEEVEKVD FKPVNHDIND ELCYSESSDN PSSSLFVSNL
DTKETFLNED NNLQISSGLD YSSETCNQGS NYSQDGIFYI SNAKAINAYG GIITQGPEAP
ILAMKVSDSM PYGDGSNKVF GYENFGNTCY CNSVLQCLYN LSSLRENILQ FPKKSRESDQ
PRKKEMRGKK PRIFTEASFE KSIAGTNGHL PNPKPQSVDD GKPTPVNSVN SNTAGPSEKK
SKFFKSFSAK HVQDNNKKEG SPAILTTGKP SSRPQDAPPL IVETPNEPGA PSRLSFENVT
DRPPDVPRKI IVGRVLNYEN PSRGSSNSNN LDLKGESNSS LSTPLDKKDT RRSSSSSQIS
PEHRKKSALI RGPVLNIDHS LNGSDKATLY SSLRDIFECI TENTYLTGVV SPSSFVDVLK
RENVLFNTTM HQDAHEFFNF LLNELSEYIE RENKKIAASD INSDSEPSKS KNFISDLFQG
TLTNQIKCLT CDNITSRDEP FLDFPIEVQG DEETDIQEIL KSYHQREMLN GSNKFYCDEC
CGLQEAERLV GLKQLPDTLT LHLKRFKYSE KQNCNIKLFN NIHYPLTLNV CSSINSKVCQ
KYELAGIVVH MGGGPQHGHY VSLCKHEKFG WLLFDDETVE AVKEETVLEF TGESPNMATA
YVLFYKAMYS NAVEKNDREN MAKEQDDNID NLIKYDDWLR TCNSGQKKKE ELPIADDLDT
AIDDSFVSNT PIKSSKKKSR MFSFRKS
