The type II restriction endonucleases specifically recognise symmetric DNA sequence of 4 to 8 base pairs and cut the DNA strand within or close to their recognition site. Fidelity of these enzymes is remarkable: a change of just one base pair in a specific recognition site can reduce cleavage rates 10⁵ to 10⁹ times. This property makes type II restriction endonucleases a useful tool for molecular biologists and an interesting model for studying DNA-protein interactions. The basis of restriction endonuclease fidelity could not been understood from analysis of their sequences alone, because these sequences share in general little similarity. It was necessary to solve three dimensional structures of typical type II restriction enzymes to find out how they interact with DNA and to suggest hypotheses explaining recognition and catalysis mechanisms of these enzymes. Surprisingly, the structures show that restriction enzymes can employ different strategies of DNA recognition even for their common inner base pairs. Thus, a minimal difference of single base pair in recognition site may select enzymes with relatively large differences in their DNA recognition machinery. We have therefore decided to investigate the variability of restriction enzymes with the same recognition sequence and chose a pair of isoshisomeric restriction endonucleases, Bse634I and Cfr10I, for our structural studies. Both enzymes recognise degenerate DNA sequence 5'-Pu/CCGGPy, and cut as indicated by /. Structure of Cfr10I is already known; in this work we report the structure of Bse634I restriction enzyme from Bacillus stearothermophilus. The two enzymes, Bse634I and Cfr10I, are the first pair of isoshisomeric restriction endonucleases where structures of both proteins in a DNA-free state are known. Comparison of the two structures shows how DNA recognition and catalysis are possibly coupled through the rearrangement of the mobile protein subdomains.     «

The type II restriction endonucleases specifically recognise symmetric DNA sequence of 4 to 8 base pairs and cut the DNA strand within or close to their recognition site. Fidelity of these enzymes is remarkable: a change of just one base pair in a specific recognition site can reduce cleavage rates 10⁵ to 10⁹ times. This property makes type II restriction endonucleases a useful tool for molecular biologists and an interesting model for studying DNA-protein interactions. The basis of restriction...     »