Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
The 2.1-A 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 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 AT versus 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.
Department of Chemistry and Interdepartmental Program in Biochemistry and Molecular Biology, University of California, Santa Barbara, California 93106-9510, USA.
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Horton
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Perona
D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D014867:Water
D014867:Water; D004247:DNA; D015252:Deoxyribonucleases, Type II Site-Specific; C027440:GATATC-specific type II deoxyribonucleases