Biopolymers and cell. 1996; 12 (3): 17 - 26

Interaction of Flp protein with its recombination site: substrate-enzyme molecular adjustment

Y. A. Voziyanov, A. I. Kornelyuk

Site-specific recombinase Flp encoded by 2 micron plasmidfrom Saccharomyces cerevisiae participates in amplification of copy number of 2 micron plasmid by inverting two parts of the plasmid relative to each other. In the paper a complex process of binding of Flp protein to its recombination site, which appears to be a series of consequent steps of recognition, is considered. An analysis of the primary structure of the Flp recombination site has been made in order to figure out whether there is a predisposition of the recombina¬tion site to the conformational changes upon the Flp protein binding. The analysis has revealed that the distribution of the dinucleotides that have a tendency to bend DNA either toward minor groove of DNA is not random. It has been suggested that a fragment of DNA molecule at the site of recombination is not a «passive» substrate for the recombination reaction, but a substrate that favour the protein to carry out recombination reaction in an optimal way. Apparently, it is a multistep process of substrate-enzyme adjust¬ment of the Flp protein and the recombination site that ensures their effective and specific binding.