Summary information and primary citation

PDB-id
2evj; SNAP-derived features in text and JSON formats; DNAproDB
Class
cell cycle-DNA
Method
X-ray (1.89 Å)
Summary
Structure of an ndt80-DNA complex (mse mutant ma9c)
Reference
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.
Abstract
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.

Cartoon-block schematics in six views (download the tarball)

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