Uracil-DNA glycosylase catalyzes the excision of uracils from DNA via a mechanism where the uracil is extrahelically flipped out of the DNA helix into the enzyme active site. A conserved leucine is inserted into the DNA duplex space vacated by the uracil leading to the paradigmatic "push-pull" mechanism of nucleotide flipping. However, the order of these two steps during catalysis has not been conclusively established. We report a complete kinetic analysis of a single catalytic turnover using a hydrolyzable duplex oligodeoxyribonucleotide substrate containing a uracil:2-aminopurine base pair. The results define for the first time the proper sequence of events during a catalytic cycle and establish a "pullpush", as opposed to a "push-pull", mechanism for nucleotide flipping.
The Escherichia coli MutY adenine glycosylase plays a critical role in repairing mismatches in DNA between adenine and the oxidatively damaged guanine base 8-oxoguanine. Crystallographic studies of the catalytic core domain of MutY show that the scissile adenine is extruded from the DNA helix to be bound in the active site of the enzyme (Guan, Y., Manuel, R. C., Arvai, A. S., Parikh, S. S., Mol, C. D., Miller, J. H., Lloyd, S., and Tainer, J. A. (1998) Nat. Struct. Biol. 5, 1058 -1064). However, the structural and mechanistic bases for the recognition of the 8-oxoguanine remain poorly understood. In experiments using a single-stranded 8-bromoguanine-containing synthetic oligodeoxyribonucleotide alone and in a duplex construct mismatched to an adenine, we observed UV cross-linking between MutY and the 8-bromoguanine probe. We further observed enhanced cross-linking in the single strand experiments, suggesting that neither the duplex context nor the mismatch with adenine is required for recognition of the 8-oxoguanine moiety. Stopped-flow fluorescence studies using 2-aminopurine-containing oligodeoxyribonucleotides further revealed the sequential extrusion of the 8-oxoguanine at 108 s ؊1 followed by the adenine at 16 s ؊1 . A protein isomerization step following base flipping at 1.9 s ؊1 was also observed and is postulated to provide additional stabilization of the extruded adenine thereby facilitating its capture by the active site for excision.The effect of cellular damages by reactive oxygen species in carcinogenesis and aging is well documented (1-3). Even in the absence of external oxidative stress, normal metabolic processes produce oxidative damages to DNA (4 -6) requiring repair. Oxidative damage of DNA bases alters their base pairing properties (5, 7) thereby interfering with replication and transcription (8). A predominant lesion found in DNA exposed to reactive oxygen species is 8-oxoguanine, which is especially deleterious due to its ability to form a stable Hoogsteen base pair with adenine in addition to the canonical Watson-Crick base pair with cytosine (9, 10). The facile by DNA polymerase misincorporation of an adenine across from the 8-oxoguanine (11) results in a mutagenic adenine:8-oxoguanine mismatch, a site where further replication prior to repair would lead to C 3 A or G 3 T transversions. In Escherichia coli, the MutY adenine glycosylase (MutY) 1 plays a critical role in preventing mutations stemming from oxidative damages to DNA by excising the adenine from the adenine:8-oxoguanine mismatch.Like all DNA-nucleotide-modifying enzymes, including DNA methylases, base-excision repair glycosylases, and endonucleases (12-15), MutY faces the 2-fold task of recognizing and accessing chemical moieties on DNA bases hidden within the double helix of duplex DNA. These enzymes have evolved an elegantly simple strategy for exposing their targets by rotating the phosphodiester bonds surrounding the nucleotide, causing the target base to be flipped out of the DNA helix (16 -21).Using the E. coli uracil-D...
MutY, an adenine glycosylase, initiates the critical repair of an adenine:8-oxo-guanine base pair in DNA arising from polymerase error at the oxidatively damaged guanine. Here we demonstrate for the first time, using presteady-state active site titrations, that MutY assembles into a dimer upon binding substrate DNA and that the dimer is the functionally active form of the enzyme. Additionally, we observed allosteric inhibition of glycosylase activity in the dimer by the concurrent binding of two lesion mispairs. Active site titration results were independently verified by gel mobility shift assays and quantitative DNA footprint titrations. A model is proposed for the potential functional role of the observed polysteric and allosteric regulation in recruiting and coordinating interactions with the methyl-directed mismatch repair system.
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