APEX1 (apurinic/apyrimidinic endodeoxyribonuclease 1)

Gene

• Entrez ID: 328
• Gene name: Apurinic/apyrimidinic endodeoxyribonuclease 1
• Gene symbol: APEX1
• Synonyms: APE, APE1, APEN, APEX, APX, HAP1, REF1
• Chromosome: 14
• Chromosome location: 14q11.2
• Summary: The APEX gene encodes the major AP endonuclease in human cells. It encodes the APEX endonuclease, a DNA repair enzyme with apurinic/apyrimidinic (AP) activity. Such AP activity sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. The AP sites are the most frequent pre-mutagenic lesions that can prevent normal DNA replication. Splice variants have been found for this gene; all encode the same protein. Disruptions in the biological functions related to APEX are associated with many various malignancies and neurodegenerative diseases.[provided by RefSeq, Dec 2019]

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT036701	hsa-miR-935	CLASH	23622248
MIRT045386	hsa-miR-185-5p	CLASH	23622248
MIRT048405	hsa-miR-100-5p	CLASH	23622248
MIRT048610	hsa-miR-99a-5p	CLASH	23622248
MIRT050830	hsa-miR-17-5p	CLASH	23622248
MIRT341107	hsa-miR-27a-5p	PAR-CLIP	23592263
MIRT341107	hsa-miR-27a-5p	PAR-CLIP	26701625
MIRT481768	hsa-miR-2909	PAR-CLIP	23592263
MIRT481769	hsa-miR-7977	PAR-CLIP	23592263
MIRT481769	hsa-miR-7977	PAR-CLIP	26701625
MIRT481770	hsa-miR-331-5p	PAR-CLIP	23592263
MIRT481770	hsa-miR-331-5p	PAR-CLIP	20371350
MIRT481771	hsa-miR-4278	PAR-CLIP	23592263
MIRT481772	hsa-miR-6789-5p	PAR-CLIP	23592263
MIRT481773	hsa-miR-6824-5p	PAR-CLIP	23592263
MIRT481774	hsa-miR-597-5p	PAR-CLIP	23592263
MIRT481774	hsa-miR-597-5p	PAR-CLIP	20371350
MIRT481775	hsa-miR-4483	PAR-CLIP	23592263
MIRT481776	hsa-miR-1293	PAR-CLIP	23592263
MIRT481777	hsa-miR-608	PAR-CLIP	23592263
MIRT481778	hsa-miR-4651	PAR-CLIP	23592263
MIRT481779	hsa-miR-6848-5p	PAR-CLIP	23592263
MIRT481779	hsa-miR-6848-5p	PAR-CLIP	26701625
MIRT481780	hsa-miR-6846-5p	PAR-CLIP	23592263
MIRT481780	hsa-miR-6846-5p	PAR-CLIP	26701625
MIRT481781	hsa-miR-4726-3p	PAR-CLIP	23592263
MIRT481781	hsa-miR-4726-3p	PAR-CLIP	26701625
MIRT481782	hsa-miR-6764-5p	PAR-CLIP	23592263
MIRT481782	hsa-miR-6764-5p	PAR-CLIP	26701625
MIRT481783	hsa-miR-1915-3p	PAR-CLIP	23592263
MIRT481783	hsa-miR-1915-3p	PAR-CLIP	26701625
MIRT481784	hsa-miR-6840-3p	PAR-CLIP	23592263
MIRT481784	hsa-miR-6840-3p	PAR-CLIP	26701625
MIRT481785	hsa-miR-484	PAR-CLIP	23592263
MIRT481785	hsa-miR-484	PAR-CLIP	26701625
MIRT481786	hsa-miR-3155b	PAR-CLIP	23592263
MIRT481786	hsa-miR-3155b	PAR-CLIP	26701625
MIRT481787	hsa-miR-3155a	PAR-CLIP	23592263
MIRT481787	hsa-miR-3155a	PAR-CLIP	26701625
MIRT481788	hsa-miR-6890-3p	PAR-CLIP	23592263
MIRT481789	hsa-miR-520h	PAR-CLIP	23592263
MIRT481789	hsa-miR-520h	PAR-CLIP	26701625
MIRT481790	hsa-miR-520g-3p	PAR-CLIP	23592263
MIRT481790	hsa-miR-520g-3p	PAR-CLIP	26701625
MIRT481791	hsa-miR-3973	PAR-CLIP	23592263
MIRT481791	hsa-miR-3973	PAR-CLIP	26701625
MIRT481792	hsa-miR-135a-3p	PAR-CLIP	23592263
MIRT481792	hsa-miR-135a-3p	PAR-CLIP	20371350
MIRT481793	hsa-miR-8062	PAR-CLIP	23592263
MIRT481794	hsa-miR-8079	PAR-CLIP	23592263
MIRT481795	hsa-miR-1245a	PAR-CLIP	23592263
MIRT481796	hsa-miR-4678	PAR-CLIP	23592263
MIRT481796	hsa-miR-4678	PAR-CLIP	20371350
MIRT481797	hsa-miR-6782-5p	PAR-CLIP	23592263
MIRT481798	hsa-miR-6805-5p	PAR-CLIP	23592263
MIRT481798	hsa-miR-6805-5p	PAR-CLIP	26701625
MIRT481799	hsa-miR-1197	PAR-CLIP	23592263
MIRT481799	hsa-miR-1197	PAR-CLIP	20371350
MIRT481800	hsa-miR-548ah-5p	PAR-CLIP	23592263
MIRT481800	hsa-miR-548ah-5p	PAR-CLIP	26701625
MIRT481801	hsa-miR-3609	PAR-CLIP	23592263
MIRT481801	hsa-miR-3609	PAR-CLIP	26701625
MIRT481802	hsa-miR-27b-3p	HITS-CLIP	22473208
MIRT481802	hsa-miR-27b-3p	PAR-CLIP	23592263
MIRT481802	hsa-miR-27b-3p	PAR-CLIP	20371350
MIRT481803	hsa-miR-27a-3p	HITS-CLIP	22473208
MIRT481803	hsa-miR-27a-3p	PAR-CLIP	23592263
MIRT481803	hsa-miR-27a-3p	PAR-CLIP	20371350
MIRT481804	hsa-miR-128-3p	PAR-CLIP	23592263
MIRT481804	hsa-miR-128-3p	PAR-CLIP	20371350
MIRT481805	hsa-miR-216a-3p	PAR-CLIP	23592263
MIRT481805	hsa-miR-216a-3p	PAR-CLIP	20371350
MIRT481806	hsa-miR-3681-3p	PAR-CLIP	23592263
MIRT481806	hsa-miR-3681-3p	PAR-CLIP	20371350
MIRT736125	hsa-miR-1226-5p	PAR-CLIP	26701625
MIRT738500	hsa-miR-1914-3p	PAR-CLIP	26701625
MIRT740850	hsa-miR-3184-5p	PAR-CLIP	26701625
MIRT743249	hsa-miR-423-5p	PAR-CLIP	26701625
MIRT749964	hsa-miR-5194	PAR-CLIP	26701625
MIRT754135	hsa-miR-6734-5p	PAR-CLIP	26701625
MIRT754259	hsa-miR-6738-5p	PAR-CLIP	26701625
MIRT757159	hsa-miR-6834-5p	PAR-CLIP	26701625

Transcription factors

Transcription factor	Regulation	Reference
HIF1A	Repression	19524065
SP1	Repression	18208837
SP1	Unknown	7534297
USF1	Unknown	7534297

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000723	Process	Telomere maintenance	IDA	24703901
GO:0000781	Component	Chromosome, telomeric region	IC	24703901
GO:0003677	Function	DNA binding	IDA	11286553
GO:0003684	Function	Damaged DNA binding	IDA	12524539, 14706345, 24703901
GO:0003691	Function	Double-stranded telomeric DNA binding	IDA	24703901
GO:0003713	Function	Transcription coactivator activity	IDA	9119221, 18809583
GO:0003714	Function	Transcription corepressor activity	TAS	7961715
GO:0003723	Function	RNA binding	HDA	22681889
GO:0003906	Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	IBA	21873635
GO:0003906	Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	IDA	8932386, 15707971, 18973764, 19188445, 24703901
GO:0003906	Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	TAS	9119221
GO:0004519	Function	Endonuclease activity	IDA	11478795
GO:0004520	Function	Endodeoxyribonuclease activity	TAS
GO:0004523	Function	RNA-DNA hybrid ribonuclease activity	TAS	11286553
GO:0004528	Function	Phosphodiesterase I activity	IBA	21873635
GO:0004528	Function	Phosphodiesterase I activity	TAS	9119221
GO:0004844	Function	Uracil DNA N-glycosylase activity	TAS
GO:0005515	Function	Protein binding	IPI	8621488, 9108029, 9207062, 11118054, 11809897, 12524539, 15518571, 15942031, 18809583, 19188445, 19465398, 19505873, 19934257, 20231292, 20696907, 20808282, 20856196, 32911434
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IDA	9119221, 15942031, 19934257, 28404743
GO:0005654	Component	Nucleoplasm	IDA	17148573
GO:0005654	Component	Nucleoplasm	TAS
GO:0005667	Component	Transcription regulator complex	IEA
GO:0005730	Component	Nucleolus	IDA	17148573, 19188445
GO:0005737	Component	Cytoplasm	IDA	9560228
GO:0005739	Component	Mitochondrion	IDA	20231292
GO:0005783	Component	Endoplasmic reticulum	TAS	12524539
GO:0005813	Component	Centrosome	IDA
GO:0005840	Component	Ribosome	TAS	12524539
GO:0006281	Process	DNA repair	IDA	9560228
GO:0006284	Process	Base-excision repair	IBA	21873635
GO:0006284	Process	Base-excision repair	IDA	8932386
GO:0006284	Process	Base-excision repair	TAS
GO:0006286	Process	Base-excision repair, base-free sugar-phosphate removal	TAS
GO:0006310	Process	DNA recombination	IEA
GO:0007568	Process	Aging	IEA
GO:0008081	Function	Phosphoric diester hydrolase activity	IDA	11478795, 18973764
GO:0008309	Function	Double-stranded DNA exodeoxyribonuclease activity	IDA	24703901
GO:0008311	Function	Double-stranded DNA 3'-5' exodeoxyribonuclease activity	IBA	21873635
GO:0008408	Function	3'-5' exonuclease activity	IDA	11832948
GO:0008408	Function	3'-5' exonuclease activity	TAS	11286553
GO:0014912	Process	Negative regulation of smooth muscle cell migration	IEA
GO:0016491	Function	Oxidoreductase activity	IDA	9119221, 12524539
GO:0016607	Component	Nuclear speck	IDA	17148573
GO:0016890	Function	Site-specific endodeoxyribonuclease activity, specific for altered base	IDA	19188445, 24703901
GO:0031490	Function	Chromatin DNA binding	IDA	11809897
GO:0042493	Process	Response to drug	IEA
GO:0042981	Process	Regulation of apoptotic process	IDA	19934257
GO:0043488	Process	Regulation of mRNA stability	IMP	19401441
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0045454	Process	Cell redox homeostasis	IEA
GO:0045892	Process	Negative regulation of transcription, DNA-templated	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	18809583
GO:0046872	Function	Metal ion binding	IDA	11286553
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	12524539
GO:0051059	Function	NF-kappaB binding	IEA
GO:0070301	Process	Cellular response to hydrogen peroxide	IEA
GO:0071320	Process	Cellular response to cAMP	IEA
GO:0071375	Process	Cellular response to peptide hormone stimulus	IEA
GO:0080111	Process	DNA demethylation	IDA	21496894
GO:0090502	Process	RNA phosphodiester bond hydrolysis, endonucleolytic	IEA
GO:0097698	Process	Telomere maintenance via base-excision repair	IDA	24703901
GO:1900087	Process	Positive regulation of G1/S transition of mitotic cell cycle	IEA

Other IDs

• MIM: 107748
• HGNC: 587
• e!Ensembl: ENSG00000100823

Protein

• UniProt ID: P27695
• Protein name: DNA-(apurinic or apyrimidinic site) endonuclease (EC 3.1.-.-) (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease 1) (AP endonuclease 1) (APE-1) (REF-1) (Redox factor-1) [Cleaved into: DNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial]
• Protein 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.
• PDB: 1BIX, 1CQG, 1CQH, 1DE8, 1DE9, 1DEW, 1E9N, 1HD7, 2ISI, 2O3H, 3U8U, 4IEM, 4LND, 4QH9, 4QHD, 4QHE, 5CFG, 5DFF, 5DFH, 5DFI, 5DFJ, 5DG0, 5WN0, 5WN1, 5WN2, 5WN3, 5WN4, 5WN5, 6BOQ, 6BOR, 6BOS, 6BOT, 6BOU, 6BOV, 6BOW, 6MK3, 6MKK, 6MKM, 6MKO, 6P93, 6P94, 6W0Q, 6W2P, 6W3L, 6W3N, 6W3Q, 6W3U, 6W43, 6W4I, 6W4T
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF03372	Exo_endo_phos	65 → 309	Endonuclease/Exonuclease/phosphatase family	Domain

• Sequence:

  MPKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPA
  TLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWS
  APSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLV
  RLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGF
  GELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKI
  RSKALGSDHCPITLYLAL

• Sequence length: 318