ID   APE3_YEAST              Reviewed;         537 AA.
AC   P37302; D6VQT1; P38154;
DT   01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1994, sequence version 1.
DT   02-SEP-2026, entry version 184.
DE   RecName: Full=Aminopeptidase Y;
DE            EC=3.4.11.15;
DE   Flags: Precursor;
GN   Name=APE3; OrderedLocusNames=YBR286W; ORFNames=YBR2024;
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], AND PROTEIN SEQUENCE OF 57-70.
RC   STRAIN=ATCC 24657 / D273-10B;
RX   PubMed=8175800; DOI=10.1016/s0021-9258(17)36879-5;
RA   Nishizawa M., Yasuhara T., Nakai T., Fujiki Y., Ohashi A.;
RT   "Molecular cloning of the aminopeptidase Y gene of Saccharomyces
RT   cerevisiae. Sequence analysis and gene disruption of a new
RT   aminopeptidase.";
RL   J. Biol. Chem. 269:13651-13655(1994).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=8091861; DOI=10.1002/yea.320100007;
RA   Holmstroem K., Brandt T., Kallesoe T.;
RT   "The sequence of a 32,420 bp segment located on the right arm of chromosome
RT   II from Saccharomyces cerevisiae.";
RL   Yeast 10:S47-S62(1994).
RN   [3]
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   [4]
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   [5]
RP   PROTEIN SEQUENCE OF 57-70, AND CHARACTERIZATION.
RC   STRAIN=D273-1B;
RX   PubMed=8175799; DOI=10.1016/s0021-9258(17)36878-3;
RA   Yasuhara T., Nakai T., Ohashi A.;
RT   "Aminopeptidase Y, a new aminopeptidase from Saccharomyces cerevisiae.
RT   Purification, properties, localization, and processing by protease B.";
RL   J. Biol. Chem. 269:13644-13650(1994).
RN   [6]
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).
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Preferentially, release of N-terminal lysine.; EC=3.4.11.15;
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000250|UniProtKB:P80561};
CC       Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000250|UniProtKB:P80561};
CC   -!- SUBUNIT: Monomer.
CC   -!- SUBCELLULAR LOCATION: Vacuole. Note=Lysosome-like vacuoles.
CC   -!- MISCELLANEOUS: Present with 4740 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the peptidase M28 family. M28A subfamily.
CC       {ECO:0000305}.
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DR   EMBL; L31635; AAA19559.1; -; Unassigned_DNA.
DR   EMBL; X76053; CAA53649.1; -; Genomic_DNA.
DR   EMBL; Z36155; CAA85251.1; -; Genomic_DNA.
DR   EMBL; BK006936; DAA07401.1; -; Genomic_DNA.
DR   PIR; A54134; A54134.
DR   RefSeq; NP_009845.2; NM_001178634.1.
DR   AlphaFoldDB; P37302; -.
DR   SMR; P37302; -.
DR   BioGRID; 32980; 97.
DR   DIP; DIP-3975N; -.
DR   FunCoup; P37302; 74.
DR   IntAct; P37302; 14.
DR   STRING; 4932.YBR286W; -.
DR   MEROPS; M28.001; -.
DR   GlyCosmos; P37302; 8 sites, No reported glycans.
DR   GlyGen; P37302; 8 sites.
DR   iPTMnet; P37302; -.
DR   PaxDb; 4932-YBR286W; -.
DR   PeptideAtlas; P37302; -.
DR   EnsemblFungi; YBR286W_mRNA; YBR286W; YBR286W.
DR   GeneID; 852589; -.
DR   KEGG; sce:YBR286W; -.
DR   AGR; SGD:S000000490; -.
DR   SGD; S000000490; APE3.
DR   VEuPathDB; FungiDB:YBR286W; -.
DR   eggNOG; KOG2195; Eukaryota.
DR   HOGENOM; CLU_024336_0_1_1; -.
DR   InParanoid; P37302; -.
DR   OMA; PNYEYEV; -.
DR   OrthoDB; 10013407at2759; -.
DR   BioCyc; YEAST:YBR286W-MONOMER; -.
DR   BioGRID-ORCS; 852589; 0 hits in 10 CRISPR screens.
DR   PRO; PR:P37302; -.
DR   Proteomes; UP000002311; Chromosome II.
DR   RNAct; P37302; protein.
DR   GO; GO:0000324; C:fungal-type vacuole; IDA:SGD.
DR   GO; GO:0004177; F:aminopeptidase activity; IDA:SGD.
DR   GO; GO:0008235; F:metalloexopeptidase activity; IEA:InterPro.
DR   GO; GO:0007039; P:protein catabolic process in the vacuole; IDA:SGD.
DR   GO; GO:0006508; P:proteolysis; IBA:GO_Central.
DR   CDD; cd03876; M28_SGAP_like; 1.
DR   CDD; cd02130; PA_ScAPY_like; 1.
DR   FunFam; 3.40.630.10:FF:000093; Peptide hydrolase; 1.
DR   Gene3D; 3.50.30.30; -; 1.
DR   Gene3D; 3.40.630.10; Zn peptidases; 1.
DR   InterPro; IPR045175; M28_fam.
DR   InterPro; IPR041756; M28_SGAP-like.
DR   InterPro; IPR046450; PA_dom_sf.
DR   InterPro; IPR003137; PA_domain.
DR   InterPro; IPR007484; Peptidase_M28.
DR   PANTHER; PTHR12147:SF17; AMINOPEPTIDASE Y; 1.
DR   PANTHER; PTHR12147; METALLOPEPTIDASE M28 FAMILY MEMBER; 1.
DR   Pfam; PF02225; PA; 1.
DR   Pfam; PF04389; Peptidase_M28; 1.
DR   SUPFAM; SSF52025; PA domain; 1.
DR   SUPFAM; SSF53187; Zn-dependent exopeptidases; 1.
PE   1: Evidence at protein level;
KW   Aminopeptidase; Direct protein sequencing; Glycoprotein; Hydrolase;
KW   Metal-binding; Metalloprotease; Protease; Reference proteome; Signal;
KW   Vacuole; Zinc; Zymogen.
FT   SIGNAL          1..21
FT                   /evidence="ECO:0000255"
FT   PROPEP          22..56
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000026847"
FT   CHAIN           57..537
FT                   /note="Aminopeptidase Y"
FT                   /id="PRO_0000026848"
FT   ACT_SITE        358
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:P80561"
FT   BINDING         314
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250|UniProtKB:P80561"
FT   BINDING         326
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250|UniProtKB:P80561"
FT   BINDING         326
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250|UniProtKB:P80561"
FT   BINDING         359
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250|UniProtKB:P80561"
FT   BINDING         387
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250|UniProtKB:P80561"
FT   BINDING         472
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250|UniProtKB:P80561"
FT   SITE            471
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000250|UniProtKB:P80561"
FT   CARBOHYD        85
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        96
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        115
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        150
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        162
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        371
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        427
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        480
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CONFLICT        14..15
FT                   /note="YA -> LR (in Ref. 2)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   537 AA;  60137 MW;  B34B7819194CF7F3 CRC64;
     MHFSLKQLAV AAFYATNLGS AYVIPQFFQE AFQQEEPIEN YLPQLNDDDS SAVAANIPKP
     HIPYFMKPHV ESEKLQDKIK VDDLNATAWD LYRLANYSTP DYGHPTRVIG SKGHNKTMEY
     ILNVFDDMQD YYDVSLQEFE ALSGKIISFN LSDAETGKSF ANTTAFALSP PVDGFVGKLV
     EIPNLGCEEK DYASVVPPRH NEKQIALIER GKCPFGDKSN LAGKFGFTAV VIYDNEPKSK
     EGLHGTLGEP TKHTVATVGV PYKVGKKLIA NIALNIDYSL YFAMDSYVEF IKTQNIIADT
     KHGDPDNIVA LGAHSDSVEE GPGINDDGSG TISLLNVAKQ LTHFKINNKV RFAWWAAEEE
     GLLGSNFYAY NLTKEENSKI RVFMDYDMMA SPNYEYEIYD ANNKENPKGS EELKNLYVDY
     YKAHHLNYTL VPFDGRSDYV GFINNGIPAG GIATGAEKNN VNNGKVLDRC YHQLCDDVSN
     LSWDAFITNT KLIAHSVATY ADSFEGFPKR ETQKHKEVDI LNAQQPQFKY RADFLII
//