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PDBsum entry 1aa3
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Double-stranded DNA binding domain
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PDB id
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1aa3
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References listed in PDB file
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Key reference
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Title
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An interaction between a specified surface of the c-Terminal domain of reca protein and double-Stranded DNA for homologous pairing.
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Authors
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H.Aihara,
Y.Ito,
H.Kurumizaka,
T.Terada,
S.Yokoyama,
T.Shibata.
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Ref.
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J Mol Biol, 1997,
274,
213-221.
[DOI no: ]
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PubMed id
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Abstract
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RecA protein and its homologs catalyze homologous pairing of dsDNA and ssDNA, a
critical reaction in homologous genetic recombination in various organisms from
a virus, microbes to higher eukaryotes. In this reaction, RecA protein forms a
nucleoprotein filament on ssDNA, which in turn binds to naked dsDNA for homology
search. We suggested that the C-terminal domain of RecA protein plays a role in
capturing the dsDNA. Here, we isolated the C-terminal domain as a soluble form
and determined the solution structure by NMR spectroscopy. The overall folding
of the NMR structure agrees with that of the corresponding part of the reported
crystal structure, but a remarkable difference was found in a solvent-exposed
region due to intermolecular contacts in the crystal. Then, we studied the
interaction between the C-terminal domain and DNA, and found that significant
chemical shift changes were induced in a specific region by titration with
dsDNA. SsDNA induced a much smaller chemical shift perturbation. The difference
of DNA concentrations to give the half-saturation of the chemical shift change
showed a higher affinity of the C-terminal region toward dsDNA. Combined with
our previous results, these provide direct evidence that the defined region in
the C-terminal domain furnishes a binding surface for DNA.
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Figure 2.
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Figure 3.
Figure 3. Superposition of backbone traces of the energy
minimized average structure derived from NMR (shown in cyan) and
the X-ray structure (shown in red) around Gly 295. The
structures were superimposed to give the lowest deviations in
the C^α positions of residues 270 to 322. The largest deviation
occurs at Gly295. Side-chains which might be involved in
electrostatic interactions with the adjacent molecule (green) in
the crystal (distance between N and O atoms is less than 4
Å) are shown in white. Plausible hydrogen bonds or salt
bridges are indicated by broken lines, with distances in
angstroms. The crystal structure is that of [Story et al 1992].
This Figure was drawn using MidasPlus [Ferrin et al 1988].
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1997,
274,
213-221)
copyright 1997.
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