P43138 (APEX1_RAT) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-(apurinic or apyrimidinic site) lyase
EC=3.1.-.-
EC=4.2.99.18

Alternative name(s):
APEX nuclease
Short name=APEN
Apurinic-apyrimidinic endonuclease 1
Short name=AP endonuclease 1
REF-1
Redox factor-1

Cleaved into the following chain:

1. DNA-(apurinic or apyrimidinic site) lyase, mitochondrial

Gene names

Name:	Apex1
Synonyms:	Ape, Apex, Ref1

Organism

Rattus norvegicus (Rat)

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	317 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Multifunctional protein that plays a central role in the cellular response to oxidative stress. The two major activities of APEX1 in 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, 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. Ref.7
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.
Enzyme regulation	NPM1 stimulates endodeoxyribonuclease activity on double-stranded DNA with AP sites, but inhibits endoribonuclease activity on single-stranded RNA containing AP sites By similarity.
Subunit structure	Monomer. Homodimer; disulfide-linked. Component of the SET complex, composed at least of APEX1, GZMA, SET, ANP32A, HMGB2 and NME1. 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. 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 By similarity. Binds to CDK5 By similarity.
Subcellular location	Nucleus. Nucleus › nucleolus By similarity. Nucleus speckle By similarity. Endoplasmic reticulum By similarity. Cytoplasm By similarity. 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. Detected in the cytoplasm of B cells stimulated to switch. Ubiquitinated form is localized predominantly in the cytoplasm By similarity. Ref.6 DNA-(apurinic or apyrimidinic site) lyase, mitochondrial: Mitochondrion. Note: The cleaved APEX2 is only detected in mitochondria. 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. Ref.6
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.
Post-translational modification	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. 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 By similarity. Acetylated on Lys-6. Acetylation is increased by the transcriptional coactivator EP300 acetyltransferase, genotoxic agents like H2O2 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 is deacetylated by SIRT1 By similarity. 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. Cys-64 and Cys-92 are nitrosylated in response to nitric oxide (NO) and lead to the exposure of the nuclear export signal (NES) By similarity. Ubiquitinated by MDM2; leading to translocation to the cytoplasm and proteasomal degradation By similarity.
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.
Sequence similarities	Belongs to the DNA repair enzymes AP/ExoA family.

Ontologies

Keywords
Biological process	DNA damage DNA recombination DNA repair Transcription Transcription regulation
Cellular component	Cytoplasm Endoplasmic reticulum Mitochondrion Nucleus
Ligand	DNA-binding Magnesium Metal-binding RNA-binding
Molecular function	Activator Endonuclease Exonuclease Hydrolase Lyase Nuclease Repressor
PTM	Acetylation Cleavage on pair of basic residues Disulfide bond Phosphoprotein S-nitrosylation Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA demethylation Inferred from sequence or structural similarity. Source: UniProtKB DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA repair Inferred from sequence or structural similarity. Source: UniProtKB aging Inferred from direct assay. Source: RGD cellular response to cAMP Inferred from expression pattern. Source: RGD cellular response to hydrogen peroxide Inferred from direct assay. Source: RGD cellular response to organic nitrogen Inferred from expression pattern. Source: RGD cellular response to peptide hormone stimulus Inferred from expression pattern. Source: RGD negative regulation of smooth muscle cell migration Inferred from mutant phenotype. Source: RGD positive regulation of DNA repair Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of S phase of mitotic cell cycle Inferred from mutant phenotype. Source: RGD positive regulation of anti-apoptosis Inferred from sequence or structural similarity. Source: UniProtKB regulation of mRNA stability Inferred from sequence or structural similarity. Source: UniProtKB regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW response to drug Inferred from expression pattern. Source: RGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	endoplasmic reticulum Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrion Inferred from direct assay Ref.6. Source: RGD nuclear speck Inferred from sequence or structural similarity. Source: UniProtKB nucleolus Inferred from sequence or structural similarity. Source: UniProtKB perinuclear region of cytoplasm Inferred from sequence or structural similarity. Source: UniProtKB transcription factor complex Inferred from direct assay. Source: RGD
Molecular function	3'-5' exonuclease activity Inferred from sequence or structural similarity. Source: UniProtKB DNA-(apurinic or apyrimidinic site) lyase activity Inferred from electronic annotation. Source: EC NF-kappaB binding Inferred from direct assay. Source: RGD RNA binding Inferred from electronic annotation. Source: UniProtKB-KW chromatin DNA binding Inferred from sequence or structural similarity. Source: UniProtKB damaged DNA binding Inferred from sequence or structural similarity. Source: UniProtKB endoribonuclease activity Inferred from direct assay Ref.7. Source: RGD metal ion binding Inferred from sequence or structural similarity. Source: UniProtKB oxidoreductase activity Inferred from sequence or structural similarity. Source: UniProtKB site-specific endodeoxyribonuclease activity, specific for altered base Inferred from sequence or structural similarity. Source: UniProtKB transcription coactivator activity Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed By similarity
	Chain	2 – 317	316	DNA-(apurinic or apyrimidinic site) lyase		PRO_0000200012
	Chain	31 – 317	287	DNA-(apurinic or apyrimidinic site) lyase, mitochondrial By similarity		PRO_0000402574
Regions
	Region	2 – 32	31	Necessary for interaction with YBX1, binding to RNA, association together with NPM1 to rRNA, endoribonuclease activity on abasic RNA and localization in the nucleoli By similarity
	Region	8 – 12	5	Nuclear localization signal (NLS) By similarity
	Region	22 – 32	11	Necessary for interaction with NPM1 and for efficient rRNA binding By similarity
	Region	63 – 79	17	Nuclear export signal (NES) By similarity
	Region	288 – 317	30	Mitochondrial targeting sequence (MTS) By similarity
Sites
	Active site	308	1	Proton acceptor By similarity
	Metal binding	67	1	Magnesium or manganese By similarity
	Metal binding	95	1	Magnesium or manganese By similarity
	Metal binding	209	1	Magnesium or manganese By similarity
	Metal binding	211	1	Magnesium or manganese By similarity
	Metal binding	307	1	Magnesium or manganese By similarity
	Metal binding	308	1	Magnesium or manganese By similarity
	Site	30 – 31	2	Cleavage; by granzyme A By similarity
Amino acid modifications
	Modified residue	6	1	N6-acetyllysine; by EP300 By similarity
	Modified residue	26	1	N6-acetyllysine By similarity
	Modified residue	30	1	N6-acetyllysine By similarity
	Modified residue	31	1	N6-acetyllysine By similarity
	Modified residue	34	1	N6-acetyllysine By similarity
	Modified residue	64	1	S-nitrosocysteine By similarity
	Modified residue	92	1	S-nitrosocysteine By similarity
	Modified residue	196	1	N6-acetyllysine By similarity
	Modified residue	232	1	Phosphothreonine; by CDK5 By similarity
	Modified residue	261	1	Phosphotyrosine By similarity
	Modified residue	309	1	S-nitrosocysteine By similarity
	Disulfide bond	64 ↔ 92		By similarity
Experimental info
	Sequence conflict	10	1	Missing in AAA21019. Ref.1
	Sequence conflict	236	1	R → A in AAA21019. Ref.1
	Sequence conflict	288	1	H → Q in AAA21019. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P43138 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: FBA6293C739E7804	FASTA	317	35,538
	10 20 30 40 50 60 MPKRGKRAAA EDGEEPKSEP ETKKSKGAAK KTEKEAAGEG PVLYEDPPDQ KTSASGKSAT 70 80 90 100 110 120 LKICSWNVDG LRAWIKKKGL DWVKEEAPDI LCLQETKCSE NKLPAELQEL PGLTHQYWSA 130 140 150 160 170 180 PSDKEGYSGV GLLSRQCPLK VSYGIGEEEH DQEGRVIVAE FESFILVTAY VPNAGRGLVR 190 200 210 220 230 240 LEYRQRWDEA FRKFLKDLAS RKPLVLCGDL NVAHEEIDLR NPKGNKKNAG FTPQERQGFG 250 260 270 280 290 300 EMLQAVPLAD SFRHLYPNTA YAYTFWTYMM NARSKNVGWR LDYFLLSHSL LPALCDSKIR 310 SKALGSDHCP ITLYLAL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning of the multifunctional rat apurinic/apyrimidinic endonuclease (rAPEN)/redox factor from an immature T cell line." Wilson T.M., Carney J.P., Kelley M.R. Nucleic Acids Res. 22:530-531(1994) [PubMed: 7510394] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: Sprague-Dawley. Tissue: Testis.
[2]	"Genomic structure of the rat major AP endonuclease gene (Apex) with an adjacent putative O-sialoglycoprotease gene (Prsmg1/Gcpl1) and a processed Apex pseudogene (Apexp1)." Yao M., Akiyama K., Tan Y., Sarker A.H., Ikeda S., Alam S.S., Tsutsui K., Yoshida M.C., Seki S. Acta Med. Okayama 53:245-252(1999) [PubMed: 10631378] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"cDNA and deduced amino acid sequence of rat APEX nuclease." Tan Y., Akiyama K., Seki S., Tabayashi T., Taniyama M. Submitted (DEC-1994) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: Sprague-Dawley. Tissue: Brain.
[4]	"Cloning of APEX cDNA gene from PC12 cell line." Xie Z.H., Liu C.Z., Wang A.M., Ma C. Submitted (SEP-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Pheochromocytoma.
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Kidney.
[6]	"Mitochondrial localization of APE/Ref-1 in thyroid cells." Tell G., Crivellato E., Pines A., Paron I., Pucillo C., Manzini G., Bandiera A., Kelley M.R., Di Loreto C., Damante G. Mutat. Res. 485:143-152(2001) [PubMed: 11182545] [Abstract] Cited for: SUBCELLULAR LOCATION.
[7]	"Identification of apurinic/apyrimidinic endonuclease 1 (APE1) as the endoribonuclease that cleaves c-myc mRNA." Barnes T., Kim W.C., Mantha A.K., Kim S.E., Izumi T., Mitra S., Lee C.H. Nucleic Acids Res. 37:3946-3958(2009) [PubMed: 19401441] [Abstract] Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	L27076 mRNA. Translation: AAA21019.1. AB023065 Genomic DNA. Translation: BAA82124.1. D44495 mRNA. Translation: BAA07938.1. AF309114 mRNA. Translation: AAG40859.1. BC078816 mRNA. Translation: AAH78816.1.
IPI	IPI00231964.
PIR	S42397.
RefSeq	NP_077062.1. NM_024148.1.
UniGene	Rn.5949.
3D structure databases
ProteinModelPortal	P43138.
SMR	P43138. Positions 39-317.
ModBase	Search...
Protein-protein interaction databases
STRING	P43138.
Proteomic databases
PRIDE	P43138.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSRNOT00000013176; ENSRNOP00000013176; ENSRNOG00000009663.
GeneID	79116.
KEGG	rno:79116.
NMPDR	fig|10116.3.peg.11232.
UCSC	NM_024148. rat.
Organism-specific databases
CTD	328.
RGD	2126. Apex1.
Phylogenomic databases
eggNOG	maNOG08727.
HOVERGEN	HBG050531.
InParanoid	P43138.
OMA	LDYRMKW.
OrthoDB	EOG44J2JD.
PhylomeDB	P43138.
Gene expression databases
ArrayExpress	P43138.
Genevestigator	P43138.
GermOnline	ENSRNOG00000009663. Rattus norvegicus.
Family and domain databases
InterPro	IPR000097. AP_endonuclease_F1. IPR020847. AP_endonuclease_F1_BS. IPR020848. AP_endonuclease_F1_CS. IPR005135. Endo/exonuclease/phosphatase. IPR004808. ExoDNase_III. [Graphical view]
KO	K10771.
PANTHER	PTHR22748. ExoIII_xth. 1 hit.
Pfam	PF03372. Exo_endo_phos. 1 hit. [Graphical view]
SUPFAM	SSF56219. Exo_endo_phos. 1 hit.
TIGRFAMs	TIGR00195. ExoDNase_III. 1 hit. TIGR00633. Xth. 1 hit.
PROSITE	PS00726. AP_NUCLEASE_F1_1. 1 hit. PS00727. AP_NUCLEASE_F1_2. 1 hit. PS00728. AP_NUCLEASE_F1_3. 1 hit. PS51435. AP_NUCLEASE_F1_4. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	614526.

Entry information

Entry name

APEX1_RAT

Accession

Primary (citable) accession number: P43138
Secondary accession number(s): Q548N9

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 110 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program