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DNA-(apurinic or apyrimidinic site) lyase 2 (EC 3.1.-.-) (EC 4.2.99.18) (AP endonuclease XTH2) (APEX nuclease 2) (APEX nuclease-like 2) (Apurinic-apyrimidinic endonuclease 2) (AP endonuclease 2)

 APEX2_HUMAN             Reviewed;         518 AA.
Q9UBZ4; Q9Y5X7;
30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
18-JUL-2018, entry version 149.
RecName: Full=DNA-(apurinic or apyrimidinic site) lyase 2;
EC=3.1.-.-;
EC=4.2.99.18;
AltName: Full=AP endonuclease XTH2;
AltName: Full=APEX nuclease 2;
AltName: Full=APEX nuclease-like 2;
AltName: Full=Apurinic-apyrimidinic endonuclease 2;
Short=AP endonuclease 2;
Name=APEX2; Synonyms=APE2, APEXL2, XTH2;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH PCNA,
SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
TISSUE=Leukemia;
PubMed=11376153; DOI=10.1093/nar/29.11.2349;
Tsuchimoto D., Sakai Y., Sakumi K., Nishioka K., Sasaki M.,
Fujiwara T., Nakabeppu Y.;
"Human APE2 protein is mostly localized in the nuclei and to some
extent in the mitochondria, while nuclear APE2 is partly associated
with proliferating cell nuclear antigen.";
Nucleic Acids Res. 29:2349-2360(2001).
[2]
NUCLEOTIDE SEQUENCE [MRNA].
TISSUE=Lung tumor;
Luna L., Rognes T., Henriksen A.C., Bjoras M., Seeberg E.;
"Putative human AP endonuclease XTH2.";
Submitted (SEP-1998) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [MRNA].
TISSUE=Bone marrow;
Akiyama K., Sarker A.H., Yao M., Tsutsui K., Seki S.;
"cDNA cloning and characterization of human APEX nuclease-like 2
(APEXL2) protein.";
Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [MRNA].
TISSUE=Lung tumor;
Hadi M.Z., Erzberger J.P., Ramirez M.H., Thelen M.P., Wilson D.M. III;
Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT CYS-141.
NIEHS SNPs program;
Submitted (JAN-2005) to the EMBL/GenBank/DDBJ databases.
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15772651; DOI=10.1038/nature03440;
Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D.,
Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A.,
Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G.,
Jones M.C., Hurles M.E., Andrews T.D., Scott C.E., Searle S.,
Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R.,
Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L.,
Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A.,
Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S.,
Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R.,
Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M.,
Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N.,
Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D.,
Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W.,
Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C.,
Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C.,
Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S.,
Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S.,
Corby N., Connor R.E., David R., Davies J., Davis C., Davis J.,
Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S.,
Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I.,
Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L.,
Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P.,
Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S.,
Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A.,
Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J.,
Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J.,
Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S.,
de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z.,
Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C.,
Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W.,
Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D.,
Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H.,
McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T.,
Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I.,
Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N.,
Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J.,
Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E.,
Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S.,
Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K.,
Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D.,
Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R.,
Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T.,
Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S.,
Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L.,
Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A.,
Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L.,
Williams G., Williams L., Williamson A., Williamson H., Wilming L.,
Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H.,
Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A.,
Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F.,
Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A.,
Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T.,
Gibbs R.A., Beck S., Rogers J., Bentley D.R.;
"The DNA sequence of the human X chromosome.";
Nature 434:325-337(2005).
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Lung;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[8]
FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF ASP-277.
PubMed=16687656; DOI=10.1093/nar/gkl259;
Burkovics P., Szukacsov V., Unk I., Haracska L.;
"Human Ape2 protein has a 3'-5' exonuclease activity that acts
preferentially on mismatched base pairs.";
Nucleic Acids Res. 34:2508-2515(2006).
[9]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=18669648; DOI=10.1073/pnas.0805139105;
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
Elledge S.J., Gygi S.P.;
"A quantitative atlas of mitotic phosphorylation.";
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
[10]
FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF TYR-396 AND
PHE-397.
PubMed=19443450; DOI=10.1093/nar/gkp357;
Burkovics P., Hajdu I., Szukacsov V., Unk I., Haracska L.;
"Role of PCNA-dependent stimulation of 3'-phosphodiesterase and 3'-5'
exonuclease activities of human Ape2 in repair of oxidative DNA
damage.";
Nucleic Acids Res. 37:4247-4255(2009).
[11]
VARIANTS TYR-269 AND HIS-392.
PubMed=20843780; DOI=10.1093/nar/gkq750;
Wang W., Shen P., Thiyagarajan S., Lin S., Palm C., Horvath R.,
Klopstock T., Cutler D., Pique L., Schrijver I., Davis R.W.,
Mindrinos M., Speed T.P., Scharfe C.;
"Identification of rare DNA variants in mitochondrial disorders with
improved array-based sequencing.";
Nucleic Acids Res. 39:44-58(2011).
-!- 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. {ECO:0000269|PubMed:11376153,
ECO:0000269|PubMed:16687656, ECO:0000269|PubMed:19443450}.
-!- 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};
-!- ENZYME REGULATION: 3'-5' exonuclease activity is activated by
sodium and manganese. 3'-5' exonuclease and 3'-phosphodiesterase
activities are stimulated in presence of PCNA.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
pH dependence:
Optimum pH is 6.0-8.0. {ECO:0000269|PubMed:16687656};
-!- SUBUNIT: Interacts with PCNA; this interaction is triggered by
reactive oxygen species and increased by misincorporation of
uracil in nuclear DNA. {ECO:0000269|PubMed:11376153}.
-!- SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Mitochondrion
{ECO:0000305}. Note=Together with PCNA, is redistributed in
discrete nuclear foci in presence of oxidative DNA damaging
agents.
-!- TISSUE SPECIFICITY: Highly expressed in brain and kidney. Weakly
expressed in the fetal brain. {ECO:0000269|PubMed:11376153}.
-!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
{ECO:0000305}.
-!- WEB RESOURCE: Name=NIEHS-SNPs;
URL="http://egp.gs.washington.edu/data/apex2/";
-----------------------------------------------------------------------
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EMBL; AB049211; BAB13764.1; -; mRNA.
EMBL; AJ011311; CAB45242.1; -; mRNA.
EMBL; AB021260; BAA78422.1; -; mRNA.
EMBL; AF119046; AAD43041.1; -; mRNA.
EMBL; AY884244; AAW56941.1; -; Genomic_DNA.
EMBL; AL020991; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BC002959; AAH02959.1; -; mRNA.
CCDS; CCDS14365.1; -.
RefSeq; NP_055296.2; NM_014481.3.
UniGene; Hs.659558; -.
ProteinModelPortal; Q9UBZ4; -.
SMR; Q9UBZ4; -.
BioGrid; 118124; 21.
IntAct; Q9UBZ4; 14.
STRING; 9606.ENSP00000364126; -.
iPTMnet; Q9UBZ4; -.
PhosphoSitePlus; Q9UBZ4; -.
DMDM; 73921676; -.
EPD; Q9UBZ4; -.
MaxQB; Q9UBZ4; -.
PaxDb; Q9UBZ4; -.
PeptideAtlas; Q9UBZ4; -.
PRIDE; Q9UBZ4; -.
ProteomicsDB; 84104; -.
DNASU; 27301; -.
Ensembl; ENST00000374987; ENSP00000364126; ENSG00000169188.
GeneID; 27301; -.
KEGG; hsa:27301; -.
UCSC; uc004dtz.5; human.
CTD; 27301; -.
DisGeNET; 27301; -.
EuPathDB; HostDB:ENSG00000169188.4; -.
GeneCards; APEX2; -.
HGNC; HGNC:17889; APEX2.
HPA; HPA048577; -.
MIM; 300773; gene.
neXtProt; NX_Q9UBZ4; -.
OpenTargets; ENSG00000169188; -.
PharmGKB; PA38474; -.
eggNOG; KOG1294; Eukaryota.
eggNOG; COG0708; LUCA.
GeneTree; ENSGT00530000063540; -.
HOGENOM; HOG000231386; -.
HOVERGEN; HBG054715; -.
InParanoid; Q9UBZ4; -.
KO; K10772; -.
OMA; GAFTCWS; -.
OrthoDB; EOG091G0IPG; -.
PhylomeDB; Q9UBZ4; -.
TreeFam; TF328442; -.
ChiTaRS; APEX2; human.
GenomeRNAi; 27301; -.
PRO; PR:Q9UBZ4; -.
Proteomes; UP000005640; Chromosome X.
Bgee; ENSG00000169188; -.
CleanEx; HS_APEX2; -.
ExpressionAtlas; Q9UBZ4; baseline and differential.
Genevisible; Q9UBZ4; HS.
GO; GO:0001650; C:fibrillar center; IDA:HPA.
GO; GO:0043231; C:intracellular membrane-bounded organelle; IDA:HPA.
GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IDA:HPA.
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.
1: Evidence at protein level;
Cell cycle; Complete proteome; Cytoplasm; DNA damage;
DNA recombination; DNA repair; DNA-binding; Endonuclease; Exonuclease;
Hydrolase; Lyase; Magnesium; Metal-binding; Mitochondrion; Nuclease;
Nucleus; Polymorphism; Reference proteome.
CHAIN 1 518 DNA-(apurinic or apyrimidinic site) lyase
2.
/FTId=PRO_0000200014.
REGION 390 397 Required for the colocalization with PCNA
in nuclear foci in presence of oxidative-
induced DNA damaging agents.
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}.
VARIANT 141 141 R -> C (in dbSNP:rs2301416).
{ECO:0000269|Ref.5}.
/FTId=VAR_023390.
VARIANT 141 141 R -> W (in dbSNP:rs2301416).
/FTId=VAR_048261.
VARIANT 269 269 H -> Y (identified in a patient with
mtDNA maintenance disorders;
dbSNP:rs145122391).
{ECO:0000269|PubMed:20843780}.
/FTId=VAR_064033.
VARIANT 392 392 N -> H (identified in a patient with
mtDNA maintenance disorders;
dbSNP:rs201964062).
{ECO:0000269|PubMed:20843780}.
/FTId=VAR_064034.
MUTAGEN 269 269 H->A: Abolishes AP endodeoxyribonuclease,
3'-5' exonuclease activity and 3'-
phosphodiesterase activities.
MUTAGEN 277 277 D->A: Abolishes AP endodeoxyribonuclease,
3'-5' exonuclease activity and 3'-
phosphodiesterase activities.
{ECO:0000269|PubMed:16687656}.
MUTAGEN 396 396 Y->A: Reduces 3'-5' exonuclease activity
in presence of PCNA. Does not abolish the
3'-5' exonuclease activity. Does only
partially redistributes together with
PCNA in nuclear foci in presence of
oxidative-induced DNA damaging agents.
{ECO:0000269|PubMed:19443450}.
MUTAGEN 397 397 F->A: Reduces 3'-5' exonuclease activity
in presence of PCNA. Does not abolish the
3'-5' exonuclease activity. Does only
partially redistributes together with
PCNA in nuclear foci in presence of
oxidative-induced DNA damaging agents.
{ECO:0000269|PubMed:19443450}.
CONFLICT 399 399 P -> S (in Ref. 4; AAD43041).
{ECO:0000305}.
SEQUENCE 518 AA; 57401 MW; 08464806153F8832 CRC64;
MLRVVSWNIN GIRRPLQGVA NQEPSNCAAV AVGRILDELD ADIVCLQETK VTRDALTEPL
AIVEGYNSYF SFSRNRSGYS GVATFCKDNA TPVAAEEGLS GLFATQNGDV GCYGNMDEFT
QEELRALDSE GRALLTQHKI RTWEGKEKTL TLINVYCPHA DPGRPERLVF KMRFYRLLQI
RAEALLAAGS HVIILGDLNT AHRPIDHWDA VNLECFEEDP GRKWMDSLLS NLGCQSASHV
GPFIDSYRCF QPKQEGAFTC WSAVTGARHL NYGSRLDYVL GDRTLVIDTF QASFLLPEVM
GSDHCPVGAV LSVSSVPAKQ CPPLCTRFLP EFAGTQLKIL RFLVPLEQSP VLEQSTLQHN
NQTRVQTCQN KAQVRSTRPQ PSQVGSSRGQ KNLKSYFQPS PSCPQASPDI ELPSLPLMSA
LMTPKTPEEK AVAKVVKGQA KTSEAKDEKE LRTSFWKSVL AGPLRTPLCG GHREPCVMRT
VKKPGPNLGR RFYMCARPRG PPTDPSSRCN FFLWSRPS


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