ID   APN2_YEAST              Reviewed;         520 AA.
AC   P38207; D6VPY1; E9P926;
DT   01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1994, sequence version 1.
DT   04-NOV-2026, entry version 177.
DE   RecName: Full=DNA-(apurinic or apyrimidinic site) endonuclease 2;
DE            EC=3.1.11.2 {ECO:0000269|PubMed:10806210, ECO:0000269|PubMed:9765213};
DE   AltName: Full=AP endonuclease 2;
DE   AltName: Full=Apurinic-apyrimidinic endonuclease 2;
GN   Name=APN2; Synonyms=ETH1; OrderedLocusNames=YBL019W; ORFNames=YBL0443;
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.
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   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   [4]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=9765213; DOI=10.1101/gad.12.19.3137;
RA   Johnson R.E., Torres-Ramos C.A., Izumi T., Mitra S., Prakash S.,
RA   Prakash L.;
RT   "Identification of APN2, the Saccharomyces cerevisiae homolog of the major
RT   human AP endonuclease HAP1, and its role in the repair of abasic sites.";
RL   Genes Dev. 12:3137-3143(1998).
RN   [5]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=10806210; DOI=10.1074/jbc.m002845200;
RA   Unk I., Haracska L., Johnson R.E., Prakash S., Prakash L.;
RT   "Apurinic endonuclease activity of yeast Apn2 protein.";
RL   J. Biol. Chem. 275:22427-22434(2000).
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   -!- FUNCTION: DNA repair enzyme that cleaves apurinic/apyrimidinic (AP)
CC       sites and removes 3'-blocking groups present at single strand breaks of
CC       damaged DNA. {ECO:0000269|PubMed:10806210, ECO:0000269|PubMed:9765213}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC         nucleoside 5'-phosphates.; EC=3.1.11.2;
CC         Evidence={ECO:0000269|PubMed:10806210, ECO:0000269|PubMed:9765213};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC       Note=Probably binds two magnesium or manganese ions per subunit.
CC       {ECO:0000250};
CC   -!- SUBCELLULAR LOCATION: Nucleus.
CC   -!- MISCELLANEOUS: Present with 414 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
CC       {ECO:0000305}.
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DR   EMBL; Z35780; CAA84838.1; -; Genomic_DNA.
DR   EMBL; AY693183; AAT93202.1; -; Genomic_DNA.
DR   EMBL; BK006936; DAA07101.1; -; Genomic_DNA.
DR   PIR; S45753; S45753.
DR   RefSeq; NP_009534.1; NM_001178259.1.
DR   PDB; 7N3Y; X-ray; 2.73 A; A/B/C/D=1-407.
DR   PDB; 7N3Z; X-ray; 1.99 A; A=1-407.
DR   AlphaFoldDB; P38207; -.
DR   SMR; P38207; -.
DR   BioGRID; 32679; 86.
DR   DIP; DIP-3930N; -.
DR   FunCoup; P38207; 577.
DR   IntAct; P38207; 4.
DR   STRING; 4932.YBL019W; -.
DR   iPTMnet; P38207; -.
DR   PaxDb; 4932-YBL019W; -.
DR   PeptideAtlas; P38207; -.
DR   EnsemblFungi; YBL019W_mRNA; YBL019W; YBL019W.
DR   GeneID; 852262; -.
DR   KEGG; sce:YBL019W; -.
DR   AGR; SGD:S000000115; -.
DR   SGD; S000000115; APN2.
DR   VEuPathDB; FungiDB:YBL019W; -.
DR   eggNOG; KOG1294; Eukaryota.
DR   HOGENOM; CLU_010374_0_0_1; -.
DR   InParanoid; P38207; -.
DR   OMA; AAGXGFF; -.
DR   OrthoDB; 391817at2759; -.
DR   BioCyc; YEAST:G3O-28922-MONOMER; -.
DR   BRENDA; 3.1.11.2; 984.
DR   BioGRID-ORCS; 852262; 2 hits in 10 CRISPR screens.
DR   PRO; PR:P38207; -.
DR   Proteomes; UP000002311; Chromosome II.
DR   RNAct; P38207; protein.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0008408; F:3'-5' exonuclease activity; IDA:SGD.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:SGD.
DR   GO; GO:0008311; F:double-stranded DNA 3'-5' DNA exonuclease activity; IDA:SGD.
DR   GO; GO:0008081; F:phosphoric diester hydrolase activity; IDA:SGD.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   GO; GO:0006284; P:base-excision repair; IGI:SGD.
DR   CDD; cd09088; Ape2-like_AP-endo; 1.
DR   FunFam; 3.60.10.10:FF:000108; AP endonuclease; 1.
DR   Gene3D; 3.60.10.10; Endonuclease/exonuclease/phosphatase; 1.
DR   InterPro; IPR004808; AP_endonuc_1.
DR   InterPro; IPR020848; AP_endonuclease_F1_CS.
DR   InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR   InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR   InterPro; IPR010666; Znf_GRF.
DR   PANTHER; PTHR22748; AP ENDONUCLEASE; 1.
DR   PANTHER; PTHR22748:SF4; DNA-(APURINIC OR APYRIMIDINIC SITE) ENDONUCLEASE 2; 1.
DR   Pfam; PF03372; Exo_endo_phos; 1.
DR   Pfam; PF06839; Zn_ribbon_GRF; 1.
DR   SUPFAM; SSF56219; DNase I-like; 1.
DR   PROSITE; PS00728; AP_NUCLEASE_F1_3; 1.
DR   PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
DR   PROSITE; PS51999; ZF_GRF; 1.
PE   1: Evidence at protein level;
KW   3D-structure; DNA damage; DNA repair; Hydrolase; Magnesium; Metal-binding;
KW   Nucleus; Reference proteome; Zinc; Zinc-finger.
FT   CHAIN           1..520
FT                   /note="DNA-(apurinic or apyrimidinic site) endonuclease 2"
FT                   /id="PRO_0000200020"
FT   ZN_FING         476..520
FT                   /note="GRF-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01343"
FT   ACT_SITE        181
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        222
FT                   /note="Proton donor/acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         59
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         222
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         224
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         353
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         476
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01343"
FT   BINDING         478
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01343"
FT   BINDING         500
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01343"
FT   BINDING         514
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01343"
FT   SITE            224
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000250"
FT   SITE            328
FT                   /note="Important for catalytic activity"
FT                   /evidence="ECO:0000250"
FT   SITE            354
FT                   /note="Interaction with DNA substrate"
FT                   /evidence="ECO:0000250"
FT   CONFLICT        15
FT                   /note="N -> D (in Ref. 3; AAT93202)"
FT                   /evidence="ECO:0000305"
FT   STRAND          16..23
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           27..30
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           36..38
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   TURN            39..41
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           43..50
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          53..58
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           64..66
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           67..70
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          76..81
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          92..97
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   TURN            104..109
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          111..120
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          123..125
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          127..129
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          131..133
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           134..136
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   TURN            138..140
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           154..160
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   TURN            161..163
FT                   /evidence="ECO:0007829|PDB:7N3Y"
FT   STRAND          166..171
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           172..174
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          175..181
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           190..213
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          216..222
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           229..231
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           233..238
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           249..255
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           257..265
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           270..276
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           285..290
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          293..295
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           296..301
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   TURN            302..304
FT                   /evidence="ECO:0007829|PDB:7N3Y"
FT   TURN            314..317
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   TURN            319..322
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          328..333
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           334..339
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          340..345
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          351..354
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   STRAND          357..361
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           375..378
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           382..385
FT                   /evidence="ECO:0007829|PDB:7N3Z"
FT   HELIX           388..390
FT                   /evidence="ECO:0007829|PDB:7N3Y"
FT   TURN            393..395
FT                   /evidence="ECO:0007829|PDB:7N3Y"
SQ   SEQUENCE   520 AA;  59445 MW;  E3947C4D904C53FB CRC64;
     MSSSENTLLD GKSENTIRFL TFNVNGIRTF FHYQPFSQMN QSLRSVFDFF RADIITFQEL
     KTEKLSISKW GRVDGFYSFI SIPQTRKGYS GVGCWIRIPE KNHPLYHALQ VVKAEEGITG
     YLTIKNGKHS AISYRNDVNQ GIGGYDSLDP DLDEKSALEL DSEGRCVMVE LACGIVIISV
     YCPANSNSSE EGEMFRLRFL KVLLRRVRNL DKIGKKIVLM GDVNVCRDLI DSADTLEQFS
     IPITDPMGGT KLEAQYRDKA IQFIINPDTP HRRIFNQILA DSLLPDASKR GILIDTTRLI
     QTRNRLKMYT VWNMLKNLRP SNYGSRIDFI LVSLKLERCI KAADILPDIL GSDHCPVYSD
     LDILDDRIEP GTTQVPIPKF EARYKYNLRN HNVLEMFAKK DTNKESNKQK YCVSKVMNTK
     KNSNIKNKSL DSFFQKVNGE KDDRIKESSE IPQQAKKRIS TPKLNFKDVF GKPPLCRHGE
     ESMLKTSKTS ANPGRKFWIC KRSRGDSNNT ESSCGFFQWV
//