Characterization of heat-like repeat superfamily of DNA glycosylases

Abstract

DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications. Bacterial HEAT-like repeat glycosylases AlkC and AlkD are specific for cationic alkylated nucleobases and have a distinctive HEAT-like repeat (HLR) fold. AlkD uses a unique non-base-flipping mechanism that enables excision of bulky lesions more commonly associated with nucleotide excision repair. In contrast, AlkC has a much narrower specificity for small lesions, principally N3-methyladenine. A crystal structure resembling a catalytic intermediate complex shows how AlkC uses unique HLR and immunoglobulin-like domains to induce a sharp kink in the DNA, exposing the damaged nucleobase to active site residues that project into the DNA. Genetic analysis of AlkC and AlkD in cells and comprehensive comparison of AlkC and AlkD with other, non-enzymatic HLR proteins provide the insights into protein structure/function/evolution relationships of this new superfamily of proteins.