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PDBsum entry 2er8
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Transcription activator/DNA
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PDB id
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2er8
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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 a leu3-Dna complex: recognition of everted cgg half-Sites by a zn2cys6 binuclear cluster protein.
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Authors
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M.X.Fitzgerald,
J.R.Rojas,
J.M.Kim,
G.B.Kohlhaw,
R.Marmorstein.
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Ref.
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Structure, 2006,
14,
725-735.
[DOI no: ]
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PubMed id
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Abstract
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Gal4 is the prototypical Zn2Cys6 binuclear cluster transcriptional regulator
that binds as a homodimer to DNA containing inverted CGG half-sites. Leu3, a
member of this protein family, binds to everted (opposite polarity to inverted)
CGG half-sites, and an H50C mutation within the Leu3 Zn2Cys6 binuclear motif
abolishes its transcriptional repression function without impairing DNA binding.
We report the X-ray crystal structures of DNA complexes with Leu3 and Leu3(H50C)
and solution DNA binding studies of selected Leu3 mutant proteins. These studies
reveal the molecular details of everted CGG half-site recognition, and suggest a
role for the H50C mutation in transcriptional repression. Comparison with the
Gal4-DNA complex shows an unexpected conservation in the DNA recognition mode of
inverted and everted CGG half-sites, and points to a critical function of a
linker region between the Zn2Cys6 binuclear cluster and dimerization regions in
DNA binding specificity. Broader implications of these findings are discussed.
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Figure 2.
Figure 2. Overall Structure of Leu3-DNA Complexes
(A) DNA
sequences used for crystallization. Half-sites recognized in
the structure are in bold. Half of each 12-mer duplex that the
complex straddles is shown, and designed half-sites are
underlined.
(B) Structures of Leu3-DNA complexes. The DNA
(red or orange), half-sites (gray), zincs (yellow), and subunits
of the homodimer (cyan or blue) are color-coded.
(C) Cα
overlay of Leu3 structures. The Leu3/15-mer is in blue, the
Leu3(H50C)/15-mer is in green, and the Leu3/12-mer is in red.
(D) Electron density map around the H50C loop of the
Leu3(H50C)-DNA complex is shown with a contour of one sigma in
gray. Each complex is color-coded: Leu3/15-mer (green),
Leu3(H50C)/15-mer (blue), and Leu3/12-mer (orange). Figure 2.
Overall Structure of Leu3-DNA Complexes(A) DNA sequences used
for crystallization. Half-sites recognized in the structure are
in bold. Half of each 12-mer duplex that the complex straddles
is shown, and designed half-sites are underlined.(B) Structures
of Leu3-DNA complexes. The DNA (red or orange), half-sites
(gray), zincs (yellow), and subunits of the homodimer (cyan or
blue) are color-coded.(C) Cα overlay of Leu3 structures. The
Leu3/15-mer is in blue, the Leu3(H50C)/15-mer is in green, and
the Leu3/12-mer is in red.(D) Electron density map around the
H50C loop of the Leu3(H50C)-DNA complex is shown with a contour
of one sigma in gray. Each complex is color-coded: Leu3/15-mer
(green), Leu3(H50C)/15-mer (blue), and Leu3/12-mer (orange).
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Figure 3.
Figure 3. Protein-DNA Contacts within the Leu3-DNA Complex
(A) Schematic diagram of protein-DNA contacts in the
Leu3/15-mer complex. Blue and cyan color-code the two subunits
of the dimer. DNA half-sites are colored in gray, while other
DNA bases are colored in red. Protein arrows distinguish between
base and phosphate interactions and, if a backbone atom is not
specified, a side chain is making the interaction.
Water-mediated contacts have been omitted for clarity.
(B)
Overall Leu3/15-mer complex with dark black boxes and letters in
italics to indicate the regions that will be enlarged in the
subsequent panels.
(C) Close-up of the interaction between
residues K78 and R79 of the Leu3 coiled-coil and the DNA.
Subunits of the homodimer are colored in blue and cyan. The DNA
(red), half-sites (gray), residues (yellow), and hydrogen bonds
(green) are also color-coded.
(D) Close-up of the
interaction between residues V38, Q42, and F73 of the Leu3
protein. Surface area from the van der Waals surface of the
residues is translucent and light blue.
(E) Close-up of the
interaction between residues K44/Y77 and DNA. Figure 3.
Protein-DNA Contacts within the Leu3-DNA Complex(A) Schematic
diagram of protein-DNA contacts in the Leu3/15-mer complex. Blue
and cyan color-code the two subunits of the dimer. DNA
half-sites are colored in gray, while other DNA bases are
colored in red. Protein arrows distinguish between base and
phosphate interactions and, if a backbone atom is not specified,
a side chain is making the interaction. Water-mediated contacts
have been omitted for clarity.(B) Overall Leu3/15-mer complex
with dark black boxes and letters in italics to indicate the
regions that will be enlarged in the subsequent panels.(C)
Close-up of the interaction between residues K78 and R79 of the
Leu3 coiled-coil and the DNA. Subunits of the homodimer are
colored in blue and cyan. The DNA (red), half-sites (gray),
residues (yellow), and hydrogen bonds (green) are also
color-coded.(D) Close-up of the interaction between residues
V38, Q42, and F73 of the Leu3 protein. Surface area from the van
der Waals surface of the residues is translucent and light
blue.(E) Close-up of the interaction between residues K44/Y77
and DNA.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2006,
14,
725-735)
copyright 2006.
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