ID APEX1_BOVIN Reviewed; 318 AA. AC P23196; Q0IIJ5; DT 01-NOV-1991, integrated into UniProtKB/Swiss-Prot. DT 23-JAN-2007, sequence version 2. DT 27-MAR-2024, entry version 181. DE RecName: Full=DNA repair nuclease/redox regulator APEX1; DE EC=3.1.11.2 {ECO:0000250|UniProtKB:P27695}; DE EC=3.1.21.- {ECO:0000250|UniProtKB:P27695}; DE AltName: Full=APEX nuclease; DE Short=APEN; DE AltName: Full=Apurinic-apyrimidinic endonuclease 1; DE Short=AP endonuclease 1; DE AltName: Full=REF-1; DE AltName: Full=Redox factor-1; DE Contains: DE RecName: Full=DNA repair nuclease/redox regulator APEX1, mitochondrial; GN Name=APEX1; Synonyms=APE, APEX, BAP1, REF1; OS Bos taurus (Bovine). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae; OC Bovinae; Bos. OX NCBI_TaxID=9913; RN [1] RP NUCLEOTIDE SEQUENCE [MRNA], AND PROTEIN SEQUENCE OF 2-19. RC TISSUE=Thymus; RX PubMed=1708495; DOI=10.1093/nar/19.5.1087; RA Robson C.N., Milne A.M., Pappin D.J.C., Hickson I.D.; RT "Isolation of cDNA clones encoding an enzyme from bovine cells that repairs RT oxidative DNA damage in vitro: homology with bacterial repair enzymes."; RL Nucleic Acids Res. 19:1087-1092(1991). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. RC STRAIN=Hereford; TISSUE=Basal ganglia; RG NIH - Mammalian Gene Collection (MGC) project; RL Submitted (AUG-2006) to the EMBL/GenBank/DDBJ databases. RN [3] RP PROTEIN SEQUENCE OF 2-23. RC TISSUE=Thymus; RX PubMed=2441359; DOI=10.1093/nar/15.14.5529; RA Henner W.D., Kiker N.P., Jorgensen T.J., Munck J.-N.; RT "Purification and amino-terminal amino acid sequence of an RT apurinic/apyrimidinic endonuclease from calf thymus."; RL Nucleic Acids Res. 15:5529-5544(1987). RN [4] RP PROTEIN SEQUENCE OF 34-38, FUNCTION, SUBCELLULAR LOCATION, AND TISSUE RP SPECIFICITY. RC TISSUE=Liver; RX PubMed=16617147; DOI=10.1093/nar/gkl177; RA Chattopadhyay R., Wiederhold L., Szczesny B., Boldogh I., Hazra T.K., RA Izumi T., Mitra S.; RT "Identification and characterization of mitochondrial abasic (AP)- RT endonuclease in mammalian cells."; RL Nucleic Acids Res. 34:2067-2076(2006). RN [5] RP 3D-STRUCTURE MODELING OF 40-318. RX PubMed=15607727; DOI=10.1016/j.bbrc.2004.11.103; RA Khurshid R., Salim A., Abbasi A.; RT "Three-dimensional structure prediction of bovine AP lyase, BAP1: RT prediction of interaction with DNA and alterations as a result of RT Arg176->Ala, Asp282->Ala, and His308->Asn mutations."; RL Biochem. Biophys. Res. Commun. 326:711-717(2005). CC -!- FUNCTION: Multifunctional protein that plays a central role in the CC cellular response to oxidative stress. The two major activities of CC APEX1 are DNA repair and redox regulation of transcriptional factors. CC Functions as an apurinic/apyrimidinic (AP) endodeoxyribonuclease in the CC DNA base excision repair (BER) pathway of DNA lesions induced by CC oxidative and alkylating agents. Initiates repair of AP sites in DNA by CC catalyzing hydrolytic incision of the phosphodiester backbone CC immediately adjacent to the damage, generating a single-strand break CC with 5'-deoxyribose phosphate and 3'-hydroxyl ends. Also incises at AP CC sites in the DNA strand of DNA/RNA hybrids, single-stranded DNA regions CC of R-loop structures, and single-stranded RNA molecules. Has 3'-5' CC exoribonuclease activity on mismatched deoxyribonucleotides at the 3' CC termini of nicked or gapped DNA molecules during short-patch BER. CC Possesses DNA 3' phosphodiesterase activity capable of removing lesions CC (such as phosphoglycolate) blocking the 3' side of DNA strand breaks. CC May also play a role in the epigenetic regulation of gene expression by CC participating in DNA demethylation. Acts as a loading factor for POLB CC onto non-incised AP sites in DNA and stimulates the 5'-terminal CC deoxyribose 5'-phosphate (dRp) excision activity of POLB. Plays a role CC in the protection from granzyme-mediated cellular repair leading to CC cell death. Also involved in the DNA cleavage step of class switch CC recombination (CSR). On the other hand, APEX1 also exerts reversible CC nuclear redox activity to regulate DNA binding affinity and CC transcriptional activity of transcriptional factors by controlling the CC redox status of their DNA-binding domain, such as the FOS/JUN AP-1 CC complex after exposure to IR. Involved in calcium-dependent down- CC regulation of parathyroid hormone (PTH) expression by binding to CC negative calcium response elements (nCaREs). Together with HNRNPL or CC the dimer XRCC5/XRCC6, associates with nCaRE, acting as an activator of CC transcriptional repression. Stimulates the YBX1-mediated MDR1 promoter CC activity, when acetylated at Lys-6 and Lys-7, leading to drug CC resistance. Acts also as an endoribonuclease involved in the control of CC single-stranded RNA metabolism. Plays a role in regulating MYC mRNA CC turnover by preferentially cleaving in between UA and CA dinucleotides CC of the MYC coding region determinant (CRD). In association with NMD1, CC plays a role in the rRNA quality control process during cell cycle CC progression. Associates, together with YBX1, on the MDR1 promoter. CC Together with NPM1, associates with rRNA. Binds DNA and RNA (By CC similarity). {ECO:0000250|UniProtKB:P27695, CC ECO:0000269|PubMed:16617147}. 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:0000250|UniProtKB:P27695}; CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; CC Evidence={ECO:0000250|UniProtKB:P27695}; CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; CC Evidence={ECO:0000250|UniProtKB:P27695}; CC Note=Probably binds two magnesium or manganese ions per subunit. CC {ECO:0000250|UniProtKB:P27695}; CC -!- ACTIVITY REGULATION: NPM1 stimulates endodeoxyribonuclease activity on CC double-stranded DNA with AP sites, but inhibits endoribonuclease CC activity on single-stranded RNA containing AP sites. CC {ECO:0000250|UniProtKB:P27695}. CC -!- SUBUNIT: Monomer. Homodimer; disulfide-linked. Component of the SET CC complex, composed of at least APEX1, SET, ANP32A, HMGB2, NME1 and CC TREX1. Associates with the dimer XRCC5/XRCC6 in a DNA-dependent manner. CC Interacts with SIRT1; the interaction is increased in the context of CC genotoxic stress. Interacts with HDAC1, HDAC2 and HDAC3; the CC interactions are not dependent on the APEX1 acetylation status. CC Interacts with XRCC1; the interaction is induced by SIRT1 and increased CC with the APEX1 acetylated form. Interacts with NPM1 (via N-terminal CC domain); the interaction is RNA-dependent and decreases in hydrogen CC peroxide-damaged cells. Interacts (via N-terminus) with YBX1 (via C- CC terminus); the interaction is increased in presence of APEX1 acetylated CC at Lys-6 and Lys-7. Interacts with HNRNPL; the interaction is DNA- CC dependent. Interacts (via N-terminus) with KPNA1 and KPNA2. Interacts CC with TXN; the interaction stimulates the FOS/JUN AP-1 complex DNA- CC binding activity in a redox-dependent manner. Interacts with GZMA, CC KRT8, MDM2, POLB, PRDX6, PRPF19, RPLP0, TOMM20 and WDR77. Binds to CDK5 CC (By similarity). {ECO:0000250|UniProtKB:P27695}. CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00764, CC ECO:0000269|PubMed:16617147}. Nucleus, nucleolus {ECO:0000250}. Nucleus CC speckle {ECO:0000255|PROSITE-ProRule:PRU00764}. Endoplasmic reticulum CC {ECO:0000250}. Cytoplasm {ECO:0000255|PROSITE-ProRule:PRU00764}. CC Note=Detected in the cytoplasm of B-cells stimulated to switch. CC Colocalized with SIRT1 in the nucleus. Colocalized with YBX1 in nuclear CC speckles after genotoxic stress. Together with OGG1 is recruited to CC nuclear speckles in UVA-irradiated cells. Colocalized with nucleolin CC and NPM1 in the nucleolus. Its nucleolar localization is cell cycle CC dependent and requires active rRNA transcription. Colocalized with CC calreticulin in the endoplasmic reticulum. Translocation from the CC nucleus to the cytoplasm is stimulated in presence of nitric oxide (NO) CC and function in a CRM1-dependent manner, possibly as a consequence of CC demasking a nuclear export signal (amino acid position 64-80). S- CC nitrosylation at Cys-93 and Cys-310 regulates its nuclear-cytosolic CC shuttling. Ubiquitinated form is localized predominantly in the CC cytoplasm. CC -!- SUBCELLULAR LOCATION: [DNA repair nuclease/redox regulator APEX1, CC mitochondrial]: Mitochondrion. Note=Translocation from the cytoplasm to CC the mitochondria is mediated by ROS signaling and cleavage mediated by CC granzyme A. Tom20-dependent translocated mitochondrial APEX1 level is CC significantly increased after genotoxic stress (By similarity). The CC cleaved APEX2 is only detected in mitochondria. {ECO:0000250}. CC -!- TISSUE SPECIFICITY: The mitochondrial form is expressed in liver (at CC protein level). Thymus. {ECO:0000269|PubMed:16617147}. CC -!- INDUCTION: By several DNA damaging agents. CC -!- DOMAIN: The N-terminus contains the redox activity while the C-terminus CC exerts the DNA AP-endodeoxyribonuclease activity; both function are CC independent in their actions. An unconventional mitochondrial targeting CC sequence (MTS) is harbored within the C-terminus, that appears to be CC masked by the N-terminal sequence containing the nuclear localization CC signal (NLS), that probably blocks the interaction between the MTS and CC Tom proteins (By similarity). {ECO:0000250}. CC -!- PTM: Phosphorylated. Phosphorylation by kinase PKC or casein kinase CK2 CC results in enhanced redox activity that stimulates binding of the CC FOS/JUN AP-1 complex to its cognate binding site. AP- CC endodeoxyribonuclease activity is not affected by CK2-mediated CC phosphorylation. Phosphorylation of Thr-233 by CDK5 in response to CC MPP(+)/MPTP (1-methyl-4-phenylpyridinium) reduces AP- CC endodeoxyribonuclease activity resulting in accumulation of DNA damage CC and contributing to neuronal death (By similarity). CC {ECO:0000250|UniProtKB:P27695}. CC -!- PTM: Acetylated on Lys-6 and Lys-7. Acetylation is increased by the CC transcriptional coactivator EP300 acetyltransferase, genotoxic agents CC like H(2)O(2) and methyl methanesulfonate (MMS). Acetylation increases CC its binding affinity to the negative calcium response element (nCaRE) CC DNA promoter. The acetylated form induces a stronger binding of YBX1 to CC the Y-box sequence in the MDR1 promoter than the unacetylated form. CC Deacetylated on lysines. Lys-6 and Lys-7 are deacetylated by SIRT1 (By CC similarity). {ECO:0000250|UniProtKB:P27695}. CC -!- PTM: Cleaved at Lys-31 by granzyme A to create the mitochondrial form; CC leading in reduction of binding to DNA, AP endodeoxyribonuclease CC activity, redox activation of transcription factors and to enhanced CC cell death. Cleaved by granzyme K; leading to intracellular ROS CC accumulation and enhanced cell death after oxidative stress (By CC similarity). {ECO:0000250|UniProtKB:P27695}. CC -!- PTM: Cys-69 and Cys-93 are nitrosylated in response to nitric oxide CC (NO) and lead to the exposure of the nuclear export signal (NES). CC {ECO:0000250|UniProtKB:P27695}. CC -!- PTM: Ubiquitinated by MDM2; leading to translocation to the cytoplasm CC and proteasomal degradation. {ECO:0000250|UniProtKB:P27695}. CC -!- MISCELLANEOUS: The specific activity of the cleaved mitochondrial CC endodeoxyribonuclease appears to be about 3-fold higher than of the CC full-length form. Extract of mitochondria, but not of nuclei or CC cytosol, cleaves recombinant APEX1 to generate a mitochondrial APEX1- CC sized product. {ECO:0000269|PubMed:1708495}. CC -!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family. CC {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; X56685; CAA40014.1; -; mRNA. DR EMBL; BC122610; AAI22611.1; -; mRNA. DR PIR; S26830; S26830. DR RefSeq; NP_788782.2; NM_176609.3. DR AlphaFoldDB; P23196; -. DR SMR; P23196; -. DR STRING; 9913.ENSBTAP00000003559; -. DR PaxDb; 9913-ENSBTAP00000003559; -. DR PeptideAtlas; P23196; -. DR GeneID; 281630; -. DR KEGG; bta:281630; -. DR CTD; 328; -. DR eggNOG; KOG1294; Eukaryota. DR HOGENOM; CLU_027539_1_3_1; -. DR InParanoid; P23196; -. DR OrthoDB; 161558at2759; -. DR TreeFam; TF315048; -. DR BRENDA; 4.2.99.18; 908. DR Proteomes; UP000009136; Unplaced. DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB. DR GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell. DR GO; GO:0005739; C:mitochondrion; ISS:UniProtKB. DR GO; GO:0016607; C:nuclear speck; ISS:UniProtKB. DR GO; GO:0005730; C:nucleolus; ISS:UniProtKB. DR GO; GO:0005654; C:nucleoplasm; ISS:UniProtKB. DR GO; GO:0005634; C:nucleus; ISS:UniProtKB. DR GO; GO:0048471; C:perinuclear region of cytoplasm; ISS:AgBase. DR GO; GO:0008408; F:3'-5' exonuclease activity; ISS:UniProtKB. DR GO; GO:0031490; F:chromatin DNA binding; ISS:UniProtKB. DR GO; GO:0052720; F:class II DNA-(apurinic or apyrimidinic site) endonuclease activity; ISS:UniProtKB. DR GO; GO:0003684; F:damaged DNA binding; ISS:UniProtKB. DR GO; GO:0003677; F:DNA binding; ISS:AgBase. DR GO; GO:0140431; F:DNA-(abasic site) binding; ISS:UniProtKB. DR GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; ISS:UniProtKB. DR GO; GO:0008311; F:double-stranded DNA 3'-5' DNA exonuclease activity; IBA:GO_Central. DR GO; GO:0046872; F:metal ion binding; ISS:AgBase. DR GO; GO:0016491; F:oxidoreductase activity; ISS:UniProtKB. DR GO; GO:0008081; F:phosphoric diester hydrolase activity; ISS:AgBase. DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW. DR GO; GO:0016890; F:site-specific endodeoxyribonuclease activity, specific for altered base; ISS:UniProtKB. DR GO; GO:0003713; F:transcription coactivator activity; ISS:AgBase. DR GO; GO:0006284; P:base-excision repair; IBA:GO_Central. DR GO; GO:0080111; P:DNA demethylation; ISS:UniProtKB. DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW. DR GO; GO:0006281; P:DNA repair; ISS:UniProtKB. DR GO; GO:0042981; P:regulation of apoptotic process; ISS:UniProtKB. DR GO; GO:0043488; P:regulation of mRNA stability; ISS:UniProtKB. DR CDD; cd09087; Ape1-like_AP-endo; 1. DR Gene3D; 3.60.10.10; Endonuclease/exonuclease/phosphatase; 1. DR InterPro; IPR004808; AP_endonuc_1. DR InterPro; IPR020847; AP_endonuclease_F1_BS. DR InterPro; IPR020848; AP_endonuclease_F1_CS. DR InterPro; IPR036691; Endo/exonu/phosph_ase_sf. DR InterPro; IPR005135; Endo/exonuclease/phosphatase. DR NCBIfam; TIGR00195; exoDNase_III; 1. DR NCBIfam; TIGR00633; xth; 1. DR PANTHER; PTHR22748; AP ENDONUCLEASE; 1. DR PANTHER; PTHR22748:SF6; DNA-(APURINIC OR APYRIMIDINIC SITE) ENDONUCLEASE; 1. DR Pfam; PF03372; Exo_endo_phos; 1. DR SUPFAM; SSF56219; DNase I-like; 1. DR PROSITE; PS00726; AP_NUCLEASE_F1_1; 1. DR PROSITE; PS00727; AP_NUCLEASE_F1_2; 1. DR PROSITE; PS00728; AP_NUCLEASE_F1_3; 1. DR PROSITE; PS51435; AP_NUCLEASE_F1_4; 1. PE 1: Evidence at protein level; KW Acetylation; Activator; Cleavage on pair of basic residues; Cytoplasm; KW Direct protein sequencing; Disulfide bond; DNA damage; DNA recombination; KW DNA repair; DNA-binding; Endonuclease; Endoplasmic reticulum; Exonuclease; KW Hydrolase; Magnesium; Metal-binding; Mitochondrion; Nuclease; Nucleus; KW Phosphoprotein; Reference proteome; Repressor; RNA-binding; KW S-nitrosylation; Transcription; Transcription regulation; Ubl conjugation. FT INIT_MET 1 FT /note="Removed" FT /evidence="ECO:0000269|PubMed:1708495, FT ECO:0000269|PubMed:2441359" FT CHAIN 2..318 FT /note="DNA repair nuclease/redox regulator APEX1" FT /id="PRO_0000200009" FT CHAIN 32..318 FT /note="DNA repair nuclease/redox regulator APEX1, FT mitochondrial" FT /id="PRO_0000402571" FT REGION 1..59 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 2..33 FT /note="Necessary for interaction with YBX1, binding to RNA, FT association together with NPM1 to rRNA, endoribonuclease FT activity on abasic RNA and localization in the nucleoli" FT /evidence="ECO:0000250" FT REGION 23..33 FT /note="Necessary for interaction with NPM1 and for FT efficient rRNA binding" FT /evidence="ECO:0000250" FT REGION 289..318 FT /note="Mitochondrial targeting sequence (MTS)" FT /evidence="ECO:0000250" FT MOTIF 8..13 FT /note="Nuclear localization signal (NLS)" FT /evidence="ECO:0000250" FT MOTIF 64..80 FT /note="Nuclear export signal (NES)" FT /evidence="ECO:0000250" FT COMPBIAS 1..41 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT ACT_SITE 171 FT /evidence="ECO:0000250" FT ACT_SITE 210 FT /note="Proton donor/acceptor" FT /evidence="ECO:0000250" FT BINDING 70 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000250" FT BINDING 96 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000250" FT BINDING 210 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000250" FT BINDING 212 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000250" FT BINDING 308 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000250" FT SITE 31..32 FT /note="Cleavage; by granzyme A" FT /evidence="ECO:0000250" FT SITE 212 FT /note="Transition state stabilizer" FT /evidence="ECO:0000250" FT SITE 283 FT /note="Important for catalytic activity" FT /evidence="ECO:0000250" FT SITE 309 FT /note="Interaction with DNA substrate" FT /evidence="ECO:0000250" FT MOD_RES 6 FT /note="N6-acetyllysine; by EP300" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 7 FT /note="N6-acetyllysine; by EP300" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 27 FT /note="N6-acetyllysine" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 31 FT /note="N6-acetyllysine" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 32 FT /note="N6-acetyllysine" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 35 FT /note="N6-acetyllysine" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 54 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 65 FT /note="S-nitrosocysteine; alternate" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 93 FT /note="S-nitrosocysteine; alternate" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 197 FT /note="N6-acetyllysine" FT /evidence="ECO:0000250|UniProtKB:P27695" FT MOD_RES 233 FT /note="Phosphothreonine; by CDK5" FT /evidence="ECO:0000250|UniProtKB:P28352" FT MOD_RES 310 FT /note="S-nitrosocysteine" FT /evidence="ECO:0000250|UniProtKB:P27695" FT DISULFID 65..93 FT /note="Alternate" FT /evidence="ECO:0000250" FT CONFLICT 21..22 FT /note="PE -> LP (in Ref. 3; AA sequence)" FT /evidence="ECO:0000305" FT CONFLICT 291 FT /note="V -> L (in Ref. 2; AAI22611)" FT /evidence="ECO:0000305" SQ SEQUENCE 318 AA; 35570 MW; 40C733FBA2EA738D CRC64; MPKRGKKGAV VEDAEEPKTE PEAKKSKAGA KKNEKEAVGE GAVLYEDPPD QKTSPSGKSA TLKICSWNVD GLRAWIKKKG LDWVKEEAPD ILCLQETKCS ENKLPVELQE LSGLSHQYWS APSDKEGYSG VGLLSRQCPL KVSYGIGEEE HDQEGRVIVA EYDAFVLVTA YVPNAGRGLV RLEYRQRWDE AFRKFLKGLA SRKPLVLCGD LNVAHEEIDL RNPKGNKKNA GFTPQERQGF GELLQAVPLT DSFRHLYPNT AYAYTFWTYM MNARSKNVGW RLDYFLLSQS VLPALCDSKI RSKALGSDHC PITLYLAL //