Biochemistry 1996, 35, 2201-2208
2201
Contribution of Facilitated Diffusion and Processive Catalysis to Enzyme Efficiency: Implications for the EcoRI Restriction-Modification System† Mark A. Surby and Norbert O. Reich* Department of Chemistry, UniVersity of California, Santa Barbara, California 93106 ReceiVed August 10, 1995; ReVised Manuscript ReceiVed December 11, 1995X
ABSTRACT:
The contribution of nonspecific DNA to enzyme efficiency (kcat/Km) is described for a sequencespecific DNA-modifying enzyme. Our investigation focuses on the EcoRI DNA methyltransferase which transfers a methyl group from the cofactor S-adenosylmethionine to the second adenine in the doublestranded DNA sequence GAATTC. kcat/Km increases 4-fold as DNA length increases from 14 to 429 base pairs and increases 2-fold as the distance from the site to the nearest end is increased from 29 to 378 base pairs. No changes in kcat/Km result from further increases in either case. A facilitated diffusion mechanism is proposed in which the methyltransferase scans an average of
