Journal Article PUBDB-2015-00218

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Structural basis of the methylation specificity of R.DpnI

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2014
Oxford Univ. Press Oxford

Nucleic acids research 42(13), 8745 - 8754 () [10.1093/nar/gku546]
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Abstract: R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winged helix domains and identify the catalytic domain residues that are involved in interactions with the substrate methyl groups. We show that these methyl groups in the Gm6ATC target sequence are positioned very close to each other. We further show that the presence of the two methyl groups requires a deviation from B-DNA conformation to avoid steric conflict. The methylation compatible DNA conformation is complementary with binding sites of both R.DpnI domains. This indirect readout of methylation adds to the specificity mediated by direct favorable interactions with the methyl groups and solvation/desolvation effects. We also present hydrogen/deuterium exchange data that support ‘crosstalk’ between the two domains in the identification of methylated DNA, which should further enhance R.DpnI methylation specificity.

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Contributing Institute(s):
  1. DOOR-User (DOOR)
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  1. PETRA Beamline P14 (POF2-54G14) (POF2-54G14)
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  1. PETRA Beamline P14 (PETRA III)

Appears in the scientific report 2014
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 Record created 2015-01-12, last modified 2025-07-30


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