APN1_YEAST
ID APN1_YEAST Reviewed; 367 AA.
AC P22936; D6VXH4;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 4.
DT 03-AUG-2022, entry version 183.
DE RecName: Full=Apurinic-apyrimidinic endonuclease 1;
DE Short=AP endonuclease 1;
DE EC=3.1.21.- {ECO:0000269|PubMed:3056935};
GN Name=APN1; OrderedLocusNames=YKL114C; ORFNames=YKL513;
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=1693433; DOI=10.1073/pnas.87.11.4193;
RA Popoff S.C., Spira A.I., Johnson A.W., Demple B.;
RT "Yeast structural gene (APN1) for the major apurinic endonuclease: homology
RT to Escherichia coli endonuclease IV.";
RL Proc. Natl. Acad. Sci. U.S.A. 87:4193-4197(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1561835; DOI=10.1002/yea.320080207;
RA Jacquier A., Legrain P., Dujon B.;
RT "Sequence of a 10.7 kb segment of yeast chromosome XI identifies the APN1
RT and the BAF1 loci and reveals one tRNA gene and several new open reading
RT frames including homologs to RAD2 and kinases.";
RL Yeast 8:121-132(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8196765; DOI=10.1038/369371a0;
RA Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V.,
RA Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P.,
RA Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L.,
RA Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A.,
RA Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H.,
RA Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L.,
RA Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M.,
RA Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H.,
RA Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J.,
RA Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H.,
RA Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J.,
RA Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S.,
RA Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F.,
RA Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R.,
RA Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W.,
RA Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M.,
RA Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C.,
RA Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H.,
RA Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L.,
RA van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S.,
RA von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M.,
RA Becker I., Mewes H.-W.;
RT "Complete DNA sequence of yeast chromosome XI.";
RL Nature 369:371-378(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 CHARACTERIZATION, PROTEIN SEQUENCE OF 2-26, AND CATALYTIC ACTIVITY.
RX PubMed=3056935; DOI=10.1016/s0021-9258(19)81316-9;
RA Johnson A.W., Demple B.;
RT "Yeast DNA diesterase for 3'-fragments of deoxyribose: purification and
RT physical properties of a repair enzyme for oxidative DNA damage.";
RL J. Biol. Chem. 263:18009-18016(1988).
RN [6]
RP METAL-BINDING STUDIES.
RX PubMed=1720775; DOI=10.1016/s0021-9258(18)54438-0;
RA Levin J.D., Shapiro R., Demple B.;
RT "Metalloenzymes in DNA repair. Escherichia coli endonuclease IV and
RT Saccharomyces cerevisiae Apn1.";
RL J. Biol. Chem. 266:22893-22898(1991).
RN [7]
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 [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-356, 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: DNA repair enzyme that cleaves apurinic/apyrimidinic (AP)
CC sites and removes 3'-blocking groups present at single strand breaks of
CC damaged DNA. APN1 accounts for > 97% of both apurinic/apyrimidinic (AP)
CC endonuclease and DNA 3'-repair diesterase activities.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Note=Binds 3 Zn(2+) ions.;
CC -!- SUBUNIT: Monomer.
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- MISCELLANEOUS: Present with 7250 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the AP endonuclease 2 family. {ECO:0000305}.
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DR EMBL; M33667; AAA34429.1; -; Genomic_DNA.
DR EMBL; S93804; AAB22003.1; -; Genomic_DNA.
DR EMBL; Z28114; CAA81954.1; -; Genomic_DNA.
DR EMBL; BK006944; DAA09044.1; -; Genomic_DNA.
DR PIR; S29871; S29871.
DR RefSeq; NP_012808.1; NM_001179680.1.
DR AlphaFoldDB; P22936; -.
DR SMR; P22936; -.
DR BioGRID; 34020; 115.
DR DIP; DIP-4106N; -.
DR IntAct; P22936; 2.
DR MINT; P22936; -.
DR STRING; 4932.YKL114C; -.
DR iPTMnet; P22936; -.
DR MaxQB; P22936; -.
DR PaxDb; P22936; -.
DR PRIDE; P22936; -.
DR EnsemblFungi; YKL114C_mRNA; YKL114C; YKL114C.
DR GeneID; 853746; -.
DR KEGG; sce:YKL114C; -.
DR SGD; S000001597; APN1.
DR VEuPathDB; FungiDB:YKL114C; -.
DR eggNOG; KOG3997; Eukaryota.
DR GeneTree; ENSGT00390000013698; -.
DR HOGENOM; CLU_025885_1_0_1; -.
DR InParanoid; P22936; -.
DR OMA; HPGSHLK; -.
DR BioCyc; YEAST:G3O-31899-MON; -.
DR BRENDA; 4.2.99.18; 984.
DR PRO; PR:P22936; -.
DR Proteomes; UP000002311; Chromosome XI.
DR RNAct; P22936; protein.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0008296; F:3'-5'-exodeoxyribonuclease activity; IDA:CACAO.
DR GO; GO:0017005; F:3'-tyrosyl-DNA phosphodiesterase 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' exodeoxyribonuclease 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; IDA:SGD.
DR CDD; cd00019; AP2Ec; 1.
DR HAMAP; MF_00152; Nfo; 1.
DR InterPro; IPR001719; AP_endonuc_2.
DR InterPro; IPR018246; AP_endonuc_F2_Zn_BS.
DR InterPro; IPR036237; Xyl_isomerase-like_sf.
DR InterPro; IPR013022; Xyl_isomerase-like_TIM-brl.
DR PANTHER; PTHR21445; PTHR21445; 1.
DR Pfam; PF01261; AP_endonuc_2; 1.
DR SMART; SM00518; AP2Ec; 1.
DR SUPFAM; SSF51658; SSF51658; 1.
DR TIGRFAMs; TIGR00587; nfo; 1.
DR PROSITE; PS00729; AP_NUCLEASE_F2_1; 1.
DR PROSITE; PS00730; AP_NUCLEASE_F2_2; 1.
DR PROSITE; PS00731; AP_NUCLEASE_F2_3; 1.
DR PROSITE; PS51432; AP_NUCLEASE_F2_4; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; DNA damage; DNA repair; Hydrolase;
KW Metal-binding; Nucleus; Phosphoprotein; Reference proteome; Zinc.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:3056935"
FT CHAIN 2..367
FT /note="Apurinic-apyrimidinic endonuclease 1"
FT /id="PRO_0000190898"
FT REGION 312..367
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 312..334
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 342..360
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 83
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 123
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 158
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 158
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 192
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 195
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 229
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 242
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 244
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 274
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT MOD_RES 356
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT CONFLICT 239
FT /note="A -> S (in Ref. 1; AAA34429)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 367 AA; 41439 MW; 76C14935B760A6D1 CRC64;
MPSTPSFVRS AVSKYKFGAH MSGAGGISNS VTNAFNTGCN SFAMFLKSPR KWVSPQYTQE
EIDKFKKNCA TYNYNPLTDV LPHGQYFINL ANPDREKAEK SYESFMDDLN RCEQLGIGLY
NLHPGSTLKG DHQLQLKQLA SYLNKAIKET KFVKIVLENM AGTGNLVGSS LVDLKEVIGM
IEDKSRIGVC IDTCHTFAAG YDISTTETFN NFWKEFNDVI GFKYLSAVHL NDSKAPLGAN
RDLHERLGQG YLGIDVFRMI AHSEYLQGIP IVLETPYEND EGYGNEIKLM EWLESKSESE
LLEDKEYKEK NDTLQKLGAK SRKEQLDKFE VKQKKRAGGT KRKKATAEPS DNDILSQMTK
KRKTKKE
