Chemical Mechanisms for Mobilizing DNA

Different types of elements, and their associated recombinases, continue to be discovered and characterized. Studies of two major classes of these recombinases have advanced to the point that detailed molecular mechanisms can be discussed. This chapter focuses on the mechanisms of protein-catalyzed recombination by these two classes to provide examples of how the chemistry of DNA mobility is catalyzed and controlled. Central to both types of DNA rearrangements are protein-catalyzed polynucleotidyl transfer steps. The chapter focuses on the likely catalytic functions of several active-site residues. The key to understanding the catalytic mechanisms used by transposases is knowledge of how the different DNA segments are positioned and repositioned within the active sites as recombination progresses. The characteristic of recombinases is related to two important biological features that distinguish the proteins from traditional enzymes. First, the physiological demand on the reaction rate for phosphoryl transfer in recombination is usually very low, with many reactions occurring less than once every cell cycle. Second, the physiology also frequently demands that essentially all substrate molecules are converted to product, even when the "substrate" and the "product" are nearly isoenergetic. The structural organization of recombination complexes is intimately related to the mechanisms used for biological control. Perhaps one of the most satisfying aspects of the continued understanding of site-specific recombination and transposition is that, as the details of the protein-DNA complex structures and catalytic strategies are elucidated, they provide insight into the molecular basis of regulation.