A1YFZ3 (APEX1_PANPA) 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, BAP1, REF1

Organism

Pan paniscus (Pygmy chimpanzee) (Bonobo)

Taxonomic identifier

9597 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Pan

Protein attributes

Sequence length	318 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

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 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 By similarity.
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.
Cofactor	Magnesium. Can also utilize manganese. Probably binds two magnesium or manganese ions per subunit By similarity.
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 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 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: Detected in the cytoplasm of B-cells stimulated to switch. 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 By similarity. 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 64-80). S-nitrosylation at Cys-93 and Cys-310 regulates its nuclear-cytosolic shuttling. Ubiquitinated form is localized predominantly in the cytoplasm By similarity. 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. The cleaved APEX2 is only detected in mitochondria By similarity.
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-233 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 and Lys-7. 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 and Lys-7 are deacetylated by SIRT1 By similarity. Cleaved at Lys-31 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-69 and Cys-93 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
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 positive regulation of DNA repair 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 transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	endoplasmic reticulum Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrion Inferred from sequence or structural similarity. Source: UniProtKB nuclear speck Inferred from sequence or structural similarity. Source: UniProtKB nucleolus Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	3'-5' exonuclease activity Inferred from sequence or structural similarity. Source: UniProtKB DNA-(apurinic or apyrimidinic site) lyase activity Inferred from sequence or structural similarity. Source: UniProtKB 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 metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW 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
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 – 318	317	DNA-(apurinic or apyrimidinic site) lyase		PRO_0000285546
	Chain	32 – 318	287	DNA-(apurinic or apyrimidinic site) lyase, mitochondrial		PRO_0000402808
Regions
	Region	2 – 33	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 By similarity
	Region	8 – 13	6	Nuclear localization signal (NLS) By similarity
	Region	23 – 33	11	Necessary for interaction with NPM1 and for efficient rRNA binding By similarity
	Region	64 – 80	17	Nuclear export signal (NES) By similarity
	Region	289 – 318	30	Mitochondrial targeting sequence (MTS) By similarity
Sites
	Active site	171	1	By similarity
	Active site	210	1	Proton donor/acceptor By similarity
	Metal binding	70	1	Magnesium 1 By similarity
	Metal binding	96	1	Magnesium 1 By similarity
	Metal binding	210	1	Magnesium 2 By similarity
	Metal binding	212	1	Magnesium 2 By similarity
	Metal binding	308	1	Magnesium 1 By similarity
	Site	31 – 32	2	Cleavage; by granzyme A By similarity
	Site	212	1	Transition state stabilizer By similarity
	Site	283	1	Important for catalytic activity By similarity
	Site	309	1	Interaction with DNA substrate By similarity
Amino acid modifications
	Modified residue	6	1	N6-acetyllysine; by EP300 By similarity
	Modified residue	7	1	N6-acetyllysine; by EP300 By similarity
	Modified residue	27	1	N6-acetyllysine By similarity
	Modified residue	31	1	N6-acetyllysine By similarity
	Modified residue	32	1	N6-acetyllysine By similarity
	Modified residue	35	1	N6-acetyllysine By similarity
	Modified residue	65	1	S-nitrosocysteine By similarity
	Modified residue	93	1	S-nitrosocysteine By similarity
	Modified residue	197	1	N6-acetyllysine By similarity
	Modified residue	233	1	Phosphothreonine; by CDK5 By similarity
	Modified residue	310	1	S-nitrosocysteine By similarity
	Disulfide bond	65 ↔ 93		By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1YFZ3 [UniParc]. Last modified February 6, 2007. Version 1. Checksum: B943A23BF487B5D3	FASTA	318	35,569
	10 20 30 40 50 60 MPKRGKKGAV AEDGDELRTE PEAKKSKTAA KKNDKEAAGE GPALYEDPPD QKTSPSGKPA 70 80 90 100 110 120 TLKICSWNVD GLRAWIKKKG LDWVKEEAPD ILCLQETKCS ENKLPAELQE LPGLSHQYWS 130 140 150 160 170 180 APSDKEGYSG VGLLSRQCPL KVSYGIGEEE HDQEGRVIVA EFDSFVLVTA YVPNAGRGLV 190 200 210 220 230 240 RLEYRQRWDE AFRKFLKGLA SRKPLVLCGD LNVAHEEIDL RNPKGNKKNA GFTPQERQGF 250 260 270 280 290 300 GELLQAVPLA DSFRHLYPNT PYAYTFWTYM MNARSKNVGW RLDYFLLSHS LLPALCDSKI 310 RSKALGSDHC PITLYLAL

References

[1]	"Positive selection in transcription factor genes on the human lineage." Nickel G.C., Tefft D.L., Trevarthen K., Funt J., Adams M.D. Submitted (AUG-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	DQ977185 Genomic DNA. Translation: ABM54218.1.
RefSeq	XP_003811777.1. XM_003811729.1. XP_003811778.1. XM_003811730.1. XP_003811779.1. XM_003811731.1.
3D structure databases
ProteinModelPortal	A1YFZ3.
SMR	A1YFZ3. Positions 40-318.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	100987860.
KEGG	pps:100987860.
Organism-specific databases
CTD	328.
Phylogenomic databases
HOVERGEN	HBG050531.
KO	K10771.
Family and domain databases
InterPro	IPR020847. AP_endonuclease_F1_BS. IPR020848. AP_endonuclease_F1_CS. IPR005135. Endo/exonuclease/phosphatase. IPR004808. ExoDNase_III. [Graphical view]
PANTHER	PTHR22748. PTHR22748. 1 hit.
Pfam	PF03372. Exo_endo_phos. 1 hit. [Graphical view]
SUPFAM	SSF56219. Exo_endo_phos. 1 hit.
TIGRFAMs	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...

Entry information

Entry name

APEX1_PANPA

Accession

Primary (citable) accession number: A1YFZ3

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 2007
Last sequence update:	February 6, 2007
Last modified:	March 6, 2013
This is version 39 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program