Recognition of Flanking DNA Sequences by EcoRV Endonuclease Involves Alternative Patterns of Water-mediated Contacts*

The 2.1-Å cocrystal structure ofEcoRV endonuclease bound to 5′-CGGGATATCCC, in a crystal lattice isomorphous with the cocrystallized undecamer 5′-AAAGATATCTT previously determined, shows novel base recognition in the major groove of the DNA flanking the GATATC target site. Lys104 of the enzyme interacts through water molecules with the exocyclic N-4 amino groups of flanking cytosines. Steric exclusion of water molecule-binding sites by the 5-methyl group of thymine drives the adoption of alternative water-mediated contacts with ATversus GC flanks. This structure provides a rare example of structural adaptability in the recognition of different DNA sequences by a protein and suggests preferred strategies for the expansion of target site specificity by EcoRV.

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