2EUX

Structure of a Ndt80-DNA complex (MSE VARIANT vA4G)

Summary for 2EUX

• Entry DOI: 10.2210/pdb2eux/pdb
• Related: 1M6U 1M7U 1MN4 1MNN 2EHI 2EHJ 2ETW 2EUV 2EUW 2EUZ 2EVF 2EVG 2EVH
• Descriptor: 5'-D(*TP*GP*CP*GP*AP*CP*GP*CP*AP*AP*AP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*CP*GP*TP*CP*GP*C)-3', NDT80 protein, ... (4 entities in total)
• Functional Keywords: beta-barrel, ig-fold transcription factor, cell cycle-dna complex, cell cycle/dna
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Cellular location: Nucleus: P38830
• Total number of polymer chains: 3
• Total formula weight: 48151.12

Authors

Lamoureux, J.S.,Glover, J.N. (deposition date: 2005-10-30, release date: 2006-03-21, Last modification date: 2023-08-23)

Primary citation

Lamoureux, J.S.,Glover, J.N.
Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes.
Structure, 14:555-565, 2006

PubMed 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.

PubMed: 16531239
DOI: 10.1016/j.str.2005.11.017

Experimental method

X-RAY DIFFRACTION (1.57 Å)