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DNA-(apurinic or apyrimidinic site) lyase 2 (EC 3.1.-.-) (EC 4.2.99.18) (APEX nuclease 2) (Apurinic-apyrimidinic endonuclease 2) (AP endonuclease 2)

 APEX2_BOVIN             Reviewed;         514 AA.
Q5E9N9; Q58D90;
30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
15-MAR-2005, sequence version 1.
12-SEP-2018, entry version 76.
RecName: Full=DNA-(apurinic or apyrimidinic site) lyase 2;
EC=3.1.-.-;
EC=4.2.99.18;
AltName: Full=APEX nuclease 2;
AltName: Full=Apurinic-apyrimidinic endonuclease 2;
Short=AP endonuclease 2;
Name=APEX2;
Bos taurus (Bovine).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia;
Pecora; Bovidae; Bovinae; Bos.
NCBI_TaxID=9913;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
PubMed=16305752; DOI=10.1186/1471-2164-6-166;
Harhay G.P., Sonstegard T.S., Keele J.W., Heaton M.P., Clawson M.L.,
Snelling W.M., Wiedmann R.T., Van Tassell C.P., Smith T.P.L.;
"Characterization of 954 bovine full-CDS cDNA sequences.";
BMC Genomics 6:166-166(2005).
-!- FUNCTION: Function as a weak apurinic/apyrimidinic (AP)
endodeoxyribonuclease in the DNA base excision repair (BER)
pathway of DNA lesions induced by oxidative and alkylating agents.
Initiates repair of AP sites in DNA by catalyzing hydrolytic
incision of the phosphodiester backbone immediately adjacent to
the damage, generating a single-strand break with 5'-deoxyribose
phosphate and 3'-hydroxyl ends. Displays also double-stranded DNA
3'-5' exonuclease, 3'-phosphodiesterase activities. Shows robust
3'-5' exonuclease activity on 3'-recessed heteroduplex DNA and is
able to remove mismatched nucleotides preferentially. Shows fairly
strong 3'-phosphodiesterase activity involved in the removal of
3'-damaged termini formed in DNA by oxidative agents. In the
nucleus functions in the PCNA-dependent BER pathway. Required for
somatic hypermutation (SHM) and DNA cleavage step of class switch
recombination (CSR) of immunoglobulin genes. Required for proper
cell cycle progression during proliferation of peripheral
lymphocytes (By similarity). {ECO:0000250}.
-!- CATALYTIC ACTIVITY: The C-O-P bond 3' to the apurinic or
apyrimidinic site in DNA is broken by a beta-elimination reaction,
leaving a 3'-terminal unsaturated sugar and a product with a
terminal 5'-phosphate. {ECO:0000255|PROSITE-ProRule:PRU00764}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Note=Probably binds two magnesium or manganese ions per subunit.
{ECO:0000250};
-!- ACTIVITY REGULATION: 3'-5' exonuclease activity is activated by
sodium and manganese. 3'-5' exonuclease and 3'-phosphodiesterase
activities are stimulated in presence of PCNA (By similarity).
{ECO:0000250}.
-!- SUBUNIT: Interacts with PCNA; this interaction is triggered by
reactive oxygen species and increased by misincorporation of
uracil in nuclear DNA. {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00764}. Cytoplasm {ECO:0000255|PROSITE-
ProRule:PRU00764}. Mitochondrion {ECO:0000250}. Note=Together with
PCNA, is redistributed in discrete nuclear foci in presence of
oxidative DNA damaging agents. {ECO:0000250}.
-!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAX46554.1; Type=Frameshift; Positions=392; Evidence={ECO:0000305};
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EMBL; BT020881; AAX08898.1; -; mRNA.
EMBL; BT021707; AAX46554.1; ALT_FRAME; mRNA.
RefSeq; NP_001015577.1; NM_001015577.1.
UniGene; Bt.1184; -.
ProteinModelPortal; Q5E9N9; -.
SMR; Q5E9N9; -.
STRING; 9913.ENSBTAP00000017537; -.
PaxDb; Q5E9N9; -.
PRIDE; Q5E9N9; -.
GeneID; 511790; -.
KEGG; bta:511790; -.
CTD; 27301; -.
eggNOG; KOG1294; Eukaryota.
eggNOG; COG0708; LUCA.
HOGENOM; HOG000231386; -.
HOVERGEN; HBG054715; -.
InParanoid; Q5E9N9; -.
KO; K10772; -.
Proteomes; UP000009136; Unplaced.
GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IBA:GO_Central.
GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IBA:GO_Central.
GO; GO:0008311; F:double-stranded DNA 3'-5' exodeoxyribonuclease activity; IBA:GO_Central.
GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0006284; P:base-excision repair; IBA:GO_Central.
GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
Gene3D; 3.60.10.10; -; 1.
InterPro; IPR004808; AP_endonuc_1.
InterPro; IPR020847; AP_endonuclease_F1_BS.
InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
InterPro; IPR005135; Endo/exonuclease/phosphatase.
InterPro; IPR010666; Znf_GRF.
PANTHER; PTHR22748; PTHR22748; 1.
Pfam; PF03372; Exo_endo_phos; 1.
Pfam; PF06839; zf-GRF; 1.
SUPFAM; SSF56219; SSF56219; 1.
TIGRFAMs; TIGR00633; xth; 1.
PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
2: Evidence at transcript level;
Cell cycle; Complete proteome; Cytoplasm; DNA damage;
DNA recombination; DNA repair; DNA-binding; Endonuclease; Exonuclease;
Hydrolase; Lyase; Magnesium; Metal-binding; Mitochondrion; Nuclease;
Nucleus; Reference proteome.
CHAIN 1 514 DNA-(apurinic or apyrimidinic site) lyase
2.
/FTId=PRO_0000200013.
REGION 390 397 Required for the colocalization with PCNA
in nuclear foci in presence of oxidative-
induced DNA damaging agents.
{ECO:0000250}.
ACT_SITE 156 156 {ECO:0000250}.
ACT_SITE 197 197 Proton donor/acceptor. {ECO:0000250}.
METAL 8 8 Magnesium 1. {ECO:0000250}.
METAL 48 48 Magnesium 1. {ECO:0000250}.
METAL 197 197 Magnesium 2. {ECO:0000250}.
METAL 199 199 Magnesium 2. {ECO:0000250}.
METAL 303 303 Magnesium 1. {ECO:0000250}.
SITE 199 199 Transition state stabilizer.
{ECO:0000250}.
SITE 277 277 Important for catalytic activity.
{ECO:0000250}.
SITE 304 304 Interaction with DNA substrate.
{ECO:0000250}.
CONFLICT 369 369 K -> Q (in Ref. 1; AAX46554).
{ECO:0000305}.
SEQUENCE 514 AA; 56938 MW; D22E64035623C993 CRC64;
MLRLVSWNIN GIRSPLQGVR CEEPSSCSAM AMGRILDKLD ADIVCLQETK VTRDVLTEPL
AIIEGYNSYF SFSRNRSGYS GVATFCKDSA TPVAAEEGLS GLLSTQNGDV GCYGNMDDFT
QEELRALDSE GRALLTQHKI CTWEGKEKTL TLINVYCPHA DPGKPERLTF KMRFYRLLQI
RAEALLAAGS HVIILGDLNT AHRPIDHWDA VNMECFEEDP GRKWMDGLLS NLGCESGSHM
GPFIDSYRCF QPKQKGAFTC WSTVSGARHL NYGSRLDYVL GDRTLVIDTF QSSFLLPEVM
GSDHCPVGAV LSVSSVPAKQ CPPLCTCFLP EFAGTQLKIL RFLVHFKQDP VFKQSALQPS
NQTQVHMRKN KARVRSTRSR PSKTGSSRGQ KNLMSYFQPS SSGPQTSNLD LPSLGTLITP
KTSEEDVMAN VVEGQTKASE AKDEKEIRTS FWKSLLGGPS PMPLCGGHRE PCVMRTVKKP
GPNLGRHFYM CARPQGPPTD PSSRCNFFLW SRPS


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