2EVI: Structure Of A Ndt80-dna Complex (mse Mutant Ma8t)

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.
PDB ID: 2EVIDownload
MMDB ID: 74615
PDB Deposition Date: 2005/10/31
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 1.8  Å
Source Organism:
Saccharomyces cerevisiae
Similar Structures:
Biological Unit for 2EVI: trimeric; determined by author
Molecular Components in 2EVI
Label Count Molecule
Protein (1 molecule)
Ndt80 Protein(Gene symbol: NDT80)
Molecule annotation
Nucleotides(2 molecules)
Molecule annotation
Molecule annotation
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Citing MMDB