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cell cycle-DNA
X-ray (1.67 Å)
Principles of protein-DNA recognition revealed in the structural analysis of ndt80-mse DNA complexes
Lamoureux JS, Glover JN (2006): "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017.
The Saccharomyces cerevisiae transcription factor Ndt80 selectively binds a DNA consensus sequence (the middle sporulation element [MSE]) to activate gene expression after the successful completion of meiotic recombination. Here we report the X-ray crystal structures of Ndt80 bound to ten distinct MSE variants. Comparison of these structures with the structure of Ndt80 bound to a consensus MSE reveals structural principles that determine the DNA binding specificity of this transcription factor. The 5' GC-rich end of the MSE contains distinct 5'-YpG-3' steps that are recognized by arginine side chains through a combination of hydrogen bonding and cation-pi interactions. The 3' AT-rich region is recognized via minor groove contacts that sterically exclude the N2 atom of GC base pairs. The conformation of the AT-rich region is fixed by interactions with the protein that favor recognition of poly(A)-poly(T) versus mixed AT sequences through an avoidance of major groove steric clashes at 5'-ApT-3' steps.

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