PRTD_YEAST
ID PRTD_YEAST Reviewed; 712 AA.
AC P25375; D6VQW0; E9P942;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1992, sequence version 1.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=Saccharolysin;
DE EC=3.4.24.37;
DE AltName: Full=Oligopeptidase YSCD;
DE AltName: Full=Protease D;
DE AltName: Full=Proteinase yscD;
GN Name=PRD1; OrderedLocusNames=YCL057W; ORFNames=YCL57W;
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].
RX PubMed=8307027; DOI=10.1111/j.1432-1033.1994.tb19978.x;
RA Buechler M., Tisljar U., Wolf D.H.;
RT "Proteinase yscD (oligopeptidase yscD). Structure, function and
RT relationship of the yeast enzyme with mammalian thimet oligopeptidase
RT (metalloendopeptidase, EP 24.15).";
RL Eur. J. Biochem. 219:627-639(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=1574125; DOI=10.1038/357038a0;
RA Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M.,
RA Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G.,
RA Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A.,
RA Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M., Carcano C.,
RA Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M.,
RA Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C.,
RA Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F.,
RA Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C.,
RA Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E.,
RA Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P.,
RA Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J.,
RA Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P.,
RA Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M.,
RA Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P.,
RA Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G.,
RA Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E.,
RA Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F.,
RA Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L.,
RA Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J.,
RA Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M.,
RA Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A.,
RA Richterich P., Roberts A.B., Rodriguez F., Sanz E.,
RA Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J.,
RA Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I.,
RA Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M.,
RA Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M.,
RA Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D.,
RA Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K.,
RA Sgouros J.G.;
RT "The complete DNA sequence of yeast chromosome III.";
RL Nature 357:38-46(1992).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
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 [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-73, AND IDENTIFICATION BY
RP 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 [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-73, 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 [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-73, 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).
CC -!- FUNCTION: Could be involved in late stage of protein degradation.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Cleavage of Pro-|-Phe and Ala-|-Ala bonds.; EC=3.4.24.37;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 1 zinc ion. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- MISCELLANEOUS: Present with 8910 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the peptidase M3 family. {ECO:0000305}.
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DR EMBL; X76504; CAA54039.1; -; Genomic_DNA.
DR EMBL; X59720; CAA42388.1; -; Genomic_DNA.
DR EMBL; AY723761; AAU09678.1; -; Genomic_DNA.
DR EMBL; BK006937; DAA07429.1; -; Genomic_DNA.
DR PIR; S19387; S19387.
DR RefSeq; NP_009874.1; NM_001178701.1.
DR AlphaFoldDB; P25375; -.
DR SMR; P25375; -.
DR BioGRID; 30929; 20.
DR DIP; DIP-4938N; -.
DR IntAct; P25375; 2.
DR MINT; P25375; -.
DR STRING; 4932.YCL057W; -.
DR MEROPS; M03.003; -.
DR iPTMnet; P25375; -.
DR MaxQB; P25375; -.
DR PaxDb; P25375; -.
DR PRIDE; P25375; -.
DR EnsemblFungi; YCL057W_mRNA; YCL057W; YCL057W.
DR GeneID; 850301; -.
DR KEGG; sce:YCL057W; -.
DR SGD; S000000562; PRD1.
DR VEuPathDB; FungiDB:YCL057W; -.
DR eggNOG; KOG2089; Eukaryota.
DR GeneTree; ENSGT00950000183171; -.
DR HOGENOM; CLU_001805_1_1_1; -.
DR InParanoid; P25375; -.
DR OMA; KNFQSAM; -.
DR BioCyc; YEAST:YCL057W-MON; -.
DR Reactome; R-SCE-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR PRO; PR:P25375; -.
DR Proteomes; UP000002311; Chromosome III.
DR RNAct; P25375; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0000324; C:fungal-type vacuole; IDA:SGD.
DR GO; GO:0005794; C:Golgi apparatus; IDA:SGD.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004222; F:metalloendopeptidase activity; IDA:SGD.
DR GO; GO:0006518; P:peptide metabolic process; IBA:GO_Central.
DR GO; GO:0006508; P:proteolysis; IDA:SGD.
DR Gene3D; 1.10.1370.10; -; 1.
DR Gene3D; 1.20.1050.40; -; 1.
DR Gene3D; 3.40.390.10; -; 1.
DR InterPro; IPR024079; MetalloPept_cat_dom_sf.
DR InterPro; IPR024077; Neurolysin/TOP_dom2.
DR InterPro; IPR024080; Neurolysin/TOP_N.
DR InterPro; IPR045090; Pept_M3A_M3B.
DR InterPro; IPR001567; Pept_M3A_M3B_dom.
DR PANTHER; PTHR11804; PTHR11804; 1.
DR Pfam; PF01432; Peptidase_M3; 1.
DR PROSITE; PS00142; ZINC_PROTEASE; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Hydrolase; Metal-binding; Metalloprotease; Phosphoprotein;
KW Protease; Reference proteome; Zinc.
FT CHAIN 1..712
FT /note="Saccharolysin"
FT /id="PRO_0000078156"
FT ACT_SITE 502
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 501
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 505
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 508
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT MOD_RES 73
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT CONFLICT 384
FT /note="L -> P (in Ref. 4; AAU09678)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 712 AA; 81934 MW; 340910B7FDAFBE37 CRC64;
MRLLLCKNWF ASPVISPLLY TRSLYSMANT TSFPIAPQAP PNWSFTPSDI SGKTNEIINN
SNNFYDSMSK VESPSVSNFV EPFMKFENEL GPIINQLTFL QHVSSDKEIR DASVNSSMKL
DELNIDLSLR HDIFLQFARV WQDVQSKADS VERETFKYVE KSYKDYIHSG LELDEGNRLK
IKEIKKKISV NSINFSKNLG EQKEYITFTK EQLEGVPDSI LTQFETIKSD KDSNETLYKV
TFKYPDIFPV MKLASSAQTR KQAFLADQNK VPENEAILLD TLKLRDELAS LLGYDTYANY
NLYDKMAEDS TTVMNFLNDL KDKLIPLGRK ELQVLQDMKA EDVKKLNQGA DPNYYIWDHR
YYDNKYLLEN FNVDLEKISE YFPLEATITG MLEIYETLFN LKFIETKDSQ NKSVWHDDVK
QIAVWNMDDP KSPNFVGWIY FDLHPRDGKY GHAANFGLSS SFMIDDTTRS YPVTALVCNF
SKSTKDKPSL LKHNEIVTFF HELGHGIHDL VGQNKESRFN GPGSVPWDFV EAPSQMLEFW
TWNKNELINL SSHYKTGEKI PESLINSLIK TKHVNGALFT LRQLHFGLFD MKVHTCKDLQ
NLSICDTWNQ LRQDISLISN GGTLSKGYDS FGHIMSDSYS AGYYGYLWAE VFATDMYHTK
FAKDPLNAKN GIQYRDIVLA RGGLYDINDN LKEFLGREPS KDAFLKELGL QN
