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DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-) (EC (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease 1) (AP endonuclease 1) (REF-1) (Redox factor-1) [Cleaved into: DNA-(apurinic or apyrimidinic site) lyase, mitochondrial]

 APEX1_MOUSE             Reviewed;         317 AA.
01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
05-DEC-2018, entry version 189.
RecName: Full=DNA-(apurinic or apyrimidinic site) lyase;
AltName: Full=APEX nuclease;
AltName: Full=Apurinic-apyrimidinic endonuclease 1;
Short=AP endonuclease 1;
AltName: Full=REF-1;
AltName: Full=Redox factor-1;
RecName: Full=DNA-(apurinic or apyrimidinic site) lyase, mitochondrial;
Name=Apex1; Synonyms=Ape, Apex, Ref1;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
Seki S., Akiyama K., Watanabe S., Hatsushika M., Ikeda S., Tsutsui K.;
"cDNA and deduced amino acid sequence of a mouse DNA repair enzyme
(APEX nuclease) with significant homology to Escherichia coli
exonuclease III.";
J. Biol. Chem. 266:20797-20802(1991).
STRAIN=129; TISSUE=Embryo;
PubMed=7533013; DOI=10.1007/BF00426079;
Takiguchi Y., Chen D.J.;
"Genomic structure of the mouse apurinic/apyrimidinic endonuclease
Mamm. Genome 5:717-722(1994).
PubMed=7782087; DOI=10.1016/0888-7543(95)80083-X;
Akiyama K., Nagao K., Oshida T., Tsutsui K., Yoshida M.C., Seki S.;
"Cloning, sequence analysis, and chromosomal assignment of the mouse
Apex gene.";
Genomics 26:63-69(1995).
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).
PubMed=1716153; DOI=10.1016/0167-4838(91)90024-T;
Seki S., Ikeda S., Watanabe S., Hatsushika M., Tsutsui K., Akiyama K.,
Zhang B.;
"A mouse DNA repair enzyme (APEX nuclease) having exonuclease and
apurinic/apyrimidinic endonuclease activities: purification and
Biochim. Biophys. Acta 1079:57-64(1991).
PubMed=16617147; DOI=10.1093/nar/gkl177;
Chattopadhyay R., Wiederhold L., Szczesny B., Boldogh I., Hazra T.K.,
Izumi T., Mitra S.;
"Identification and characterization of mitochondrial abasic (AP)-
endonuclease in mammalian cells.";
Nucleic Acids Res. 34:2067-2076(2006).
PubMed=18025127; DOI=10.1084/jem.20071289;
Guikema J.E., Linehan E.K., Tsuchimoto D., Nakabeppu Y., Strauss P.R.,
Stavnezer J., Schrader C.E.;
"APE1- and APE2-dependent DNA breaks in immunoglobulin class switch
J. Exp. Med. 204:3017-3026(2007).
PubMed=19556307; DOI=10.1093/intimm/dxp061;
Sabouri Z., Okazaki I.M., Shinkura R., Begum N., Nagaoka H.,
Tsuchimoto D., Nakabeppu Y., Honjo T.;
"Apex2 is required for efficient somatic hypermutation but not for
class switch recombination of immunoglobulin genes.";
Int. Immunol. 21:947-955(2009).
TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung,
Pancreas, Spleen, and Testis;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
Cell 143:1174-1189(2010).
PubMed=20473298; DOI=10.1038/ncb2058;
Huang E., Qu D., Zhang Y., Venderova K., Haque M.E., Rousseaux M.W.C.,
Slack R.S., Woulfe J.M., Park D.S.;
"The role of Cdk5-mediated apurinic/apyrimidinic endonuclease 1
phosphorylation in neuronal death.";
Nat. Cell Biol. 12:563-571(2010).
-!- FUNCTION: Multifunctional protein that plays a central role in the
cellular response to oxidative stress. The two major activities of
APEX1 are DNA repair and redox regulation of transcriptional
factors. Functions as a 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. Does also incise at AP sites in
the DNA strand of DNA/RNA hybrids, single-stranded DNA regions of
R-loop structures, and single-stranded RNA molecules. Has a 3'-5'
exoribonuclease activity on mismatched deoxyribonucleotides at the
3' termini of nicked or gapped DNA molecules during short-patch
BER. Possesses a DNA 3' phosphodiesterase activity capable of
removing lesions (such as phosphoglycolate) blocking the 3' side
of DNA strand breaks. May also play a role in the epigenetic
regulation of gene expression by participating in DNA
demethylation. Acts as a loading factor for POLB onto non-incised
AP sites in DNA and stimulates the 5'-terminal deoxyribose 5'-
phosphate (dRp) excision activity of POLB. Plays a role in the
protection from granzymes-mediated cellular repair leading to cell
death. Also involved in the DNA cleavage step of class switch
recombination (CSR). On the other hand, APEX1 also exerts
reversible nuclear redox activity to regulate DNA binding affinity
and transcriptional activity of transcriptional factors by
controlling the redox status of their DNA-binding domain, such as
the FOS/JUN AP-1 complex after exposure to IR. Involved in
calcium-dependent down-regulation of parathyroid hormone (PTH)
expression by binding to negative calcium response elements
(nCaREs). Together with HNRNPL or the dimer XRCC5/XRCC6,
associates with nCaRE, acting as an activator of transcriptional
repression. Stimulates the YBX1-mediated MDR1 promoter activity,
when acetylated at Lys-6 and Lys-7, leading to drug resistance.
Acts also as an endoribonuclease involved in the control of
single-stranded RNA metabolism. Plays a role in regulating MYC
mRNA turnover by preferentially cleaving in between UA and CA
dinucleotides of the MYC coding region determinant (CRD). In
association with NMD1, plays a role in the rRNA quality control
process during cell cycle progression. Associates, together with
YBX1, on the MDR1 promoter. Together with NPM1, associates with
rRNA. Binds DNA and RNA. {ECO:0000269|PubMed:18025127,
Reaction=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.; EC=; Evidence={ECO:0000255|PROSITE-
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.
-!- ACTIVITY REGULATION: NPM1 stimulates endodeoxyribonuclease
activity on double-stranded DNA with AP sites, but inhibits
endoribonuclease activity on single-stranded RNA containing AP
sites. {ECO:0000250}.
-!- SUBUNIT: Monomer. Homodimer; disulfide-linked. Component of the
SET complex, composed of at least APEX1, SET, ANP32A, HMGB2, NME1
and TREX1. Associates with the dimer XRCC5/XRCC6 in a DNA-
dependent manner. Interacts with SIRT1; the interaction is
increased in the context of genotoxic stress. Interacts with
HDAC1, HDAC2 and HDAC3; the interactions are not dependent on the
APEX1 acetylation status. Interacts with XRCC1; the interaction is
induced by SIRT1 and increased with the APEX1 acetylated form.
Interacts with NPM1 (via N-terminal domain); the interaction is
RNA-dependent and decreases in hydrogen peroxide-damaged cells.
Interacts (via N-terminus) with YBX1 (via C-terminus); the
interaction is increased in presence of APEX1 acetylated at Lys-6
and Lys-7. Interacts with HNRNPL; the interaction is DNA-
dependent. Interacts (via N-terminus) with KPNA1 and KPNA2.
Interacts with TXN; the interaction stimulates the FOS/JUN AP-1
complex DNA-binding activity in a redox-dependent manner.
Interacts with GZMA, KRT8, MDM2, POLB, PRDX6, PRPF19, RPLP0,
TOMM20 and WDR77. Binds to CDK5. {ECO:0000269|PubMed:20473298}.
-!- SUBCELLULAR LOCATION: Nucleus. Nucleus, nucleolus {ECO:0000250}.
Nucleus speckle {ECO:0000255|PROSITE-ProRule:PRU00764}.
Endoplasmic reticulum {ECO:0000250}. Cytoplasm. Note=Colocalized
with SIRT1 in the nucleus. Colocalized with YBX1 in nuclear
speckles after genotoxic stress. Together with OGG1 is recruited
to nuclear speckles in UVA-irradiated cells. Colocalized with
nucleolin and NPM1 in the nucleolus. Its nucleolar localization is
cell cycle dependent and requires active rRNA transcription.
Colocalized with calreticulin in the endoplasmic reticulum.
Translocation from the nucleus to the cytoplasm is stimulated in
presence of nitric oxide (NO) and function in a CRM1-dependent
manner, possibly as a consequence of demasking a nuclear export
signal (amino acid position 63-79). S-nitrosylation at Cys-92 and
Cys-309 regulates its nuclear-cytosolic shuttling. Ubiquitinated
form is localized predominantly in the cytoplasm. Detected in the
cytoplasm of B-cells stimulated to switch (By similarity).
-!- SUBCELLULAR LOCATION: DNA-(apurinic or apyrimidinic site) lyase,
mitochondrial: Mitochondrion. Note=Translocation from the
cytoplasm to the mitochondria is mediated by ROS signaling and
cleavage mediated by granzyme A. Tom20-dependent translocated
mitochondrial APEX1 level is significantly increased after
genotoxic stress (By similarity). The cleaved APEX2 is only
detected in mitochondria. {ECO:0000250}.
-!- TISSUE SPECIFICITY: Expressed in both resting and stimulated B
cells stimulated to switch (at protein level).
-!- DOMAIN: The N-terminus contains the redox activity while the C-
terminus exerts the DNA AP-endodeoxyribonuclease activity; both
function are independent in their actions. An unconventional
mitochondrial targeting sequence (MTS) is harbored within the C-
terminus, that appears to be masked by the N-terminal sequence
containing the nuclear localization signal (NLS), that probably
blocks the interaction between the MTS and Tom proteins (By
similarity). {ECO:0000250}.
-!- PTM: Phosphorylated. Phosphorylation by kinase PKC or casein
kinase CK2 results in enhanced redox activity that stimulates
binding of the FOS/JUN AP-1 complex to its cognate binding site.
AP-endodeoxyribonuclease activity is not affected by CK2-mediated
phosphorylation (By similarity). Phosphorylation of Thr-232 by
CDK5 in response to MPP(+)/MPTP (1-methyl-4-phenylpyridinium)
reduces AP-endodeoxyribonuclease activity resulting in
accumulation of DNA damage and contributing to neuronal death.
{ECO:0000250, ECO:0000269|PubMed:20473298}.
-!- PTM: Acetylated on Lys-6 and Lys-7. Acetylation is increased by
the transcriptional coactivator EP300 acetyltransferase, genotoxic
agents like H(2)O(2) and methyl methanesulfonate (MMS).
Acetylation increases its binding affinity to the negative calcium
response element (nCaRE) DNA promoter. The acetylated form induces
a stronger binding of YBX1 to the Y-box sequence in the MDR1
promoter than the unacetylated form. Deacetylated on lysines. Lys-
6 and Lys-7 are deacetylated by SIRT1 (By similarity).
-!- PTM: Cleaved at Lys-30 by granzyme A to create the mitochondrial
form; leading in reduction of binding to DNA, AP
endodeoxyribonuclease activity, redox activation of transcription
factors and to enhanced cell death. Cleaved by granzyme K; leading
to intracellular ROS accumulation and enhanced cell death after
oxidative stress (By similarity). {ECO:0000250}.
-!- PTM: Cys-64 and Cys-92 are nitrosylated in response to nitric
oxide (NO) and lead to the exposure of the nuclear export signal
(NES). {ECO:0000250}.
-!- PTM: Ubiquitinated by MDM2; leading to translocation to the
cytoplasm and proteasomal degradation. {ECO:0000250}.
-!- MISCELLANEOUS: The specific activity of the cleaved mitochondrial
endodeoxyribonuclease appeared to be about 3-fold higher than of
the full-length form. Extract of mitochondria, but not of nuclei
or cytosol, cleaves recombinant APEX1 to generate a mitochondrial
APEX1-sized product (By similarity). {ECO:0000250}.
-!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
Distributed under the Creative Commons Attribution (CC BY 4.0) License
EMBL; D90374; BAA14382.1; -; mRNA.
EMBL; U12273; AAC13769.1; -; Genomic_DNA.
EMBL; D38077; BAA07270.1; -; Genomic_DNA.
EMBL; BC052401; AAH52401.1; -; mRNA.
CCDS; CCDS27027.1; -.
PIR; A39500; A39500.
RefSeq; NP_033817.1; NM_009687.2.
UniGene; Mm.203; -.
UniGene; Mm.239117; -.
ProteinModelPortal; P28352; -.
SMR; P28352; -.
BioGrid; 198145; 8.
ELM; P28352; -.
IntAct; P28352; 4.
MINT; P28352; -.
STRING; 10090.ENSMUSP00000042602; -.
iPTMnet; P28352; -.
PhosphoSitePlus; P28352; -.
SwissPalm; P28352; -.
EPD; P28352; -.
PaxDb; P28352; -.
PeptideAtlas; P28352; -.
PRIDE; P28352; -.
Ensembl; ENSMUST00000049411; ENSMUSP00000042602; ENSMUSG00000035960.
GeneID; 11792; -.
KEGG; mmu:11792; -.
UCSC; uc007tly.2; mouse.
CTD; 328; -.
MGI; MGI:88042; Apex1.
eggNOG; KOG1294; Eukaryota.
eggNOG; COG0708; LUCA.
GeneTree; ENSGT00530000063540; -.
HOGENOM; HOG000034586; -.
HOVERGEN; HBG050531; -.
InParanoid; P28352; -.
KO; K10771; -.
OrthoDB; EOG091G0FDG; -.
PhylomeDB; P28352; -.
TreeFam; TF315048; -.
Reactome; R-MMU-110357; Displacement of DNA glycosylase by APEX1.
Reactome; R-MMU-110362; POLB-Dependent Long Patch Base Excision Repair.
Reactome; R-MMU-110373; Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
Reactome; R-MMU-5651801; PCNA-Dependent Long Patch Base Excision Repair.
Reactome; R-MMU-73930; Abasic sugar-phosphate removal via the single-nucleotide replacement pathway.
Reactome; R-MMU-73933; Resolution of Abasic Sites (AP sites).
ChiTaRS; Apex1; mouse.
PRO; PR:P28352; -.
Proteomes; UP000000589; Chromosome 14.
Bgee; ENSMUSG00000035960; Expressed in 319 organ(s), highest expression level in optic fissure.
CleanEx; MM_APEX1; -.
ExpressionAtlas; P28352; baseline and differential.
Genevisible; P28352; MM.
GO; GO:0005813; C:centrosome; ISO:MGI.
GO; GO:0005737; C:cytoplasm; IDA:MGI.
GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell.
GO; GO:0005739; C:mitochondrion; ISS:UniProtKB.
GO; GO:0016607; C:nuclear speck; ISS:UniProtKB.
GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
GO; GO:0005654; C:nucleoplasm; ISS:UniProtKB.
GO; GO:0005634; C:nucleus; IDA:MGI.
GO; GO:0048471; C:perinuclear region of cytoplasm; ISS:UniProtKB.
GO; GO:0005667; C:transcription factor complex; ISO:MGI.
GO; GO:0008408; F:3'-5' exonuclease activity; ISS:UniProtKB.
GO; GO:0031490; F:chromatin DNA binding; ISS:UniProtKB.
GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
GO; GO:0003684; F:damaged DNA binding; ISS:UniProtKB.
GO; GO:0003677; F:DNA binding; ISS:UniProtKB.
GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; ISS:UniProtKB.
GO; GO:0008311; F:double-stranded DNA 3'-5' exodeoxyribonuclease activity; IBA:GO_Central.
GO; GO:0008309; F:double-stranded DNA exodeoxyribonuclease activity; ISO:MGI.
GO; GO:0003691; F:double-stranded telomeric DNA binding; ISO:MGI.
GO; GO:0004521; F:endoribonuclease activity; ISO:MGI.
GO; GO:0046872; F:metal ion binding; ISS:UniProtKB.
GO; GO:0051059; F:NF-kappaB binding; ISO:MGI.
GO; GO:0016491; F:oxidoreductase activity; ISS:UniProtKB.
GO; GO:0004528; F:phosphodiesterase I activity; IBA:GO_Central.
GO; GO:0008081; F:phosphoric diester hydrolase activity; ISO:MGI.
GO; GO:0044877; F:protein-containing complex binding; ISO:MGI.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0016890; F:site-specific endodeoxyribonuclease activity, specific for altered base; ISS:UniProtKB.
GO; GO:0003713; F:transcription coactivator activity; ISS:UniProtKB.
GO; GO:0007568; P:aging; ISO:MGI.
GO; GO:0006284; P:base-excision repair; ISO:MGI.
GO; GO:0045454; P:cell redox homeostasis; IDA:MGI.
GO; GO:0071320; P:cellular response to cAMP; IEA:Ensembl.
GO; GO:0070301; P:cellular response to hydrogen peroxide; ISO:MGI.
GO; GO:0071375; P:cellular response to peptide hormone stimulus; IEA:Ensembl.
GO; GO:0080111; P:DNA demethylation; ISS:UniProtKB.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
GO; GO:0006281; P:DNA repair; ISS:UniProtKB.
GO; GO:0014912; P:negative regulation of smooth muscle cell migration; ISO:MGI.
GO; GO:1900087; P:positive regulation of G1/S transition of mitotic cell cycle; ISO:MGI.
GO; GO:0042981; P:regulation of apoptotic process; ISS:UniProtKB.
GO; GO:0043488; P:regulation of mRNA stability; ISS:UniProtKB.
GO; GO:0000723; P:telomere maintenance; ISO:MGI.
GO; GO:0097698; P:telomere maintenance via base-excision repair; ISO:MGI.
Gene3D;; -; 1.
InterPro; IPR004808; AP_endonuc_1.
InterPro; IPR020847; AP_endonuclease_F1_BS.
InterPro; IPR020848; AP_endonuclease_F1_CS.
InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
InterPro; IPR005135; Endo/exonuclease/phosphatase.
PANTHER; PTHR22748; PTHR22748; 1.
Pfam; PF03372; Exo_endo_phos; 1.
SUPFAM; SSF56219; SSF56219; 1.
TIGRFAMs; TIGR00633; xth; 1.
1: Evidence at protein level;
Acetylation; Activator; Cleavage on pair of basic residues;
Complete proteome; Cytoplasm; Direct protein sequencing;
Disulfide bond; DNA damage; DNA recombination; DNA repair;
DNA-binding; Endonuclease; Endoplasmic reticulum; Exonuclease;
Hydrolase; Lyase; Magnesium; Metal-binding; Mitochondrion; Nuclease;
Nucleus; Phosphoprotein; Reference proteome; Repressor; RNA-binding;
S-nitrosylation; Transcription; Transcription regulation;
Ubl conjugation.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:1716153}.
CHAIN 2 317 DNA-(apurinic or apyrimidinic site)
CHAIN 31 317 DNA-(apurinic or apyrimidinic site)
lyase, mitochondrial. {ECO:0000250}.
REGION 2 32 Necessary for interaction with YBX1,
binding to RNA, association together with
NPM1 to rRNA, endoribonuclease activity
on abasic RNA and localization in the
nucleoli. {ECO:0000250}.
REGION 22 32 Necessary for interaction with NPM1 and
for efficient rRNA binding.
REGION 288 317 Mitochondrial targeting sequence (MTS).
MOTIF 8 12 Nuclear localization signal (NLS).
MOTIF 63 79 Nuclear export signal (NES).
ACT_SITE 170 170 {ECO:0000250}.
ACT_SITE 209 209 Proton donor/acceptor. {ECO:0000250}.
METAL 69 69 Magnesium 1. {ECO:0000250}.
METAL 95 95 Magnesium 1. {ECO:0000250}.
METAL 209 209 Magnesium 2. {ECO:0000250}.
METAL 211 211 Magnesium 2. {ECO:0000250}.
METAL 307 307 Magnesium 1. {ECO:0000250}.
SITE 30 31 Cleavage; by granzyme A. {ECO:0000250}.
SITE 211 211 Important for substrate recognition.
SITE 211 211 Transition state stabilizer.
SITE 282 282 Important for catalytic activity.
SITE 308 308 Interaction with DNA substrate.
MOD_RES 6 6 N6-acetyllysine; by EP300.
MOD_RES 7 7 N6-acetyllysine; by EP300.
MOD_RES 18 18 Phosphoserine.
MOD_RES 26 26 N6-acetyllysine.
MOD_RES 30 30 N6-acetyllysine.
MOD_RES 31 31 N6-acetyllysine.
MOD_RES 34 34 N6-acetyllysine.
MOD_RES 53 53 Phosphoserine.
MOD_RES 64 64 S-nitrosocysteine; alternate.
MOD_RES 92 92 S-nitrosocysteine; alternate.
MOD_RES 196 196 N6-acetyllysine.
MOD_RES 232 232 Phosphothreonine; by CDK5.
MOD_RES 309 309 S-nitrosocysteine.
DISULFID 64 92 Alternate. {ECO:0000250}.
MUTAGEN 53 53 S->A: Reduced CDK5-mediated
phosphorylation. Loss of CDK5-mediated
phosphorylation; when associated with T-
MUTAGEN 232 232 T->A: Reduced CDK5-mediated
phosphorylation. Confers neuron
resistance to MPP(+)/MPTP (1-methyl-4-
phenylpyridinium). Loss of CDK5-mediated
phosphorylation; when associated with S-
53. {ECO:0000269|PubMed:20473298}.
MUTAGEN 232 232 T->E: Confers neuron sensitivity to
MPP(+)/MPTP (1-methyl-4-
SEQUENCE 317 AA; 35490 MW; CF086691FAC89C4A CRC64;

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