DNA Distortion and Specificity in a Sequence-Specific Endonuclease

Andrea C. Babic, Elizabeth J. Little, Veena M. Manohar, Jurate Bitinaite, Nancy C. Horton

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Five new structures of the Q138F HincII enzyme bound to a total of three different DNA sequences and three different metal ions (Ca2+, Mg2+, and Mn2+) are presented. While previous structures were produced from soaking Ca2+ into preformed Q138F HincII/DNA crystals, the new structures are derived from cocrystallization with Ca2+, Mg2+, or Mn2+. The Mn2+-bound structure provides the first view of a product complex of Q138F HincII with cleaved DNA. Binding studies and a crystal structure show how Ca2+ allows trapping of a Q138F HincII complex with noncognate DNA in a catalytically incompetent conformation. Many Q138F HincII/DNA structures show asymmetry, despite the binding of a symmetric substrate by a symmetric enzyme. The various complexes are fit into a model describing the different conformations of the DNA-bound enzyme and show how DNA conformational energetics determine DNA-cleavage rates by the Q138F HincII enzyme.

Original languageEnglish (US)
Pages (from-to)186-204
Number of pages19
JournalJournal of Molecular Biology
Issue number1
StatePublished - Oct 31 2008


  • indirect readout
  • protein-DNA complex
  • restriction endonuclease

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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