RECOGNITION OF FLANKING DNA-SEQUENCES BY ECORV ENDONUCLEASE INVOLVES ALTERNATIVE PATTERNS OF WATER-MEDIATED CONTACTS

The 2.1-Angstrom cocrystal structure of EcoRV endonuclease bound to 5' -CGGGATATCCC, in a crystal lattice isomorphous with the cocrystallized undecamer 5'-AAAGATATCTT previously determined, shows novel base reco gnition in the major groove of the DNA flanking the GATATC target site . Lys(104) Of the enzyme interacts through water molecules with the ex ocyclic N-4 amino groups of flanking cytosines. Steric exclusion of wa ter molecule-binding sites by the 5-methyl group of thymine drives the adoption of alternative water-mediated contacts with AT versus GC fla nks. This structure provides a rare example of structural adaptability in the recognition of different DNA sequences by a protein and sugges ts preferred strategies for the expansion of target site specificity b y EcoRV.