Structural Features of DNA Glycosylases and AP Endonucleases

The most common and perhaps the most important type of DNA damage is base damage, which occurs at the rate of several thousand base pairs per cell per day in humans (1). This damage is primarily caused by endogenous metabolic and immune processes rather than environmental toxins, with the exception of UV damage to the skin from sunlight and oxidative damage to lung and blood from cigarette smoke (2,3). While the repair of DNA base damage can be complex, most such damage is prevented from becoming mutagenic or toxic by the base excision repair (BER) pathway. All base damage repair is initiated and, in special cases, completed by proteins that specifically recognize the damaged bases and either remove them to begin BER or repair them by direct damage reversal. Three-dimensional crystal structures of representatives of all major components of the BER pathway have been determined. Here, we review the enzymes that act in the initiation of BER and the proteins that complete the direct damage reversal process. The BER involves the remarkably specific detection and removal of damaged bases in the context of an enormous background of normal DNA, followed by DNA backbone cleavage. In the damage-general steps of BER that follow, DNA polymerases and ligases complete repair by synthesizing new DNA and rejoining the deoxyribonucleotide phosphate backbone. The elucidation of the initial steps of damaged base repair have provided critical insights into protein-DNA interactions and chemistry with broad and profound impacts on our understanding of biochemistry, cell biology, and life itself. For example, the DNA glycosylases that initiate BER use unique DNAbinding motifs, flip damaged nucleotides 180 into damage-specific pockets, and initiate a choreographed and coordinated handoff of damaged DNA intermediates to downstream pathway components. As will be discussed in the following sections, experimental characterizations of DNA base repair processes are providing an integrated understanding of structural cell biology at escalating levels of complexity, from DNA base damage to protein-DNA complexes to dynamically assembled macromolecular machines.