Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase

Abstract

The genomes of aerobic organisms suffer chronic oxidation of guanine to the genotoxic product 8-oxoguanine (oxoG). Replicative DNA polymerases misread oxoG residues and insert adenine instead of cytosine opposite the oxidized base. Both bases in the resulting A*oxoG mispair are mutagenic lesions, and both must undergo base-specific replacement to restore the original C*G pair. Doing so represents a formidable challenge to the DNA repair machinery, because adenine makes up roughly 25% of the bases in most genomes. The evolutionarily conserved enzyme adenine DNA glycosylase (called MutY in bacteria and hMYH in humans) initiates repair of A*oxoG to C*G by removing the inappropriately paired adenine base from the DNA backbone. A central issue concerning MutY function is the mechanism by which A*oxoG mispairs are targeted among the vast excess of A*T pairs. Here we report the use of disulphide crosslinking to obtain high-resolution crystal structures of MutY-DNA lesion-recognition complexes. These structures reveal the basis for recognizing both lesions in the A*oxoG pair and for catalysing removal of the adenine base.

DNA repair glycosylases with a [4Fe–4S] cluster: A redox cofactor for DNA-mediated charge transport?

“…In E. coli MutY, the corresponding mutations (Y82C and G253D) lead to modest decreases in substrate binding affinity and rate of excision [77]. In addition, structural studies show that Y82 and G253 interact with the DNA near the 8-oxoguanine lesion site [39][40]. It is likely that Y82 and G253 are involved in substrate recognition, but it is still not completely understood how all of the mutations implicated in MAP give rise to cancer.…”

“…Crystal structures are available for MutY and Endo III both free and bound to DNA [18][19][20][39][40]. These provide many clues about the environment of the cluster in both states.…”

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

“…Such configurations are relatively common, as, for example, in structures of the conserved motif IVof the 4.5 S RNA alone, 46 the SRP RNA complex with Ffh M domain, 47 the RNA complexes of the SRP Alu domain, 48 and DNA-editing complexes involved in repair and excision of 8-oxoguanine:adenine mispairs. 49,50 Previously, mutations of residues associated with the activation region, in particular Arg195, have been assayed in the context of the assembled SRP: FtsY complex 15 and found to exhibit deficiencies in GTPase activation. It is possible that these defects, rather than reflecting a contribution to the chemistry of GTP hydrolysis per se (as in an arginine finger mechanism 51 ), reflect instead interactions of the activation region with the 4.5 S RNA of the SRP.…”

Unnatural substrates reveal the importance of 8-oxoguanine for in vivo mismatch repair by MutY

“…1). 24 In addition, the removal of N3 is unlikely to affect base pairing with OG, and therefore should not globally alter the recognition features of the mismatched base pair or the ease with which MutY mediates base pair disruption. Thus, the reduced ability of MutY to remove Z3 relative to A is likely due to alterations of the electronic properties of the base.…”

“…DNA bending and distortion that is associated with forming the catalytically competent DNA-MutY intermediate is expected to be facilitated by electrostatic and hydrogenbonding interactions of DNA backbone phosphates with amino acid side chains and backbone amides. 24 In the case of G:A substrates, accessing the catalytically competent intermediate must rely heavily on nonspecific electrostatic interactions to explain the sensitivity to the increased salt concentration. 36,37 In contrast, with OG:A substrates, nonspecific electrostatic interactions are not as critical for efficient adenine removal.…”