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P43138 (APEX1_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 132. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended 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
Gene names
Name:Apex1
Synonyms:Ape, Apex, Ref1
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length317 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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.

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 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. 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 By similarity.

Subcellular location

Nucleus. Nucleusnucleolus 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 processDNA damage
DNA recombination
DNA repair
Transcription
Transcription regulation
   Cellular componentCytoplasm
Endoplasmic reticulum
Mitochondrion
Nucleus
   LigandDNA-binding
Magnesium
Metal-binding
RNA-binding
   Molecular functionActivator
Endonuclease
Exonuclease
Hydrolase
Lyase
Nuclease
Repressor
   PTMAcetylation
Cleavage on pair of basic residues
Disulfide bond
Phosphoprotein
S-nitrosylation
Ubl conjugation
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA catabolic process, endonucleolytic

Inferred from sequence or structural similarity. Source: GOC

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

RNA phosphodiester bond hydrolysis, endonucleolytic

Inferred from direct assay Ref.7. Source: GOC

aging

Inferred from direct assay PubMed 12742531. Source: RGD

cell redox homeostasis

Inferred from electronic annotation. Source: Ensembl

cellular response to cAMP

Inferred from expression pattern PubMed 12173070. Source: RGD

cellular response to hydrogen peroxide

Inferred from direct assay PubMed 12884291. Source: RGD

cellular response to organonitrogen compound

Inferred from expression pattern PubMed 12173070. Source: RGD

cellular response to peptide hormone stimulus

Inferred from expression pattern PubMed 12173070. Source: RGD

negative regulation of smooth muscle cell migration

Inferred from mutant phenotype PubMed 19038866. Source: RGD

nucleic acid phosphodiester bond hydrolysis

Inferred from sequence or structural similarity. Source: GOC

positive regulation of DNA repair

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of G1/S transition of mitotic cell cycle

Inferred from mutant phenotype PubMed 12730053. Source: RGD

regulation of mRNA stability

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

response to drug

Inferred from expression pattern PubMed 17264098. Source: RGD

response to organonitrogen compound

Inferred from expression pattern PubMed 15344903. Source: RGD

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcentrosome

Inferred from electronic annotation. Source: Ensembl

cytoplasm

Inferred from direct assay PubMed 12173070. Source: RGD

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

nucleus

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 PubMed 15084519. Source: RGD

   Molecular_function3'-5' exonuclease activity

Inferred from sequence or structural similarity. Source: UniProtKB

DNA binding

Inferred from sequence or structural similarity. Source: UniProtKB

DNA-(apurinic or apyrimidinic site) lyase activity

Inferred from sequence or structural similarity. Source: UniProtKB

NF-kappaB binding

Inferred from direct assay PubMed 17602955. 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

phosphoric diester hydrolase activity

Inferred from electronic annotation. Source: Ensembl

protein binding

Inferred from physical interaction PubMed 17280489. Source: RGD

protein complex binding

Inferred from physical interaction PubMed 15084519. Source: RGD

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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 317316DNA-(apurinic or apyrimidinic site) lyase
PRO_0000200012
Chain31 – 317287DNA-(apurinic or apyrimidinic site) lyase, mitochondrial By similarity
PRO_0000402574

Regions

Region2 – 3231Necessary 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
Region8 – 125Nuclear localization signal (NLS) By similarity
Region22 – 3211Necessary for interaction with NPM1 and for efficient rRNA binding By similarity
Region63 – 7917Nuclear export signal (NES) By similarity
Region288 – 31730Mitochondrial targeting sequence (MTS) By similarity

Sites

Active site1701 By similarity
Active site2091Proton donor/acceptor By similarity
Metal binding691Magnesium 1 By similarity
Metal binding951Magnesium 1 By similarity
Metal binding2091Magnesium 2 By similarity
Metal binding2111Magnesium 2 By similarity
Metal binding3071Magnesium 1 By similarity
Site30 – 312Cleavage; by granzyme A By similarity
Site2111Transition state stabilizer By similarity
Site2821Important for catalytic activity By similarity
Site3081Interaction with DNA substrate By similarity

Amino acid modifications

Modified residue61N6-acetyllysine; by EP300 By similarity
Modified residue261N6-acetyllysine By similarity
Modified residue301N6-acetyllysine By similarity
Modified residue311N6-acetyllysine By similarity
Modified residue341N6-acetyllysine By similarity
Modified residue641S-nitrosocysteine; alternate By similarity
Modified residue921S-nitrosocysteine; alternate By similarity
Modified residue1961N6-acetyllysine By similarity
Modified residue2321Phosphothreonine; by CDK5 By similarity
Modified residue3091S-nitrosocysteine By similarity
Disulfide bond64 ↔ 92Alternate By similarity

Experimental info

Sequence conflict101Missing in AAA21019. Ref.1
Sequence conflict2361R → A in AAA21019. Ref.1
Sequence conflict2881H → Q in AAA21019. Ref.1

Sequences

Sequence LengthMass (Da)Tools
P43138 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: FBA6293C739E7804

FASTA31735,538
        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 

« Hide

References

« Hide '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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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.
PIRS42397.
RefSeqNP_077062.1. NM_024148.1.
XP_006251975.1. XM_006251913.1.
UniGeneRn.5949.

3D structure databases

ProteinModelPortalP43138.
SMRP43138. Positions 39-317.
ModBaseSearch...
MobiDBSearch...

PTM databases

PhosphoSiteP43138.

Proteomic databases

PaxDbP43138.
PRIDEP43138.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000013176; ENSRNOP00000013176; ENSRNOG00000009663.
GeneID79116.
KEGGrno:79116.
UCSCRGD:2126. rat.

Organism-specific databases

CTD328.
RGD2126. Apex1.

Phylogenomic databases

eggNOGCOG0708.
GeneTreeENSGT00530000063540.
HOGENOMHOG000034586.
HOVERGENHBG050531.
InParanoidP43138.
KOK10771.
OMATYDKRWS.
OrthoDBEOG7C8GJ6.
PhylomeDBP43138.
TreeFamTF315048.

Gene expression databases

GenevestigatorP43138.

Family and domain databases

Gene3D3.60.10.10. 1 hit.
InterProIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PANTHERPTHR22748. PTHR22748. 1 hit.
PfamPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
SUPFAMSSF56219. SSF56219. 1 hit.
TIGRFAMsTIGR00633. xth. 1 hit.
PROSITEPS00726. 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]
ProtoNetSearch...

Other

NextBio614526.
PROP43138.

Entry information

Entry nameAPEX1_RAT
AccessionPrimary (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: June 11, 2014
This is version 132 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families