Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase

Abstract

7,8-dihydro-8-oxoguanine (8-oxoG) is the major oxidative product of guanine and the most prevalent base lesion observed in DNA molecules. Because 8-oxoG has the capability to form a Hoogsteen pair with adenine (8-oxoG:A) in addition to a normal Watson-Crick pair with cytosine (8-oxoG:C), this lesion can lead to a G:C → T:A transversion after replication. However, 8-oxoG is recognized and excised by the 8-oxoguanine DNA glycosylase (Ogg) of the base excision repair pathway. Members of the Ogg1 family usually display a strong preference for a C opposite the lesion. In contrast, the atypical Ogg1 from Clostridium actetobutylicum (CacOgg) can excise 8-oxoG when paired with either one of the four bases, albeit with a preference for C and A. Here we describe the first high resolution crystal structures of CacOgg in complex with duplex DNA containing the lesion 8-oxoG paired to cytosine and to adenine. A structural comparison with human OGG1 provides a rationale for the lack of opposite base specificity displayed by the bacterial Ogg.

The C-terminal Lysine of Ogg2 DNA Glycosylases is a Major Molecular Determinant for Guanine/8-Oxoguanine Distinction

“…The identity of the metal ion was deduced based on geometry (octahedral), bound distances (average of 2.5 Å) and the previously determined structure of CacOgg. 16 …”

“…The Ogg1 family encompasses the largest number of members including the well-studied human OGG1 (hOGG1) 7; 8; 9; 10; 11; 12; 13 and the atypical bacterial Ogg1 from Clostridium acetobutylicum (CacOgg) 14; 15; 16 . Even though the Ogg1 gene products can vary considerably in size these enzymes all share a similar tertiary fold composed of three domains.…”

“…This second feature of 8-oxoG appears to be a major contributor to 8-oxoG recognition by Ogg1: The N7-H atom participates in a hydrogen bond with the main chain carbonyl of a conserved glycine (Gly42 in hOGG1 and Gly30 in CacOgg 16; 24 ) located in the αA-βB recognition loop of domain A. 14; 16; 24; 25 If G is bound instead of 8-oxoG, then the attractive interaction between the glycine carbonyl and the 8-oxoG N7-H is predicted to be replaced by a repulsive interaction between the same carbonyl and the N7 lone pair of G. 26 AGOG, on the other hand, seems to recognize the two features that distinguish 8-oxoG from guanine, interacting with both C8-oxygen and N7-H atom. 22 Moreover, the interactions between AGOG and 8-oxoG involve the side chains of two residues and not a main chain carbonyl as seen in Ogg1.…”

“…In addition, the structure revealed conformational changes upon binding DNA by MjaOgg of a magnitude similar to that reported for Ogg1. 16; 25 Furthermore, analysis of the interactions between the enzyme and the estranged base provides an explanation for the lack of opposite base specificity displayed by Ogg2 compared to hOGG1.…”

Recognition of Damaged DNA: Structure and Dynamic Markers

“…83 BER DNA Polymerase b has an activity that preferentially inserts a C opposite an 8-oxoG, thus creating the original 8-oxoG:C base pair giving OGG1 another opportunity for repair. 87 Finally, the MMR dimer MSH2-MSH6 also recognizes 8-oxoG damage opposite A, G, and T but not C. The enzyme recruits the necessary repair enzymes to remove the nascent nucleotide, and depending on the identity of the nucleotide is either fully corrected or reverts to an 8-oxoG:C base pair (Fig. 3).…”