New Recognition Mode for a TG Mismatch: The Atomic Structure of a Very Short Patch Repair Endonuclease-DNA Complex
1
Citation
11
Reference
10
Related Paper
Citation Trend
Abstract:
The crystal structure determination of the T4 endo-Vpyrimidine photodimer DNA glycosylase provided thefirst direct view of DNA lesion recognition by a repair enzyme (Vassylyev et al. 1995). Similar damaged DNArecognition modes, involving nucleotide flipping, wereobserved in various base excision repair enzymes (Parikhet al. 1997; Vassylyev and Morikawa 1997; Mol et al.1999). The implications of nucleotide flipping raised thenew question of how DNA endonucleases other than baseexcision repair enzymes recognize mismatched basepairs. The Escherichia coli very short patch repair (Vsr)endonuclease is a good target to address this question interms of three-dimensional structures. The Vsr endonuclease is involved in the initial reaction for the repair ofmismatched TG base pairs generated through spontaneous deamination of a methylated cytosine. This enzyme recognizes a TG mismatch within the duplex5′CT(A/T)GG, where the second T forms the mismatchand all of the other bases are in standard Watson-Crickbase pairing. It catalyzes the cleavage at the 5′ side of thethymine, leaving a 5′ phosphate and a 3′ hydroxyl at thetermini. The crystal structure of a truncated form of thisendonuclease was determined at 1.8 Å resolution (Tsutakawa et al. 1999b). The protein was found to containone structural zinc-binding module. Unexpectedly, itsoverall topology resembles members of the type II restriction endonuclease family, although the catalytic center with critical histidines is distinct from those of restriction enzymes. More recently, the crystal structure of Vsrendonuclease in complex with DNA has been determinedat 2.3 Å resolution (Tsutakawa et al. 1999a). This endonuclease has been found to employ a novel mismatchbase-pair recognition scheme that does not involve baseflipping-out. Extensive interactions between the DNAand the protein characterize the recognition mechanism,where three aromatic residues intercalate from the majorgroove into the DNA to strikingly deform the base-pairstacking. An amino-terminal α-helix is accommodatedinto the expanded minor groove so that the amino acidside chains make additional contacts with the DNA duplexes. With the presence of a cleaved DNA intermediatein the active center, the structure of the Vsr/DNA complex provides detailed insights into the catalytic mechanism for endonuclease activity...Keywords:
AP endonuclease
Deamination
Cytosine
Abstract The six major mammalian DNA repair pathways were discovered as independent processes, each dedicated to remove specific types of lesions, but the past two decades have brought into focus the significant interplay between these pathways. In particular, several studies have demonstrated that certain proteins of the nucleotide excision repair (NER) and base excision repair (BER) pathways work in a cooperative manner in the removal of oxidative lesions. This review focuses on recent data showing how the NER proteins, XPA, XPC, XPG, CSA, CSB and UV-DDB, work to stimulate known glycosylases involved in the removal of certain forms of base damage resulting from oxidative processes, and also discusses how some oxidative lesions are probably directly repaired through NER. Finally, since many glycosylases are inhibited from working on damage in the context of chromatin, we detail how we believe UV-DDB may be the first responder in altering the structure of damage containing-nucleosomes, allowing access to BER enzymes.
Cite
Citations (88)
AP endonuclease
Hypoxanthine
Cite
Citations (19)
AP endonuclease
DNA polymerase beta
Cite
Citations (464)
Human alkyladenine DNA glycosylase (AAG) locates and excises a wide variety of damaged purine bases from DNA, including hypoxanthine that is formed by the oxidative deamination of adenine. We used steady state, pre-steady state, and single-turnover kinetic assays to show that the multiple-turnover excision of hypoxanthine in vitro is limited by release of the abasic DNA product. This suggests the possibility that the product release step is regulated in vivo by interactions with other base excision repair (BER) proteins. Such coordination of BER activities would protect the abasic DNA repair intermediate and ensure its correct processing. AP endonuclease 1 (APE1) is the predominant enzyme for processing abasic DNA sites in human cells. Therefore, we have investigated the functional effects of added APE1 on the base excision activity of AAG. We find that APE1 stimulates the multiple-turnover excision of hypoxanthine by AAG but has no effect on single-turnover excision. Since the amino terminus of AAG has been implicated in other protein-protein interactions, we also characterize the deletion mutant lacking the first 79 amino acids. We find that APE1 fully stimulates the multiple-turnover glycosylase activity of this mutant, demonstrating that the amino terminus of AAG is not strictly required for this functional interaction. These results are consistent with a model in which APE1 displaces AAG from the abasic site, thereby coordinating the first two steps of the base excision repair pathway.
AP endonuclease
Hypoxanthine
Cite
Citations (50)
The eukaryotic 8-oxoguanine−DNA glycosylase 1 (OGG1) provides the major activity for repairing mutagenic 7,8-dihydro-8-oxoguanine (8-oxoG) induced in the genome due to oxidative stress. Earlier in vitro studies showed that, after excising the base lesion, the human OGG1 remains bound to the resulting abasic (AP) site in DNA and does not turn over efficiently. The human AP-endonuclease (APE1), which cleaves the phosphodiester bond 5' to the AP site, in the next step of repair, displaces the bound OGG1 and thus increases its turnover. Here we show that NEIL1, a DNA glycosylase/AP lyase specific for many oxidized bases but with weak 8-oxoG excision activity, stimulates turnover of OGG1 in a fashion similar to that of APE1 and carries out βδ-elimination at the AP site. This novel collaboration of two DNA glycosylases, which do not stably interact with each other, in stimulating 8-oxoguanine repair is possible because of higher AP site affinity and stronger AP lyase activity of NEIL1 relative to OGG1. Comparable levels of NEIL1 and OGG1 in some human cells raise the possibility that NEIL1 serves as a backup enzyme to APE1 in stimulating 8-oxoG repair in vivo.
AP endonuclease
Cite
Citations (73)
Base excision repair (BER) is considered the most important pathway involved in removing DNA damage. Base excision repair pathway is initiated by recognition of a DNA glycosylase (OGG1-oxoguanine glycosylase 1 and MUTYH -MutY homolog)/. This glycosylase catalyzes the cleavage of an N-glycosidic bond, effectively removing the damaged base The DNA backbone is cleaved by a DNA AP endonuclease/APE1/ and creating an apurinic or apyrmidinic site (AP site). DNA polymeraseX-ray repair cross-complementing group 1(XRCC1) fills in the gap with the correct nucleotide. Finally, DNA ligase completes the repair process and restores the integrity of the helix by sealing the nick. Many genes encoding DNA damage repair proteins involved in BER are highly polymorphic. Those polymorphisms have a great influence on pertinent protein functions and they are associated with individual susceptibility into neoplastic events. XRCC1 plays an important role in BER system, which is critical for genome maintenance. Polymorphisms in XRCC1 that result alteration of DNA repair capacity are reportedly associated with cancer risk and treatment response.
XRCC1
AP endonuclease
MUTYH
Cite
Citations (11)
The base excision repair (BER) pathway repairs a wide variety of damaged nucleobases in DNA. This pathway is initiated by a DNA repair glycosylase, which locates the site of damage and catalyzes the excision of the damaged nucleobase. The resulting abasic site is further processed by apurinic/apyrimidinic site endonuclease 1 (APE1) to create a single-strand nick with the 3'-hydroxyl that serves as a primer for DNA repair synthesis. Because an abasic site is highly mutagenic, it is critical that the steps of the BER pathway be coordinated. Most human glycosylases bind tightly to their abasic product. APE1 displaces the bound glycosylase, thereby stimulating multiple-turnover base excision. It has been proposed that direct protein-protein interactions are involved in the stimulation by APE1, but no common interaction motifs have been identified among the glycosylases that are stimulated by APE1. We characterized the APE1 stimulation of alkyladenine DNA glycosylase (AAG) using a variety of symmetric and asymmetric lesion-containing oligonucleotides. Efficient stimulation of a wide variety of substrates favors a model in which both AAG and APE1 can simultaneously bind to DNA but may not interact directly. Rather, nonspecific DNA binding by both AAG and APE1 enables APE1 to replace AAG at the abasic site. AAG is not displaced into solution but remains bound to an adjacent undamaged site. We propose that nonspecific DNA binding interactions allow transient exposure of the abasic site so that it can be captured by APE1.
AP endonuclease
Uracil-DNA glycosylase
Cite
Citations (21)
Adenine-DNA glycosylase MutY of Escherichia coli catalyzes the cleavage of adenine when mismatched with 7,8-dihydro-8-oxoguanine (GO), an oxidatively damaged base. The biological outcome is the prevention of C/G→A/T transversions. The molecular mechanism of base excision repair (BER) of A/GO in mammals is not well understood. In this study we report stimulation of mammalian adenine-DNA glycosylase activity by apurinic/apyrimidinic (AP) endonuclease using murine homolog of MutY (Myh) and human AP endonuclease (Ape1), which shares 94% amino acid identity with its murine homolog Apex. After removal of adenine by the Myh glycosylase activity, intact AP DNA remains due to lack of an efficient Myh AP lyase activity. The study of wild-type Ape1 and its catalytic mutant H309N demonstrates that Ape1 catalytic activity is required for formation of cleaved AP DNA. It also appears that Ape1 stimulates Myh glycosylase activity by increasing formation of the Myh–DNA complex. This stimulation is independent of the catalytic activity of Ape1. Consequently, Ape1 preserves the Myh preference for A/GO over A/G and improves overall glycosylase efficiency. Our study suggests that protein–protein interactions may occur in vivo to achieve efficient BER of A/GO.
AP endonuclease
MUTYH
Cite
Citations (129)
Summary The chronological life span of yeast, the survival of stationary (G 0 ) cells over time, provides a model for investigating certain of the factors that may influence the aging of non‐dividing cells and tissues in higher organisms. This study measured the effects of defined defects in the base excision repair (BER) system for DNA repair on this life span. Stationary yeast survives longer when it is pregrown on respiratory, as compared to fermentative (glucose), media. It is also less susceptible to viability loss as the result of defects in DNA glycosylase/AP lyases (Ogg1p, Ntg1p, Ntg2p), apurinic/apyrimidinic (AP) endonucleases (Apn1p, Apn2p) and monofunctional DNA glycosylase (Mag1p). Whereas single BER glycosylase/AP lyase defects exerted little influence over such optimized G 0 survival, this survival was severely shortened with the loss of two or more such enzymes. Equally, the apn1 Δ and apn2 Δ single gene deletes survived as well as the wild type, whereas a apn1 Δ apn2 Δ double mutant totally lacking in any AP endonuclease activity survived poorly. Both this shortened G 0 survival and the enhanced mutagenicity of apn1 Δ apn2 Δ cells were however rescued by the overexpression of either Apn1p or Apn2p. The results highlight the vital importance of BER in the prevention of mutation accumulation and the attainment of the full yeast chronological life span. They also reveal an appreciable overlap in the G 0 maintenance functions of the different BER DNA glycosylases and AP endonucleases.
AP endonuclease
Cite
Citations (42)
Nitric oxide and nitrous acid induce deamination of DNA bases, resulting in uracil, hypoxanthine, xanthine, and oxanine (Oxa) as major damage. Oxa reacts further with polyamines and DNA binding proteins, generating bulky cross-link adducts. Recently we have shown Oxa and cross-link adducts are potentially genotoxic lesions. In the present study, we have assessed the role of base excision repair (BER) and nucleotide excision repair (NER) systems in the repair of Oxa and Oxa-spermine (Oxa-Sp) cross-link adducts. Oxa was very poorly removed from DNA by both BER glycosylases and NER enzymes, whereas Oxa-Sp was efficiently excised by E. coli and human NER enzymes.
Deamination
Hypoxanthine
Uracil
Cite
Citations (8)