Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts

Nancy C Horton, John J. Perona

Research output: Contribution to journalArticle

32 Scopus citations


The 2.1-Å 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.

Original languageEnglish (US)
Pages (from-to)21721-21729
Number of pages9
JournalJournal of Biological Chemistry
Issue number34
Publication statusPublished - Aug 21 1998
Externally publishedYes


ASJC Scopus subject areas

  • Biochemistry

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