EndonucleaseCleaving the phosphodiesterPhosphodiester bondEndonucleasesMechanismBasesHydrogenEnzymeRepairOppositePolymeraseGlycosylaseGlycosylasesAPE1APEX1LesionsProteinsDeaminationNucleotide excisiReplicationHAP1CellsMammalianNHEJExcisionAriseMutationRecognitionBiochemistryCleavageDamageLigaseBaseCleaveActivityProteinHumanOGG1ReactionMultiplePartialFormationStructure
Endonuclease4
- Apurinic/apyrimidinic (AP) endonuclease is an enzyme that is involved in the DNA base excision repair pathway (BER). (wikipedia.org)
- Human AP endonuclease (APE1), like most AP endonucleases, is of class II and requires an Mg2+ in its active site in order to carry out its role in base excision repair. (wikipedia.org)
- Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. (ox.ac.uk)
- Ribosomal protein S3 (RpS3) is involved in protein biosynthesis as a component of the ribosome complex and possesses endonuclease activity to repair damaged DNA. (bmbreports.org)
Cleaving the phosphodiester1
- Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5' to the abasic site. (ox.ac.uk)
Phosphodiester bond1
- Both of these structures possess rings attached to short chains, which appear similar to the deoxyribose sugar ring without a base attached and phosphodiester bond in DNA. (wikipedia.org)
Endonucleases4
- There are four types of AP endonucleases that have been classified according to their mechanism and site of incision. (wikipedia.org)
- Class I AP endonucleases (EC 4.2.99.18) cleave 3′ to AP sites by a β-lyase mechanism, leaving an unsaturated aldehyde, termed a 3′-(4-hydroxy-5-phospho-2-pentenal) residue, and a 5′-phosphate. (wikipedia.org)
- Class II AP endonucleases incise DNA 5′ to AP sites by a hydrolytic mechanism, leaving a 3′-hydroxyl and a 5′-deoxyribose phosphate residue. (wikipedia.org)
- Class III and class IV AP endonucleases also cleave DNA at the phosphate groups 3′ and 5′ to the baseless site, but they generate a 3′-phosphate and a 5′-OH. (wikipedia.org)
Mechanism2
- The APE1 enzyme creates a nick in the phosphodiester backbone at an abasic (baseless) site through a simple acyl substitution mechanism. (wikipedia.org)
- Furthermore, the structural mechanism for AP-site cleavage is incomplete. (ox.ac.uk)
Bases1
- This active site is bordered by Phe266, Trp280, and Leu282, which pack tightly with the hydrophobic side of the AP site, discriminating against sites that do have bases. (wikipedia.org)
Hydrogen4
- The AP site is then further stabilized through hydrogen bonding of the phosphate group 5´ to the AP site with Asn174, Asn212, His309, and the Mg2+ ion while its orphan base partner is stabilized through hydrogen bonding with Met270. (wikipedia.org)
- The phosphate group 3' to the AP site is stabilized through hydrogen bonding to Arg177. (wikipedia.org)
- Meanwhile, an Asp210 in the active site, which is made more reactive due to the increase in its pKa (or the negative log of acid dissociation constant) caused through its stabilization through its hydrogen bonding between Asn68 and Asn212, activates the nucleophile that attacks and cleaves the phosphodiester backbone and probably results in the observed maximal APE1 activity at a pH of 7.5. (wikipedia.org)
- The increase in ethylene emission resulted in enhanced hydrogen peroxide concentration, phenylalanine ammonia-lyase activity, ß-1,3 glucanase activity, and expression profiles of WRKY, CaPR1, and CaPTI1 genes that are typical salt stress and PR signaling factors. (bvsalud.org)
Enzyme1
- Further, both contain many H-bond acceptors which may interact with the H-bond donors in the active site of APE1, causing these inhibitors to stick in the active site and preventing the enzyme from catalyzing other reactions. (wikipedia.org)
Repair5
- Its main role in the repair of damaged or mismatched nucleotides in DNA is to create a nick in the phosphodiester backbone of the AP site created when DNA glycosylase removes the damaged base. (wikipedia.org)
- Because APE1 performs an essential function in DNA base-excision repair pathway, it has become a target for researchers looking for means to prevent cancer cells from surviving chemotherapy. (wikipedia.org)
- Not only is APE1 needed in and of itself to create the nick in the DNA backbone so that the enzymes involved later in the BER pathway can recognize the AP-site, it also has a redox function that helps activate other enzymes involved in DNA repair. (wikipedia.org)
- Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. (ox.ac.uk)
- Lyn, a tyrosine kinase that is activated by double-stranded DNA-damaging agents, is involved in various signaling pathways, such as proliferation, apoptosis, and DNA repair. (bmbreports.org)
Opposite2
- Three APE1 residues (Arg73, Ala74, and Lys78) contact three consecutive DNA phosphates on the strand opposite the one containing the AP site while Tyr128 and Gly127 span and widen the minor groove, anchoring the DNA for the extreme kinking caused by the interaction between positive residues found in four loops and one α-helix and the negative phosphate groups found in the phosphodiester backbone of DNA. (wikipedia.org)
- DNA polymerase (pol) η is responsible for error-free translesion DNA synthesis (TLS) opposite ultraviolet light (UV)-induced cis-syn cyclobutane thymine dimers (CTDs) and cisplatin-induced intrastrand guanine crosslinks. (bvsalud.org)
Polymerase10
- During short-patch BER, 5′dRP is displaced by DNA polymerase β (Polβ), which inserts a single nucleotide. (springer.com)
- When DNA polymerase encounters an abasic site, DNA replication is usually blocked, which may itself lead to a single-stranded or double-stranded break in the DNA helix. (wikipedia.org)
- UV-DDB increased both OGG1 and APE1 strand cleavage and stimulated subsequent DNA polymerase β-gap filling activity by 30-fold. (nih.gov)
- Our findings indicate that AP sites are highly cytotoxic and mutagenic in eukaryotes, and that the REV3, REV7-encoded DNA polymerase ζ mediates the mutagenic bypass of AP sites. (houstonmethodist.org)
- Wilson, S.H. and Kuff, E.L. A novel DNA polymerase activity found in association with intracisternal A-type particles. (nih.gov)
- An oligonucleotide substrate containing a reduced abasic site, which was pre-incised with APE1, was employed to reconstitute the excision step of long-patch BER with purified human DNA polymerase beta and FEN1. (ox.ac.uk)
- In this sense, during the last years we have been studying the catalytic functions of the B. subtilis DNA polymerase belonging to family X (PolXBs). (uam.es)
- DNA polymerase (pol) η is responsible for error-free translesion DNA synthesis (TLS) opposite ultraviolet light (UV)-induced cis-syn cyclobutane thymine dimers (CTDs) and cisplatin-induced intrastrand guanine crosslinks. (bvsalud.org)
- Moreover, judging from the repair requirements and sensitivity to specific polymerase inhibitors, there were overlapping repair activities in processing of dI in DNA. (biomedcentral.com)
- From radionucleotide incorporation fine mapping, the resulting apurinic/apyrimidinic (AP) sites are further processed by both the short patch pathway (1-nucleotide gap filling) with DNA polymerase (Pol) β and the long patch pathway (2-6 nucleotide resynthesis) with Pol δ and PCNA [ 7 ]. (biomedcentral.com)
Glycosylase5
- A damaged base is recognized by a specific DNA glycosylase, which cleaves the bond between the base and sugar, creating an abasic site (AP), which is a mutagenic and cytotoxic intermediate. (springer.com)
- In this process, a DNA glycosylase recognizes a damaged base and cleaves the N-glycosidic bond to release the base, leaving an AP site. (wikipedia.org)
- In alternative fashion, bifunctional glycosylase-lyases can cleave the AP site, leaving a 5' phosphate adjacent to a 3' α,β-unsaturated aldehyde. (wikipedia.org)
- The excision of base damage is initiated by a specific DNA glycosylase: Hypoxanthine is bound and excised efficiently by human N -methylpurine-DNA glycosylase (MPG, also known as AAG, ANPG, APNG, or MDG) [ 6 ]. (biomedcentral.com)
- In Escherichia coli , early studies indicated that the DNA glycosylase encoded by alkA gene could recognize and release hypoxanthine residues from DNA [ 1 ]. (biomedcentral.com)
Glycosylases5
- The resulting AP site is further processed by the AP lyase activity associated with bifunctional DNA glycosylases and AP endonucleases cleaving 3′or 5′at the AP site, respectively. (springer.com)
- BER is initiated by a specific DNA glycosylases, which recognize and remove damaged or incorrect bases, creating AP sites. (springer.com)
- A variety of glycosylases that recognize different types of damage exist, including oxidized or methylated bases, or uracil in DNA. (wikipedia.org)
- Enzymes, namely DNA glycosylases, also commonly create AP sites, as part of the base excision repair pathway. (wikipedia.org)
- DNA glycosylases first create abasic sites by recognizing and removing modified bases. (wikipedia.org)
APE11
APEX11
Lesions4
- It appears from literature that human cytomegalovirus enhances DNA repair capacity in host cells, without producing detectable lesions in cellular DNA or inhibiting DNA synthesis (Nishiyama and Rapp 1981 ). (springer.com)
- The base excision repair (BER) pathway corrects most endogenous base lesions, including alkylation, oxidation and deamination, apurinic/apyrimidinic (AP) sites as well as single-strand breaks. (springer.com)
- Many bacterial members are provided with a nonhomologous end joining system (NHEJ) responsible for repairing double strand breaks (DSB), the most hazardous DNA lesions as they are lethal to dividing cells if they are not repaired in a timely fashion. (uam.es)
- AP sites are the most common genomic DNA lesions frequently associated with DSBs. (uam.es)
Proteins5
- Changes in the activity of DNA repair proteins during viral infection can cause disturbances in the DNA repair system and change its mechanisms. (springer.com)
- Recent data from our laboratory has shown that the nucleotide excision repair (NER) proteins UV-damaged DNA-binding protein (UV-DDB), xeroderma pigmentosum group C (XPC), and xeroderma pigmentosum group A (XPA) play important roles in the processing of 8-oxoG. (nih.gov)
- We further discuss our single-molecule studies showing that UV-DDB associates with these proteins at abasic moieties on DNA damage arrays. (nih.gov)
- To understand the mechanism involved in the coordination of the sequential repair reactions that lead to long-patch BER, we have investigated interactions between proteins involved in this pathway. (ox.ac.uk)
- Our main objective is to get insights on the molecular mechanisms responsible for maintaining genome stability in bacteria, by functional analysis of the enzymatic features of purified repair proteins from model organisms as the gram positive bacterium Bacillus subtilis whose vegetative cells and spores have to handle DNA damage induced by extreme environmental conditions, and the gram negative Pseudomonas aeruginosa . (uam.es)
Deamination3
- Alkylation, deamination, and oxidation of individual bases can all lead to the weakening of the glycosyl bond, so exposure to agents that cause those modifications can encourage AP site formation. (wikipedia.org)
- Deoxyinosine (hypoxanthine deoxyribonucleotide, dI) in DNA can arise from spontaneous deamination of deoxyadenosine residue, and is also induced by ROS produced from normal aerobic respiration. (biomedcentral.com)
- Deoxyinosine derived from deamination of deoxyadenosine in DNA is potentially mutagenic since it prefers to pair with dCTP during replication, yielding A:T to G:C transition mutations at sites of adenine deamination [ 5 ]. (biomedcentral.com)
Nucleotide excisi2
- There are six known systems of DNA repair: pathway of direct reversion of damage, base excision repair (BER), nucleotide-excision repair (NER), mismatch repair (MMR), homologous recombination (HR) and nonhomologous DNA end joining (NHEJ). (springer.com)
- UV-DDB, a key protein in human global nucleotide excision repair (NER), binds avidly to abasic sites and 8-oxo-guanine (8-oxoG), suggesting a noncanonical role in base excision repair (BER). (nih.gov)
Replication4
- If left unrepaired, AP sites can lead to mutation during semiconservative replication. (wikipedia.org)
- If AP sites in DNA are not repaired, DNA replication cannot proceed normally, and significant mutations can result. (wikipedia.org)
- Maintenance of genome stability largely relies on faithful DNA replication. (uam.es)
- Hypoxanthine in DNA can pair with cytosine which results in A:T to G:C transition mutations after DNA replication. (biomedcentral.com)
HAP11
- We identify APN2, the yeast homolog of HAP1 and provide evidence that Apn1 and Apn2 represent alternate pathways for repairing AP sites. (houstonmethodist.org)
Cells4
- The control aspects of the five DNA repair mechanisms in virus-infected cells have not been well characterized. (springer.com)
- AP sites in living cells can cause various and severe consequences, including cell death. (wikipedia.org)
- Furthermore, UV-DDB moves to sites of 8-oxoG repair in cells, and UV-DDB depletion sensitizes cells to oxidative DNA damage. (nih.gov)
- In mammalian cells, base excision repair (BER) was thought to be the major pathway for dI repair. (biomedcentral.com)
Mammalian1
- In a given mammalian cell, 5000-10,000 apurinic sites are estimated to form per day. (wikipedia.org)
NHEJ1
- Therefore, LigD has in the same polypeptidic chain the three activities required in the last steps of BER, suggesting that its DNA repair role is not restricted to the NHEJ pathway, but expands beyond, being potentially active in additional repair pathways. (uam.es)
Excision4
- Various types of DNA damage are repaired through multiple repair pathways, such as base excision, nucleotide excision, homologous recombination and nonhomologous end joining. (springer.com)
- AP sites can be formed by spontaneous depurination, but also occur as intermediates in base excision repair. (wikipedia.org)
- AP sites are an important feature of the base excision repair pathway. (wikipedia.org)
- This activity coordinates with the polymerization and ligase activities to allow efficient repairing of an AP site-containing DNA in an in vitro reconstituted Base Excision Repair (BER) reaction. (uam.es)
Arise1
- Abasic (AP) sites arise in DNA through spontaneous base loss and enzymatic removal of damaged bases. (houstonmethodist.org)
Mutation2
- DNA damages can lead to cell mutation, death, apoptosis and immune system activation. (springer.com)
- Unrepaired DNA damage can lead to mutation, development of various diseases or cell death (Bartek et al. (springer.com)
Recognition1
- We propose that UV-DDB is a general sensor of DNA damage in both NER and BER pathways, facilitating damage recognition in the context of chromatin. (nih.gov)
Biochemistry1
- In biochemistry and molecular genetics, an AP site (apurinic/apyrimidinic site), also known as an abasic site, is a location in DNA (also in RNA but much less likely) that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage. (wikipedia.org)
Cleavage1
- Coupling of AP sites cleavage to the end-joining reaction by the B. subtilis LigD. (uam.es)
Damage3
- The viruses that induce cellular DNA damage include members of the herpesvirus group, adenovirus, mumps-virus, measles-virus, rubella-virus, poliovirus and papilloma-virus (Fortunato et al. (springer.com)
- It is known that HCMV can act as mutagen inducing various DNA damage (AbuBakar et al. (springer.com)
- Those experimental studies focused on repairs of exogenously introduced damage in cellular DNA in the context of single viral protein expression (Becker et al. (springer.com)
Ligase1
- We have recently characterized the additional presence of an unexpected 5'-2-deoxyribose-5-phosphate (dRP) lyase activity in the ligase domain (LigDom) of the LigD from B. subtilis and P.aeruginosa . (uam.es)
Base4
- AP sites form when deoxyribose is cleaved from its nitrogenous base, breaking the glycosidic linkage between the two. (wikipedia.org)
- AP site formation can also be caused by various base-modifying chemicals. (wikipedia.org)
- Hydroxyl radicals can attack the glycosidic linkages, directly creating an AP site, or make the glycosyl bond less favorable by linking to the base or the deoxyribose ring. (wikipedia.org)
- The templating nucleotide opposite the AP site directs the binding of the complementary ribonucleotide, forming a Watson-Crick base pair at the polymerization site of the PolDom ( c ). (uam.es)
Cleave1
- The AP endonucleases cleave an AP site to yield a 3′ hydroxyl adjacent to a 5′ deoxyribosephosphate (dRP). (springer.com)
Activity1
- The increase in ethylene emission resulted in enhanced hydrogen peroxide concentration, phenylalanine ammonia-lyase activity, ß-1,3 glucanase activity, and expression profiles of WRKY, CaPR1, and CaPTI1 genes that are typical salt stress and PR signaling factors. (bvsalud.org)
Protein1
- Once the preternary-precatalytic complex is stabilized, the protein incises at the AP site, releasing the cleaved strand and giving rise to a new 5'-P end ( d ). (uam.es)
Human1
- Herpesvirus infections, such as those induced by human cytomegalovirus (HCMV), induce specific DNA damages. (springer.com)
OGG11
- Data from cell experiments are then described showing that UV-DDB interacts with OGG1 at sites of 8-oxoG. (nih.gov)
Reaction1
- This reaction can be catalyzed by AP lyase. (wikipedia.org)
Multiple1
- Irradiated environments contain radicals, which can contribute to AP sites in multiple ways. (wikipedia.org)
Partial1
- The location of the AP site proximal to the 5'-end could promote the partial melting of the 5'-end making the AP site accessible. (uam.es)
Formation2
- Ionizing radiation can also lead to AP site formation. (wikipedia.org)
- Apyrimidinic sites form at a rate roughly 20 times slower, with estimates at around 500 formation events per day, per cell. (wikipedia.org)