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PDBsum entry 6n2s
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Gene regulation/DNA
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PDB id
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6n2s
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References listed in PDB file
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Key reference
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Title
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Molecular basis for the faithful replication of 5-Methylcytosine and its oxidized forms by DNA polymerase β.
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Authors
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M.J.Howard,
K.G.Foley,
D.D.Shock,
V.K.Batra,
S.H.Wilson.
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Ref.
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J Biol Chem, 2019,
294,
7194-7201.
[DOI no: ]
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PubMed id
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Abstract
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DNA methylation is an epigenetic mark that regulates gene expression in mammals.
One method of methylation removal is through ten-eleven translocation-catalyzed
oxidation and the base excision repair pathway. The iterative oxidation of
5-methylcytosine catalyzed by ten-eleven translocation enzymes produces three
oxidized forms of cytosine: 5-hydroxmethylcytosine, 5-formylcytosine, and
5-carboxycytosine. The effect these modifications have on the efficiency and
fidelity of the base excision repair pathway during the repair of opposing base
damage, and in particular DNA polymerization, remains to be elucidated. Using
kinetic assays, we show that the catalytic efficiency for the incorporation of
dGTP catalyzed by human DNA polymerase β is not affected when 5-methylcytosine,
5-hydroxmethylcytosine, and 5-formylcytosine are in the DNA template. In
contrast, the catalytic efficiency of dGTP insertion decreases ∼20-fold when
5-carboxycytosine is in the templating position, as compared with unmodified
cytosine. However, DNA polymerase fidelity is unaltered when these modifications
are in the templating position. Structural analysis reveals that the methyl,
hydroxymethyl, and formyl modifications are easily accommodated within the
polymerase active site. However, to accommodate the carboxyl modification, the
phosphate backbone on the templating nucleotide shifts ∼2.5 Å to avoid a
potential steric/repulsive clash. This altered conformation is stabilized by
lysine 280, which makes a direct interaction with the carboxyl modification and
the phosphate backbone of the templating strand. This work provides the
molecular basis for the accommodation of epigenetic base modifications in a
polymerase active site and suggests that these modifications are not
mutagenically copied during base excision repair.
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