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evolution
basic human AP endonuclease is a multifunctional protein. AP endonucleases fall into two families depending on the similarity of their amino acid sequence with exonuclease III (ExoIII or Xth) or endonuclease IV (EndoIV or Nfo) from Escherichia coli. APE1 belongs to the large nuclease family related to ExoIII from Escherichia coli. Enzymes of the ExoIII family including APE1 exhibit several enzymatic activities manifested more or less effectively: AP endonuclease, 3'-phosphodiesterase, 3'-phosphatase, and 3'-5'-exonuclease
evolution
endonuclease III belongs to the DNA glycosylases of the helix-hairpin-helix-GPD structural superfamily
evolution
AP endonucleases have been classified into XthA and Nfo families based on sequence homology and structural conservation studies involving Escherichia coli exonuclease III (ExoIII) or endonuclease IV (EndoIV) respectively. The catalytic site in AP endonucleases is highly conserved from bacteria to humans and consists of residues involved in the binding of metal ions
evolution
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AP endonucleases have been classified into XthA and Nfo families based on sequence homology and structural conservation studies involving Escherichia coli exonuclease III (ExoIII) or endonuclease IV (EndoIV) respectively. The catalytic site in AP endonucleases is highly conserved from bacteria to humans and consists of residues involved in the binding of metal ions
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evolution
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AP endonucleases have been classified into XthA and Nfo families based on sequence homology and structural conservation studies involving Escherichia coli exonuclease III (ExoIII) or endonuclease IV (EndoIV) respectively. The catalytic site in AP endonucleases is highly conserved from bacteria to humans and consists of residues involved in the binding of metal ions
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malfunction
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APE1 knockdown abrogates neuroprotection against cerebral ischemia
malfunction
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knockdown of ZAP1 levels does not alter base excision repair in early embryogenesis
malfunction
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knocking down Ape1/Ref-1 expression enhances estrogen responsiveness of the progesterone receptor and pS2 genes but does not alter the expression of the constitutively active 36B4 gene
malfunction
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short hairpin RNA-mediated stable suppression of APE-1 results in increased apoptosis in gastric epithelial cells after Helicobacter pylori infection
malfunction
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siRNA knockdown of endogenous APE1 impairs high-mobility group box 1-mediated cytokine expression and MAPK activation in THP-1 cells
malfunction
APE1 lacking the first 34 amino acids at the Nterminus, unlike wild-type enzyme, is unable to form cross-links with BS-AP DNAs that testifies to the involvement of disordered N-terminal extension, which is enriched in lysine residues, in the interaction with AP sites.
malfunction
disruption of the disulfide bond connecting beta8 and beta9 sheets only has a slight effect on the AP endonuclease activity
malfunction
inactivation of the APE1 gene causes early embryonic lethality in mice
malfunction
mutation of active site residue D144 in HpXth predicted to be essential for catalysis results in a complete loss of enzyme activities
malfunction
protein acetylation is an important protein modification in living cells and has an impact on pathological conditions. A profound deregulation of APE1/Ref-1 acetylation (on Lys35) status in triple negative breast cancer is revealed
malfunction
the expression of transforming growth factor beta (TGFbeta) is significantly reduced in APE1-deficient osteosarcoma cells. Transforming growth factor beta promotes cancer metastasis through various mechanisms including immunosuppression, angiogenesis, and invasion. APE1, TGFbeta, and microvessel density (MVD) have a pairwise correlation in osteosarcoma tissue samples, whereas TGFbeta, tumor size, and MVD are inversely related to the prognosis of the cohort. High expression of APE1, TGFbeta, and microvessel density (MVD) correlate with poor prognosis of osteosarcoma patients. Apurinic/apyrimidinic endonuclease 1-siRNA-mediated downregulation in osteosarcoma cells inhibits expression of TGFbeta1. Apurinic/apyrimidinic endonuclease 1-siRNA inhibits the capability to enhance HUVEC migration and tube formation of tumor cells through the TGFbeta/Smad3 signaling pathway. Tumor angiogenesis and growth in xenografts are suppressed by APE1-siRNA
malfunction
the redox-deficient truncated APE1 protein lacking the first N-terminal 61 amino acid residues (APE1-N?61) cannot stimulate DNA glycosylase activities of OGG1, MBD4, and ANPG on duplex DNA substrates
malfunction
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disruption of the disulfide bond connecting beta8 and beta9 sheets only has a slight effect on the AP endonuclease activity
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malfunction
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mutation of active site residue D144 in HpXth predicted to be essential for catalysis results in a complete loss of enzyme activities
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metabolism
mechanisms of AP site cleavage by enzymes from the base excision repair system (BER), overview. Enzyme Polbeta in combination with APE1 is able to perform synthesis with strand displacement and simultaneously correction of Polbeta errors with catalysis by 3'-5'-exonuclease activity of the APE1. A Schiff base is formed as an intermediate in the reactions catalyzed by AP lyases and 5'-dRP lyases. One of the repair proteins interacting with the AP sites via formation of a Schiff base is poly(ADP-ribose)polymerase 1 (PARP1). PARP1 is known as a sensor of single-stranded breaks and as a protein regulator of BER. If exogenous APE1 is added prior to irradiation, the efficiency of the PARP1 and FEN1 labeling decreases (but not of the Polbeta), these proteins compete for binding to this DNA substrate. Interaction between various enzymes and proteins participating in BER, overview
metabolism
a nucleophilic residue of ALKBH1 reacts with the electrophilic C3' of the alpha,beta-unsaturated aldehyde of the 5'-product. The addition of a competing nucleophile, specifically 2-mercaptoethanol, reduces the extent of adduct formation
physiological function
AP endonuclease and proliferating cell nuclear antigen form a functional complex to generate a gap of several nucleotides for efficient DNA repair synthesis
physiological function
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AP endonuclease pE296R is essential for virus growth in swine macrophages. DNA repair functions of pE296R are AP endonucleolytic, 3'-5' exonuclease, 3-diesterase and nucleotide incision repair activities
physiological function
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APE1 functions as a critical rate-limiting enzyme in DNA base excision repair and accounts for nearly all of the AP site incision activities in cell extracts, APE1 also exerts unique redox activity to regulate the DNA-binding affinity of certain transcriptional factors by controlling the redox status of their DNA-binding domain
physiological function
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APE1 has a central role in the coordination of base excision repair
physiological function
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APE1 is a dual regulator of inflammatory signaling to high-mobility group box 1 by human monocytes/macrophages. Forced cytoplasmic overexpression of APE1 profoundly attenuates the upregulation of high-mobility group box 1-mediated reactive oxygen species generation, cytokine secretion, and cyclooxygenase-2 expression by primary monocytes and macrophage-like THP-1 cell lines, the extracellular release of high-mobility group box 1 by activated macrophages is inhibited by APE1 transfection
physiological function
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APE1 is a key multifunctional protein involved in DNA base excision repair
physiological function
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APE1 is a key upstream regulator in TLR2-dependent keratinocyte inflammatory responses
physiological function
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APE1 is a multifunctional enzyme that plays a central role in base excision repair of DNA and is also involved in the alternative nucleotide incision repair pathway
physiological function
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APE1 is required for pituitary adenylate cyclase-activating polypeptide-induced neuroprotection against global cerebral ischemia
physiological function
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APE1 is the major nuclease for excising abasic sites and particular 3'-obstructive termini from DNA, and is an integral participant in the base excision repair pathway
physiological function
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APE1 regulates c-myc mRNA level possibly via its endoribonuclease activity
physiological function
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APE1 regulates c-myc mRNA level possibly via its endoribonuclease activity
physiological function
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APE1 stimulates the multiple-turnover excision of hypoxanthine by alkyladenine DNA glycosylase but has no effect on single-turnover excision
physiological function
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Ape1/Ref-1 enhances the interaction of estrogen receptor alpha with estrogen-response elements in DNA, Ape1/Ref-1 alters expression of the endogenous, estrogen-responsive progesterone receptor and pS2 genes in MCF-7 cells and associates with estrogen-response elements-containing regions of these genes in native chromatin
physiological function
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both DNA repair and acetylation functions of APE-1 modulate programmed cell death, the DNA repair activity of APE-1 inhibits the mitochondrial pathway, whereas the acetylation function inhibits the extrinsic pathway during Helicobacter pylori infection
physiological function
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in addition to the apurinic/apyrimidinic DNA endonuclease activity, APE1 has 3'-5' DNA exonuclease, 3' phosphodiesterase, and RNase H activities
physiological function
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in addition to the apurinic/apyrimidinic DNA endonuclease activity, APE1 has 3'-5' DNA exonuclease, 3'-phosphodiesterase, and RNase H activities
physiological function
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nuclear factor -kappaB is activated by cytoplasmic, but not nuclear, Ape1 to cause Cox-2 expression. Ape1 can enhance lung tumor malignancy through nuckear factor-kappaB activation
physiological function
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overexpression of Nfo about 50fold in spores increases the wet heat resistance of exoA nfo Bacillus subtilis spores that lack most alpha/beta-type small, acid-soluble spore proteins, but has no effect on these spores' UV-C resistance. Nfo overexpression also increases these spores' dry heat resistance, and to levels slightly greater than that of wild type spores
physiological function
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mice deficient for the base excision repair enzyme, apurinic/apyrimidinic endonuclease APE2 protein develop relatively normally, but they display defects in lymphopoiesis. Mice nullizygous for APE2 show an inhibition of the pro-B to pre-B cell transition. APE2 is not required for V(D)J recombination and the turnover rate of APE2-deficient progenitor B cells is nearly normal. The production rate of pro- and pre-B cells is reduced due to a p53-dependent DNA damage response. Progenitors from APE2-deficient mice differentiate normally in response to IL-7 in in vitro stromal cell cocultures, but pro-B cells show defective expansion. APE2-deficient mice show a delay in recovery of B lymphocyte progenitors following bone marrow depletion by 5-fluorouracil, with the pro-B and pre-B cell pools still markedly decreased 2 weeks after a single treatment
physiological function
over-expression of APN in Toxoplasma gondii confers protection from DNA damage, and viable knockouts of APN are not obtainable. An inducible APN knockdown mutant demonstrates that APN is critical for Toxoplasma to recover from DNA damage
physiological function
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overexpression of APE/Ref-1 using adenovirus and restoration of APE small peptides significantly reduces kainic acid-induced hippocampal cell death. Both silencing of APE/Ref-1 by siRNA and inhibition of endonuclease by an antibody significantly increase caspase-3 activity and apoptotic cell death triggered from the early time after exposure to kainic acid. Findings suggest that cell death is initiated by reducing APE/Ref-1 protein and inhibiting its repair function in spite of enough protein amounts
physiological function
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spores lacking both AP endonucleases Nfo and ExoA and major alpha/beta-type small acid-soluble spore proteins are significantly more sensitive to 254-nm UVC, environmental UV >280 nm, X-ray exposure, and high-energy charged particle bombardment and have elevated mutation frequencies compared to those of wild-type spores and spores lacking only one or both AP endonucleases or major alpha/beta-type small acid-soluble spore proteins
physiological function
the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates. Bifunctional enzyme that catalyzes the excision of 8-oxoguanine by cleaving the N-glycosylic bond between the base and the deoxyribose moiety (glycosylase activity) and subsequently cleave the DNA backbone (lyase activity, EC 4.2.99.18)
physiological function
isoform Ape1 is an essential factor stabilizing telomeric DNA, and its deficiency is associated with telomere dysfunction and segregation defects in immortalized cells maintaining telomeres by either the alternative lengthening of telomeres pathway or telomerase expression or in normal human fibroblasts
physiological function
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isoform APE1-deficient cell lines derived from bloodstream stage trypanosomes, confirm that the AP endonuclease is not essential for viability in this cell type under in vitro culture conditions. An inverse correlation exists between the level of AP endonuclease in the cell and the number of endogenously generated abasic sites in its genomic DNA. Depletion of APE1 renders cells hypersensitive to AP site and strand break-inducing agents such as methotrexate and phleomycin, respectively, but not to alkylating agents. The increased susceptibility of APE1-depleted cells to nitric oxide suggests an essential role in protection against the immune defenses of the mammalian host
physiological function
overexpression of isoform AP1 increases epimastigotes viability when they are exposed to acute ROS/RNS attack. This protective effect is more evident when parasites are submitted to persistent reactive oxygen species/reactive nitrogen species exposition
physiological function
AP endonuclease 1 (APE1) is a multifunctional protein abundant in human cells that is essential in maintaining multiple cellular functions. AP endonuclease 1 (APE1) takes part in the base excision repair (BER). It prevents trinucleotide repeat (TNR) expansions via its 3'-5'-exonuclease activity and stimulatory effect on DNA ligation during BER in a hairpin loop. Coordinating with flap endonuclease 1, the APE1 3'-5'-exonuclease activity cleaves the annealed upstream 3'-flap of a double-flap intermediate resulting from 5'-incision of an abasic site in the hairpin loop. Furthermore, APE1 stimulates DNA ligase I to resolve a long double-flap intermediate, thereby promoting hairpin removal and preventing TNR expansions
physiological function
APE1 is one of the key enzymes taking part in the repair of damage to DNA. The primary role of APE1 is the initiation of the repair of AP-sites by catalyzing the hydrolytic incision of the phosphodiester bond immediately 5' to the damage. In addition to the AP-endonuclease activity, APE1 possesses 3'-5'-exonuclease activity, which presumably is responsible for cleaning up nonconventional 3'-ends that were generated as a result of DNA damage or as transition intermediates in DNA repair pathways
physiological function
APE1 is unable to cleave apurinic/apyrimidinic (AP) sites in spite of formation of the Schiff-base-dependent intermediate, which is prerequisite for the beta-elimination mechanism. Clustered AP sites are more cytotoxic than isolated AP lesions because double strand breaks (DSB) can be formed during repair of closely positioned bistranded AP sites. Formation of DSB due to simultaneous cleavage of bistranded AP sites may be regulated by proteins specifically interacting with this complex lesion
physiological function
apurinic/apyrimidinic (AP) endonucleases play critical roles in the repair of abasic sites and strand breaks in DNA. Helicobacter pylori contains one single AP endonuclease. The DNA substrate specificity of Helicobacter pylori AP endonuclease HpXth counteracts the genotoxic effects of DNA damage generated by endogenous and host-imposed factors. The presence of Helicobacter pylori Xth protein in AP endonuclease-deficient Escherichia coli xth nfo strain significantly reduces the sensitivity to an alkylating agent and H2O2
physiological function
Apurinic/apyrimidinic (AP) sites, the most frequently formed DNA lesions in the genome, inhibit transcription and block replication. The primary enzyme that repairs AP sites in mammalian cells is the AP endonuclease (APE1), which functions through the base excision repair (BER) pathway. Human DNA repair enzyme APE1 is a ubiquitous and multifunctional protein. It plays a central role in the repair of spontaneously generated AP sites and oxidative and alkylated DNA damage in the genome via the BER pathwayMammalian cells, unlike Saccharomyces cerevisiae or Escherichia coli cells, require acetylation of APE1 for the efficient repair of AP sites and base damage in the genome. APE1 acetylation is an integral part of the BER pathway for maintaining genomic integrity. Apart from its DNA repair function, APE1 functions as a redox activator of many transcription factors, as well as a direct transcriptional coregulator of many genes. APE1 is essential for embryonic development and for cell viability and/or proliferation in cultures. Human APE1 is unique in that it has an N-terminal disordered 42 amino acids and has both DNA repair and transcriptional regulatory activities. AcAPE1 is exclusively associated with chromatin throughout the cell cycle. Acetylation of APE1 enhances its AP catalytic efficiency, and APE1 acetylation enhances its interaction with downstream BER proteins and stability on chromatin. APE1 acetylation plays a role in cell survival and/or proliferation in response to genotoxic stress
physiological function
apurinic/apyrimidinic endonuclease 1 (Ape1) is an important enzyme in the base excision repair mechanism, responsible for the backbone cleavage of abasic DNA through a phosphate hydrolysis reaction
physiological function
apurinic/apyrimidinic endonuclease 1 is a multifunctional protein playing crucial roles in DNA base excision repair and redox regulation of gene expression, activities that are functionally and structurally independent of each other. The APE1 redox activity stimulates numerous transcriptional factors, including activator protein-1 (AP-1), nuclear factor-kappaB (NF-happaB), and HIF-1. These factors are involved in mediating VEGF gene expression; HIF-1 and NF-kappaB, in particular, increased VEGF expression in response to hypoxia. Apurinic/apyrimidinic endonuclease 1 (APE1) is a dually functional protein possessing both base excision repair and redox activities, it is involved in tumor angiogenesis. APE1, TGFbeta, and microvessel density (MVD) have a pairwise correlation in osteosarcoma tissue samples, whereas TGFbeta, tumor size, and MVD are inversely related to the prognosis of the cohort. High expression of APE1, TGFbeta, and microvessel density (MVD) correlate with poor prognosis of osteosarcoma patients. APE1 may indirectly regulate angiogenesis through a TGFbeta-dependent pathway
physiological function
apurinic/apyrimidinic endonuclease Apn1 of Saccharomyces cerevisiae is known as a key player of the base excision DNA repair (BER) pathway in yeast. BER is initiated by DNA glycosylases, whereas Apn1 can start DNA repair individually in the nucleotide incision repair (NIR) pathway. More delicate regulation of Apn1's NIR activity is necessary due to the more complicated kinetic mechanism, as compared to BER
physiological function
apurinic/apyrimidinic sites (AP sites) are among the most abundant DNA damages. They can emerge because of spontaneous hydrolysis of the N-glycoside bond and during removal of the damaged DNA bases by DNA glycosylases. In mammalian cells up to 10000 AP sites emerge daily primarily due to apurinization of DNA. The number of such damages increases dramatically during intensive oxidative stress, X-ray and UV irradiation, and other actions. The deoxyribose residues in the AP sites exist in different forms that are in equilibrium. The acyclic aldehyde form of an AP site can form a Schiff base with amino groups in proteins, most often with the epsilon-NH2 group of lysine residues. AP endonucleases are the most important enzymes involved in the DNA repair that initiates the repair of AP sites. APE1 exhibits 3'-phosphodiesterase, 3'-5'-exonuclease, and 3'-phosphatase activities. Role of APE1 in the DNA repair process and in other metabolic processes, overview. APE1 stimulates the activity of the mouse adeninex02DNA glycosylase (Myh) and enhances affinity of this enzyme to adenine/8-oxoguanine pairs in comparison with adenine/guanine pairs
physiological function
apurinic/apyrimidinic sites (AP sites) are among the most abundant DNA damages. They can emerge because of spontaneous hydrolysis of the N-glycoside bond and during removal of the damaged DNA bases by DNA glycosylases. In mammalian cells up to 10000 AP sites emerge daily primarily due to apurinization of DNA. The number of such damages increases dramatically during intensive oxidative stress, X-ray and UV irradiation, and other actions. The deoxyribose residues in the AP sites exist in different forms that are in equilibrium. The acyclic aldehyde form of an AP site can form a Schiff base with amino groups in proteins, most often with the epsilon-NH2 group of lysine residues. AP endonucleases are the most important enzymes involved in the DNA repair that initiates the repair of AP sites. Human apurinic/apyrimidinic endonuclease 1 (APE1) is one of the key participants in the DNA base excision repair system. The major contribution to AP site cleavage in mammalian cells is provided by APE1 (over 95% of damages). APE1 hydrolyzes DNA adjacent to the 5'-end of an AP site to produce a nick with a 3'-hydroxyl group and a 5'-deoxyribose phosphate moiety. APE1 exhibits 3'-phosphodiesterase, 3'-5'-exonuclease, and 3'-phosphatase activities. APE1 is also identified as a redox factor (Ref-1). Role of APE1 in the DNA repair process and in other metabolic processes, overview. The APE1 protein is required for viability of human cell culture. APE1 is required not only for hydrolysis of AP sites generated by monofunctional DNA glycosylases, but also for processing of the products of bifunctional DNA glycosylases catalyzing beta-elimination. The enzyme is obviously involved in the cell response system to the action of some genotoxic agents. Participation of APE1 in stimulation of the DNA glycosylase, lyase, polymerase, flap endonuclease, and DNA ligase activities of BER enzymes likely reflects the role of this enzyme in coordination of different stages of DNA repair to achieve its optimal efficiency
physiological function
Endonuclease III (Endo III) is a bifunctional DNA glycosylase possessing N-glycosylase and AP lyase activities. Endonuclease III is responsible for base excision repair of oxidized or reduced pyrimidine bases
physiological function
human apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1) is a multifunctional protein which is essential in the base excision repair (BER) pathway of DNA lesions caused by oxidation and alkylation. This protein hydrolyzes DNA adjacent to the 5'-end of an apurinic/apyrimidinic (AP) site to produce a nick with a 3'-hydroxyl group and a 5'-deoxyribose phosphate moiety or activates the DNA binding activity of certain transcription factors through its redox function. Role for APE1/Ref-1 in the pathogenesis of cancer and in resistance to DNA-interactive drugs. APE1/Ref-1 plays a vital role in mammalian cells with implication in human pathologies. DNA damage and chronic oxidative stress are involved in various neurodegenerative disorders, including Alzheimer's, Parkinson's, Huntington's diseases, and amyotrophic lateral sclerosis. APE1/Ref-1 signaling pathway in hepatocellular carcinoma stimulates cellular proliferation, enhances anti-apoptosis, and facilitates metastasis
physiological function
human apurinic/apyrimidinic endonuclease APE1 is one of the key enzymes of the base excision DNA repair system. The main biological function of APE1 is the hydrolysis of the phosphodiester bond on the 5'-side of an apurinic/apyrimidinic site (AP-site) to give the 5'-phosphate and 3'-hydroxyl group. The level of enzymatic activity of human AP-endonuclease APE1 has a considerable influence on the process of the removal of DNA lesions. APE1 is an extremely active enzyme which is able to process many synthetic analogues of the AP-site such as tetrahydrofuran (F-site) or alpha,omega-alkane diols
physiological function
human enzyme APE2 performs most of the essential functional residues of the exonuclease III-like proteins. APE2 has 518 amino acids. Unlike APE1/Ref-1, APE2 shows only weak capacity to exhibit AP site repair activity. APE2 has no the N-terminal tail that is present in APE1/Ref-1 and as such does not possess redox activity
physiological function
most of the biological importance of APE1 in the DNA repair pathways is associated with the high affinity for the abasic nucleotide and nicking of DNA hydrolytically 5' to the AP-site. APE1 has the ability to incise the DNA sugar-phosphate backbone 5' to structurally unrelated lesions such as alpha-anomeric 2'-deoxynucleosides, various red/ox-modified pyrimidines and etheno-adducts
physiological function
the apurinic/apyrimidinic (AP) endonuclease Apn1 from Saccharomyces cerevisiae is a key enzyme involved in the base excision repair (BER) at the cleavage stage of abasic sites (AP sites) in DNA
physiological function
the base excision repair (BER) pathway consists of sequential action of DNA glycosylase and apurinic/apyrimidinic (AP) endonuclease necessary to remove a damaged base and generate a single-strand break in duplex DNA. Human multifunctional AP endonuclease 1 (APE1) plays essential roles in BER by acting downstream of DNA glycosylases to incise a DNA duplex at AP sites and remove 3'-blocking sugar moieties at DNA strand breaks. Human apurinic/apyrimidinic (AP) endonuclease, APE1, stimulates DNA glycosylases, e.g. human 8-oxoguanine-DNA glycosylase (OGG1), by increasing their turnover rate on duplex DNA substrates, overview. The redox domain of APE1 is necessary for the active mode of stimulation of DNA glycosylases (e.g. of uracil-DNA glycosylase activity of MBD4). Consequently, APE1 shows DNA length dependence with preferential repair of short DNA duplexes. APE1-catalyzed oligomerization along DNA induces helix distortions, which in turn enable conformational selection and stimulation of DNA glycosylases
physiological function
MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. the sliding DNA beta-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA-binding domain of XthA is found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of beta-clamp located on different domains interact with XthA. The beta-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. Addition of beta-clamp binding peptides disrupts the MtbXthA-clamp complex and inhibits clamp-dependent stimulation of MtbXthA, overview. In the AP incision activities, the control experiments involving a random peptide had no effect on activity stimulation, while addition of peptides derived from alpha subunit, delta subunit, and MtbXthA, respectively, result in 2.0-2.5fold decreased stimulation of MtbXthA activity. The beta-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the beta-clamp onto DNA is required for activity stimulation. In the absence of DNA, the PBG located on the second domain of the beta-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. The C-terminal domain of beta-clamp predominantly mediates interactions with XthA in the presence of DNA
physiological function
Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair. The enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as AP-endonuclease at high ionic environments, while the 3'-5' exonuclease activity is predominant at low ionic environments
physiological function
the 6-methyl adenine demethylase activity is very low. The demethylase activity is less than half that of the apurinic/apyrimidinic lyase activity when ALKBH1 samples are assayed using identical buffer conditions. The two enzymatic activities are located in distinct but partially overlapping active sites for the two reactions
physiological function
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the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates. Bifunctional enzyme that catalyzes the excision of 8-oxoguanine by cleaving the N-glycosylic bond between the base and the deoxyribose moiety (glycosylase activity) and subsequently cleave the DNA backbone (lyase activity, EC 4.2.99.18)
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physiological function
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the apurinic/apyrimidinic (AP) endonuclease Apn1 from Saccharomyces cerevisiae is a key enzyme involved in the base excision repair (BER) at the cleavage stage of abasic sites (AP sites) in DNA
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physiological function
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apurinic/apyrimidinic endonuclease Apn1 of Saccharomyces cerevisiae is known as a key player of the base excision DNA repair (BER) pathway in yeast. BER is initiated by DNA glycosylases, whereas Apn1 can start DNA repair individually in the nucleotide incision repair (NIR) pathway. More delicate regulation of Apn1's NIR activity is necessary due to the more complicated kinetic mechanism, as compared to BER
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physiological function
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overexpression of isoform AP1 increases epimastigotes viability when they are exposed to acute ROS/RNS attack. This protective effect is more evident when parasites are submitted to persistent reactive oxygen species/reactive nitrogen species exposition
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physiological function
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overexpression of Nfo about 50fold in spores increases the wet heat resistance of exoA nfo Bacillus subtilis spores that lack most alpha/beta-type small, acid-soluble spore proteins, but has no effect on these spores' UV-C resistance. Nfo overexpression also increases these spores' dry heat resistance, and to levels slightly greater than that of wild type spores
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physiological function
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Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair. The enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as AP-endonuclease at high ionic environments, while the 3'-5' exonuclease activity is predominant at low ionic environments
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physiological function
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MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. the sliding DNA beta-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA-binding domain of XthA is found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of beta-clamp located on different domains interact with XthA. The beta-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. Addition of beta-clamp binding peptides disrupts the MtbXthA-clamp complex and inhibits clamp-dependent stimulation of MtbXthA, overview. In the AP incision activities, the control experiments involving a random peptide had no effect on activity stimulation, while addition of peptides derived from alpha subunit, delta subunit, and MtbXthA, respectively, result in 2.0-2.5fold decreased stimulation of MtbXthA activity. The beta-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the beta-clamp onto DNA is required for activity stimulation. In the absence of DNA, the PBG located on the second domain of the beta-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. The C-terminal domain of beta-clamp predominantly mediates interactions with XthA in the presence of DNA
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physiological function
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Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair. The enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as AP-endonuclease at high ionic environments, while the 3'-5' exonuclease activity is predominant at low ionic environments
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physiological function
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MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. the sliding DNA beta-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA-binding domain of XthA is found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of beta-clamp located on different domains interact with XthA. The beta-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. Addition of beta-clamp binding peptides disrupts the MtbXthA-clamp complex and inhibits clamp-dependent stimulation of MtbXthA, overview. In the AP incision activities, the control experiments involving a random peptide had no effect on activity stimulation, while addition of peptides derived from alpha subunit, delta subunit, and MtbXthA, respectively, result in 2.0-2.5fold decreased stimulation of MtbXthA activity. The beta-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the beta-clamp onto DNA is required for activity stimulation. In the absence of DNA, the PBG located on the second domain of the beta-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. The C-terminal domain of beta-clamp predominantly mediates interactions with XthA in the presence of DNA
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physiological function
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isoform APE1-deficient cell lines derived from bloodstream stage trypanosomes, confirm that the AP endonuclease is not essential for viability in this cell type under in vitro culture conditions. An inverse correlation exists between the level of AP endonuclease in the cell and the number of endogenously generated abasic sites in its genomic DNA. Depletion of APE1 renders cells hypersensitive to AP site and strand break-inducing agents such as methotrexate and phleomycin, respectively, but not to alkylating agents. The increased susceptibility of APE1-depleted cells to nitric oxide suggests an essential role in protection against the immune defenses of the mammalian host
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physiological function
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apurinic/apyrimidinic (AP) endonucleases play critical roles in the repair of abasic sites and strand breaks in DNA. Helicobacter pylori contains one single AP endonuclease. The DNA substrate specificity of Helicobacter pylori AP endonuclease HpXth counteracts the genotoxic effects of DNA damage generated by endogenous and host-imposed factors. The presence of Helicobacter pylori Xth protein in AP endonuclease-deficient Escherichia coli xth nfo strain significantly reduces the sensitivity to an alkylating agent and H2O2
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additional information
a set of AP DNA duplexes containing AP sites in both strands in different mutual orientation (BS-AP DNAs) is used for search in the extracts of human cells proteins specifically recognizing clustered AP sites
additional information
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a set of AP DNA duplexes containing AP sites in both strands in different mutual orientation (BS-AP DNAs) is used for search in the extracts of human cells proteins specifically recognizing clustered AP sites
additional information
association of APE1 with undamaged DNA reduces effective concentration of the enzyme and subsequently decreases APE1-catalyzed cleavage rates on long DNA substrates. APE1 oligomers on DNA induce helix distortions thereby enhancing molecular recognition of DNA lesions by DNA glycosylases via a conformational proofreading/selection mechanism. Thus, APE1-mediated structural deformations of the DNA helix stabilize the enzyme-substrate complex and promote dissociation of human DNA glycosylases from the AP site with a subsequent increase in their turnover rate. APE1 shows DNA length dependence with preferential repair of short DNA duplexes. Electron microscopic analysis of DNA complexes with the APE1 protein
additional information
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association of APE1 with undamaged DNA reduces effective concentration of the enzyme and subsequently decreases APE1-catalyzed cleavage rates on long DNA substrates. APE1 oligomers on DNA induce helix distortions thereby enhancing molecular recognition of DNA lesions by DNA glycosylases via a conformational proofreading/selection mechanism. Thus, APE1-mediated structural deformations of the DNA helix stabilize the enzyme-substrate complex and promote dissociation of human DNA glycosylases from the AP site with a subsequent increase in their turnover rate. APE1 shows DNA length dependence with preferential repair of short DNA duplexes. Electron microscopic analysis of DNA complexes with the APE1 protein
additional information
endonuclease III uses a multistep mechanism of damage recognition, which likely involves Gln41 and Leu81 as lesion sensors. The principal amino acids involved in the catalysis are Lys120 and Asp138. The former is the nucleophile that attacks the C1' atom of deoxyribose, resulting in the cleavage of the N-glycosydic bond and subsequent formation of a Schiff base covalent intermediate. The following beta-elimination reaction leads to the departure of the 3'-phosphate. The subsequent Schiff base hydrolysis releases the enzyme and leads to formation of a single-strand break in DNA duplex with an alpha/beta-unsaturated aldehyde at the 3'-end and a phosphate at the 5'-end
additional information
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endonuclease III uses a multistep mechanism of damage recognition, which likely involves Gln41 and Leu81 as lesion sensors. The principal amino acids involved in the catalysis are Lys120 and Asp138. The former is the nucleophile that attacks the C1' atom of deoxyribose, resulting in the cleavage of the N-glycosydic bond and subsequent formation of a Schiff base covalent intermediate. The following beta-elimination reaction leads to the departure of the 3'-phosphate. The subsequent Schiff base hydrolysis releases the enzyme and leads to formation of a single-strand break in DNA duplex with an alpha/beta-unsaturated aldehyde at the 3'-end and a phosphate at the 5'-end
additional information
enzyme HpXth homology modeling
additional information
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enzyme HpXth homology modeling
additional information
molecular dynamics simulations elucidates the structural features of complexes of the enzyme with DHU-containing DNAs. Enzyme three-dimensional structure homology modeling using the structure of Endo IV (PDB ID 1QTW) as template
additional information
molecular dynamics simulations of Ape1 complexed to its substrate DNA performed for models containing 1 or 2 Mg21-ions as cofactor located at different positions show a complex with 1 metal ion bound on the leaving group site of the scissile phosphate to be the most likely reaction-competent conformation. Active-site residue His309 is found to be protonated based on pKa calculations and the higher conformational stability of the Ape1-DNA substrate complex compared to scenarios with neutral His309. Simulations of the D210N mutant further support the prevalence of protonated His309 and strongly suggest Asp210 as the general base for proton acceptance by a nucleophilic water molecule. Enzyme modelling based on the crystal structure of the phosphorothioate substrate complex with Mn2+ as metal cofactor (PDB ID 5DG0). Residue His309 is essential for substrate binding and the phosphate hydrolysis step. In terms of substrate binding, Tyr171 has the possibility to form a hydrogen bond with the non-bridging oxygen atom of the AP-site
additional information
residue His83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Substrate binding structure analysis using DNA duplex crystal structure (PDB ID 2NQJ) for molecular dynamics simulations
additional information
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residue His83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Substrate binding structure analysis using DNA duplex crystal structure (PDB ID 2NQJ) for molecular dynamics simulations
additional information
stopped-flow fluorescence techniques are used to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Analysis of enzyme-substrate complexes with bound Mg2+
additional information
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stopped-flow fluorescence techniques are used to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Analysis of enzyme-substrate complexes with bound Mg2+
additional information
substrate specificity and substrate binding, molecular dynamics simulations. Molecular modelling of the APE1 complex with 13 ntDNA duplexes containing 1,N6-ethenoadenosine, alpha-adenosine, 5,6-dihydrouridine or F-site. Model structures of APE1-DNA complexes show that the pocket of the active site is formed by amino acid residues Asn174, Asn212, Asn229, Ala230, Phe266 and Trp280
additional information
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substrate specificity and substrate binding, molecular dynamics simulations. Molecular modelling of the APE1 complex with 13 ntDNA duplexes containing 1,N6-ethenoadenosine, alpha-adenosine, 5,6-dihydrouridine or F-site. Model structures of APE1-DNA complexes show that the pocket of the active site is formed by amino acid residues Asn174, Asn212, Asn229, Ala230, Phe266 and Trp280
additional information
the N-terminal domain (about 6 kDa, 60 amino acids) is responsible for the redox function of APE1, which is independent of the repair functions of this enzyme, and it contains the nuclear export signal. The second human AP endonuclease (APE2) also belongs to the ExoIII family, but the level of its endonuclease activity is significantly lower than of APE1. Amino acids such as Asp219, Asp90, and Asp308 are functionally important, D219 in APE1 plays a key function in repair. Tyr171 does not interact directly with the AP site, but participates in the catalysis of the APE1 endonuclease reaction in the form of a phenolate ion, i.e. it attacks phosphate at the 5'-side of the AP site
additional information
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the N-terminal domain (about 6 kDa, 60 amino acids) is responsible for the redox function of APE1, which is independent of the repair functions of this enzyme, and it contains the nuclear export signal. The second human AP endonuclease (APE2) also belongs to the ExoIII family, but the level of its endonuclease activity is significantly lower than of APE1. Amino acids such as Asp219, Asp90, and Asp308 are functionally important, D219 in APE1 plays a key function in repair. Tyr171 does not interact directly with the AP site, but participates in the catalysis of the APE1 endonuclease reaction in the form of a phenolate ion, i.e. it attacks phosphate at the 5'-side of the AP site
additional information
enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Determinants of abasic-site recognition: the first three determinants, i.e. the base opposite the abasic site, the abasic ribose ring itself, and local distortions in the AP-site, do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, conserved residues located near the active site, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision. MtbXthA binds with high affinity to abasic sites in DNA e.g. to a 5'-FAM labelled duplex DNA substrate N1 that has an abasic site analogue, tetrahydrofuran (THF), incorporated into it. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
additional information
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enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Determinants of abasic-site recognition: the first three determinants, i.e. the base opposite the abasic site, the abasic ribose ring itself, and local distortions in the AP-site, do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, conserved residues located near the active site, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision. MtbXthA binds with high affinity to abasic sites in DNA e.g. to a 5'-FAM labelled duplex DNA substrate N1 that has an abasic site analogue, tetrahydrofuran (THF), incorporated into it. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
additional information
the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
additional information
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residue His83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Substrate binding structure analysis using DNA duplex crystal structure (PDB ID 2NQJ) for molecular dynamics simulations
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additional information
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molecular dynamics simulations elucidates the structural features of complexes of the enzyme with DHU-containing DNAs. Enzyme three-dimensional structure homology modeling using the structure of Endo IV (PDB ID 1QTW) as template
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additional information
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enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Determinants of abasic-site recognition: the first three determinants, i.e. the base opposite the abasic site, the abasic ribose ring itself, and local distortions in the AP-site, do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, conserved residues located near the active site, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision. MtbXthA binds with high affinity to abasic sites in DNA e.g. to a 5'-FAM labelled duplex DNA substrate N1 that has an abasic site analogue, tetrahydrofuran (THF), incorporated into it. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
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additional information
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the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
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additional information
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enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Determinants of abasic-site recognition: the first three determinants, i.e. the base opposite the abasic site, the abasic ribose ring itself, and local distortions in the AP-site, do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, conserved residues located near the active site, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision. MtbXthA binds with high affinity to abasic sites in DNA e.g. to a 5'-FAM labelled duplex DNA substrate N1 that has an abasic site analogue, tetrahydrofuran (THF), incorporated into it. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
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additional information
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the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
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additional information
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enzyme HpXth homology modeling
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