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PDBsum entry 6ph6
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Transcription/DNA
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PDB id
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6ph6
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References listed in PDB file
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Key reference
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Title
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Dna polymerase β nucleotide-Stabilized template misalignment fidelity depends on local sequence context.
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Authors
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M.J.Howard,
N.A.Cavanaugh,
V.K.Batra,
D.D.Shock,
W.A.Beard,
S.H.Wilson.
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Ref.
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J Biol Chem, 2020,
295,
529-538.
[DOI no: ]
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PubMed id
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Abstract
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DNA polymerase β has two DNA-binding domains that interact with the opposite
sides of short DNA gaps. These domains contribute two activities that modify the
5' and 3' margins of gapped DNA during base excision repair. DNA gaps greater
than 1 nucleotide (nt) pose an architectural and logistical problem for the two
domains to interact with their respective DNA termini. Here, crystallographic
and kinetic analyses of 2-nt gap-filling DNA synthesis revealed that the
fidelity of DNA synthesis depends on local sequence context. This was due to
template dynamics that altered which of the two template nucleotides in the gap
served as the coding nucleotide. We observed that, when a purine nucleotide was
in the first coding position, DNA synthesis fidelity was similar to that
observed with a 1-nt gap. However, when the initial templating nucleotide was a
pyrimidine, fidelity was decreased. If the first templating nucleotide was a
cytidine, there was a significantly higher probability that the downstream
template nucleotide coded for the incoming nucleotide. This dNTP-stabilized
misalignment reduced base substitution and frameshift deletion fidelities. A
crystal structure of a binary DNA product complex revealed that the cytidine in
the first templating site was in an extrahelical position, permitting the
downstream template nucleotide to occupy the coding position. These results
indicate that DNA polymerase β can induce a strain in the DNA that modulates
the position of the coding nucleotide and thereby impacts the identity of the
incoming nucleotide. Our findings demonstrate that "correct" DNA
synthesis can result in errors when template dynamics induce coding ambiguity.
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