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Title
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Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition.
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Authors
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S.Datta,
N.Ganesh,
N.R.Chandra,
K.Muniyappa,
M.Vijayan.
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Ref.
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Proteins, 2003,
50,
474-485.
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PubMed id
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Abstract
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RecA protein plays a crucial role in homologous recombination and repair of DNA.
Central to all activities of RecA is its binding to Mg(+2)-ATP. The active form
of the protein is a helical nucleoprotein filament containing the nucleotide
cofactor and single-stranded DNA. The stability and structure of the helical
nucleoprotein filament formed by RecA are modulated by nucleotide cofactors.
Here we report crystal structures of a MtRecA-ADP complex, complexes with
ATPgammaS in the presence and absence of magnesium as well as a complex with
dATP and Mg+2. Comparison with the recently solved crystal structures of the apo
form as well as a complex with ADP-AlF4 confirms an expansion of the P-loop
region in MtRecA, compared to its homologue in Escherichia coli, correlating
with the reduced affinity of MtRecA for ATP. The ligand bound structures reveal
subtle variations in nucleotide conformations among different nucleotides that
serve in maintaining the network of interactions crucial for nucleotide binding.
The nucleotide binding site itself, however, remains relatively unchanged. The
analysis also reveals that ATPgammaS rather than ADP-AlF4 is structurally a
better mimic of ATP. From among the complexed structures, a definition for the
two DNA-binding loops L1 and L2 has clearly emerged for the first time and
provides a basis to understand DNA binding by RecA. The structural information
obtained from these complexes correlates well with the extensive biochemical
data on mutants available in the literature, contributing to an understanding of
the role of individual residues in the nucleotide binding pocket, at the
molecular level. Modeling studies on the mutants again point to the relative
rigidity of the nucleotide binding site. Comparison with other NTP binding
proteins reveals many commonalties in modes of binding by diverse members in the
structural family, contributing to our understanding of the structural signature
of NTP recognition.
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