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PDBsum entry 1mn4
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Transcription
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PDB id
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1mn4
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References listed in PDB file
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Key reference
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Title
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Structure of the sporulation-Specific transcription factor ndt80 bound to DNA.
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Authors
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J.S.Lamoureux,
D.Stuart,
R.Tsang,
C.Wu,
J.N.Glover.
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Ref.
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EMBO J, 2002,
21,
5721-5732.
[DOI no: ]
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PubMed id
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Abstract
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Progression through the middle phase of sporulation in Saccharomyces cerevisiae
is promoted by the successful completion of recombination at the end of prophase
I. Completion of meiotic recombination allows the activation of the
sporulation-specific transcription factor Ndt80, which binds to a specific DNA
sequence, the middle sporulation element (MSE), and activates approximately 150
genes to enable progression through meiosis. Here, we isolate the DNA-binding
domain of Ndt80 and determine its crystal structure both free and in complex
with an MSE-containing DNA. The structure reveals that Ndt80 is a member of the
Ig-fold family of transcription factors. The structure of the DNA-bound form,
refined at 1.4 A, reveals an unexpected mode of recognition of 5'-pyrimidine-
guanine-3' dinucleotide steps by arginine residues that simultaneously recognize
the 3'-guanine base through hydrogen bond interactions and the 5'-pyrimidine
through stacking/van der Waals interactions. Analysis of the DNA-binding
affinities of MSE mutants demonstrates the central importance of these
interactions, and of the AT-rich portion of the MSE. Functional similarities
between Ndt80 and the Caenorhabditis elegans p53 homolog suggest an evolutionary
link between Ndt80 and the p53 family.
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Figure 6.
Figure 6 Schematic of Ndt80–DNA interactions. The MSE bases
are highlighted in blue and are numbered 1–9. The
complementary strand is distinguished with a prime following the
number. Protein residues are colored as described in Figure 4.
Electrostatic and polar interactions are indicated with arrows,
while van der Waals contacts are represented by hash marks. The
blue circles are water molecules that are highly ordered in the
DNA–protein interface.
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Figure 7.
Figure 7 5'-YpG-3' recognition by Ndt80. (A) View down the DNA
helix axis showing base stacking between the C–G base pair at
position 5 and the A–T pair at position 6. van der Waals
surface representations of R177 (yellow), P57 (red) and T6'
(gray) are displayed and hydrogen bonding interactions are
indicated in green. (B) An equivalent CG–AT is shown from the
structure of a similar DNA sequence determined in the absence of
bound protein (Nelson et al., 1987). The view is such that the
C–G base pairs in both panels are in identical orientations.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
5721-5732)
copyright 2002.
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