Computational approaches to restriction endonucleases

Type II restriction endonucleases catalyze phosphodiester bond hydrolysis in bacteria to protect the host cell from invading phage DNA. Due to their exquisite sequence selectivity type II restriction endonucleases serve as excellent model systems for studying protein-nucleic acid interactions. Crystal structures of the PD-(D/E)XK superfamily revealed a common alpha/beta core motif and similar active site. In contrast, these enzymes show little sequence similarity and use different strategies to interact with their substrate DNA. Computational approaches have been applied to unify the mechanism of restriction endonucleases and rationalize their diversity. The first step of type II restriction endonuclease catalysis has been studied on Bam HI by semi-microscopic version of the Protein Dipoles Langevin Dipoles method. The substrate-assisted catalysis and the general base mechanism have been concluded as less likely than the metal-catalyzed reaction. A general model for catalysis has been proposed based on the group contributions to the reduction of the activation free energy. Factors contributing to structural stability of PD-(D/E)XK type II restriction endonucleases have been analyzed to elucidate evolutionary relationship between these enzymes. Residues playing role in catalysis and recognition were highly correlated with those participating in stabilization centers. Thus the main functional motifs were concluded to be evolutionary more conserved than other parts of the structure. This observation is consistent with the proposal that these enzymes have developed from a common ancestor with divergent evolution. (C) 2003 Elsevier B.V. All rights reserved.