ULP1_YEAST
ID ULP1_YEAST Reviewed; 621 AA.
AC Q02724; D6W3Z2;
DT 18-OCT-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 184.
DE RecName: Full=Ubiquitin-like-specific protease 1;
DE EC=3.4.22.68 {ECO:0000269|PubMed:10882122};
GN Name=ULP1; OrderedLocusNames=YPL020C; ORFNames=LPB11C;
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=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [2]
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 [3]
RP FUNCTION.
RX PubMed=10094048; DOI=10.1038/18457;
RA Li S.J., Hochstrasser M.;
RT "A new protease required for cell-cycle progression in yeast.";
RL Nature 398:246-251(1999).
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-21; SER-25 AND THR-179, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-179 AND SER-264, AND
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 ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 401-621 IN COMPLEX WITH SMT3, AND
RP CATALYTIC ACTIVITY.
RX PubMed=10882122; DOI=10.1016/s1097-2765(00)80326-3;
RA Mossessova E., Lima C.D.;
RT "Ulp1-SUMO crystal structure and genetic analysis reveal conserved
RT interactions and a regulatory element essential for cell growth in yeast.";
RL Mol. Cell 5:865-876(2000).
CC -!- FUNCTION: Protease that catalyzes two essential functions in the SUMO
CC pathway: processing of full-length SMT3 to its mature form and
CC deconjugation of SMT3 from targeted proteins. Has an essential role in
CC the G2/M phase of the cell cycle. {ECO:0000269|PubMed:10094048}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of the alpha-linked peptide bond in the sequence
CC Gly-Gly-|-Ala-Thr-Tyr at the C-terminal end of the small ubiquitin-
CC like modifier (SUMO) propeptide, Smt3, leading to the mature form of
CC the protein. A second reaction involves the cleavage of an epsilon-
CC linked peptide bond between the C-terminal glycine of the mature SUMO
CC and the lysine epsilon-amino group of the target protein.;
CC EC=3.4.22.68; Evidence={ECO:0000269|PubMed:10882122};
CC -!- MISCELLANEOUS: Present with 377 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the peptidase C48 family. {ECO:0000305}.
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DR EMBL; U36624; AAB68167.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11408.1; -; Genomic_DNA.
DR PIR; S63462; S63462.
DR RefSeq; NP_015305.1; NM_001183834.1.
DR PDB; 1EUV; X-ray; 1.60 A; A=403-621.
DR PDB; 2HKP; X-ray; 2.10 A; A=403-621.
DR PDB; 2HL8; X-ray; 2.00 A; A=403-621.
DR PDB; 2HL9; X-ray; 1.90 A; A=403-621.
DR PDB; 5H2V; X-ray; 2.80 A; B=1-150.
DR PDB; 5H2W; X-ray; 2.50 A; B/D=150-340.
DR PDB; 5H2X; X-ray; 2.20 A; B=150-172.
DR PDBsum; 1EUV; -.
DR PDBsum; 2HKP; -.
DR PDBsum; 2HL8; -.
DR PDBsum; 2HL9; -.
DR PDBsum; 5H2V; -.
DR PDBsum; 5H2W; -.
DR PDBsum; 5H2X; -.
DR AlphaFoldDB; Q02724; -.
DR SMR; Q02724; -.
DR BioGRID; 36157; 463.
DR DIP; DIP-4041N; -.
DR IntAct; Q02724; 13.
DR MINT; Q02724; -.
DR STRING; 4932.YPL020C; -.
DR MEROPS; C48.001; -.
DR iPTMnet; Q02724; -.
DR MaxQB; Q02724; -.
DR PaxDb; Q02724; -.
DR PRIDE; Q02724; -.
DR TopDownProteomics; Q02724; -.
DR EnsemblFungi; YPL020C_mRNA; YPL020C; YPL020C.
DR GeneID; 856087; -.
DR KEGG; sce:YPL020C; -.
DR SGD; S000005941; ULP1.
DR VEuPathDB; FungiDB:YPL020C; -.
DR eggNOG; KOG0778; Eukaryota.
DR GeneTree; ENSGT00940000167730; -.
DR HOGENOM; CLU_021050_0_0_1; -.
DR InParanoid; Q02724; -.
DR OMA; CGIYVCM; -.
DR BioCyc; YEAST:G3O-33938-MON; -.
DR BRENDA; 3.4.22.68; 984.
DR Reactome; R-SCE-3065679; SUMO is proteolytically processed.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR EvolutionaryTrace; Q02724; -.
DR PRO; PR:Q02724; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q02724; protein.
DR GO; GO:0005635; C:nuclear envelope; IDA:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0008234; F:cysteine-type peptidase activity; IDA:SGD.
DR GO; GO:0016929; F:deSUMOylase activity; IDA:SGD.
DR GO; GO:0044877; F:protein-containing complex binding; IDA:SGD.
DR GO; GO:0000086; P:G2/M transition of mitotic cell cycle; IMP:SGD.
DR GO; GO:0016926; P:protein desumoylation; IDA:SGD.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR003653; Peptidase_C48_C.
DR Pfam; PF02902; Peptidase_C48; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS50600; ULP_PROTEASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Hydrolase; Phosphoprotein; Protease;
KW Reference proteome; Thiol protease; Ubl conjugation pathway.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..621
FT /note="Ubiquitin-like-specific protease 1"
FT /id="PRO_0000101731"
FT REGION 116..150
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 169..196
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 432..621
FT /note="Protease"
FT /evidence="ECO:0000269|PubMed:10882122"
FT COMPBIAS 120..146
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 176..196
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 514
FT /evidence="ECO:0000269|PubMed:10882122"
FT ACT_SITE 531
FT /evidence="ECO:0000269|PubMed:10882122"
FT ACT_SITE 580
FT /evidence="ECO:0000269|PubMed:10882122"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 21
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950"
FT MOD_RES 25
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950"
FT MOD_RES 179
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956"
FT MOD_RES 264
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT HELIX 409..419
FT /evidence="ECO:0007829|PDB:1EUV"
FT STRAND 426..430
FT /evidence="ECO:0007829|PDB:1EUV"
FT STRAND 433..436
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 437..440
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 441..443
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 451..464
FT /evidence="ECO:0007829|PDB:1EUV"
FT STRAND 468..470
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 474..482
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 484..486
FT /evidence="ECO:0007829|PDB:1EUV"
FT TURN 487..491
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 492..494
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 498..500
FT /evidence="ECO:0007829|PDB:1EUV"
FT STRAND 502..510
FT /evidence="ECO:0007829|PDB:1EUV"
FT TURN 511..513
FT /evidence="ECO:0007829|PDB:1EUV"
FT STRAND 514..521
FT /evidence="ECO:0007829|PDB:1EUV"
FT TURN 522..525
FT /evidence="ECO:0007829|PDB:1EUV"
FT STRAND 526..530
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 539..555
FT /evidence="ECO:0007829|PDB:1EUV"
FT STRAND 558..560
FT /evidence="ECO:0007829|PDB:1EUV"
FT STRAND 565..569
FT /evidence="ECO:0007829|PDB:1EUV"
FT STRAND 575..578
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 580..592
FT /evidence="ECO:0007829|PDB:1EUV"
FT HELIX 601..616
FT /evidence="ECO:0007829|PDB:1EUV"
FT TURN 617..620
FT /evidence="ECO:0007829|PDB:1EUV"
SQ SEQUENCE 621 AA; 72378 MW; F71132817FAF0B41 CRC64;
MSVEVDKHRN TLQYHKKNPY SPLFSPISTY RCYPRVLNNP SESRRSASFS GIYKKRTNTS
RFNYLNDRRV LSMEESMKDG SDRASKAGFI GGIRETLWNS GKYLWHTFVK NEPRNFDGSE
VEASGNSDVE SRSSGSRSSD VPYGLRENYS SDTRKHKFDT STWALPNKRR RIESEGVGTP
STSPISSLAS QKSNCDSDNS ITFSRDPFGW NKWKTSAIGS NSENNTSDQK NSYDRRQYGT
AFIRKKKVAK QNINNTKLVS RAQSEEVTYL RQIFNGEYKV PKILKEERER QLKLMDMDKE
KDTGLKKSII DLTEKIKTIL IENNKNRLQT RNENDDDLVF VKEKKISSLE RKHKDYLNQK
LKFDRSILEF EKDFKRYNEI LNERKKIQED LKKKKEQLAK KKLVPELNEK DDDQVQKALA
SRENTQLMNR DNIEITVRDF KTLAPRRWLN DTIIEFFMKY IEKSTPNTVA FNSFFYTNLS
ERGYQGVRRW MKRKKTQIDK LDKIFTPINL NQSHWALGII DLKKKTIGYV DSLSNGPNAM
SFAILTDLQK YVMEESKHTI GEDFDLIHLD CPQQPNGYDC GIYVCMNTLY GSADAPLDFD
YKDAIRMRRF IAHLILTDAL K
