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PDBsum entry 2evh
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Cell cycle/DNA
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PDB id
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2evh
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References listed in PDB file
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Key reference
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Title
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Principles of protein-Dna recognition revealed in the structural analysis of ndt80-Mse DNA complexes.
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Authors
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J.S.Lamoureux,
J.N.Glover.
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Ref.
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Structure, 2006,
14,
555-565.
[DOI no: ]
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PubMed id
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Abstract
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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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Figure 4.
Figure 4. Stereoview of the Changes in the mC5T Structure
The mutation of the guanine recognized by Arg177 to an
adenosine forces the side chain to reorient, displacing two
water molecules. The wild-type structure is semitransparent, and
illustrated in orange and teal for DNA and protein,
respectively; waters are red and hydrogen bonds are yellow. The
mutant structure is colored blue and purple for DNA and protein,
respectively. The waters in the mutant are colored green and the
hydrogen bonds are beige. The surface of the protein, excluding
the side chain for Arg177, from the mutant structure is rendered
in grey and is essentially identical to that of the wild-type
structure.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2006,
14,
555-565)
copyright 2006.
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