Summary information and primary citation
- PDB-id
- 3e3y; DSSR-derived features in text and JSON formats
- Class
- hydrolase-DNA
- Method
- X-ray (2.13 Å)
- Summary
- Q138f hincii bound to gttaac and cocrystallized with 5 mm ca2+
- Reference
- Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC (2008): "DNA distortion and specificity in a sequence-specific endonuclease." J.Mol.Biol., 383, 186-204. doi: 10.1016/j.jmb.2008.08.032.
- Abstract
- Five new structures of the Q138F HincII enzyme bound to a total of three different DNA sequences and three different metal ions (Ca(2+), Mg(2+), and Mn(2+)) are presented. While previous structures were produced from soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new structures are derived from cocrystallization with Ca(2+), Mg(2+), or Mn(2+). The Mn(2)(+)-bound structure provides the first view of a product complex of Q138F HincII with cleaved DNA. Binding studies and a crystal structure show how Ca(2+) 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.
