PMID: 16963084 , Related PDB id: 2I13

Authors:

Segal DJ, Crotty JW, Bhakta MS, Barbas CF 3rd, Horton NC

Title:

Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA.

Journal:

J Mol Biol. 2006 Oct 20;363(2):405-21. Epub 2006 Aug 11.

Abstract:

Cys2-His2 zinc fingers are one of the most common types of DNA-binding domains. Modifications to zinc-finger binding specificity have recently enabled custom DNA-binding proteins to be designed to a wide array of target sequences. We present here a 1.96 A structure of Aart, a designed six-zinc finger protein, bound to a consensus DNA target site. This is the first structure of a designed protein with six fingers, and was intended to provide insights into the unusual affinity and specificity characteristics of this protein. Most protein-DNA contacts were found to be consistent with expectations, while others were unanticipated or insufficient to explain specificity. Several were unexpectedly mediated by glycerol, water molecules or amino acid-base stacking interactions. These results challenge some conventional concepts of recognition, particularly the finding that triplets containing 5'A, C, or T are typically not specified by direct interaction with the amino acid in position 6 of the recognition helix.