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PDBsum entry 6fbh
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DNA binding protein
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PDB id
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6fbh
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References listed in PDB file
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Key reference
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Title
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Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
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Authors
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H.M.Kropp,
S.L.Dürr,
C.Peter,
K.Diederichs,
A.Marx.
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Ref.
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Proc Natl Acad Sci U S A, 2018,
115,
9992-9997.
[DOI no: ]
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PubMed id
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Abstract
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DNA polymerases have evolved to process the four canonical nucleotides
accurately. Nevertheless, these enzymes are also known to process modified
nucleotides, which is the key to numerous core biotechnology applications.
Processing of modified nucleotides includes incorporation of the modified
nucleotide and postincorporation elongation to proceed with the synthesis of the
nascent DNA strand. The structural basis for postincorporation elongation is
currently unknown. We addressed this issue and successfully crystallized KlenTaq
DNA polymerase in six closed ternary complexes containing the enzyme, the
modified DNA substrate, and the incoming nucleotide. Each structure shows a
high-resolution snapshot of the elongation of a modified primer, where the
modification "moves" from the 3'-primer terminus upstream to the sixth
nucleotide in the primer strand. Combining these data with quantum
mechanics/molecular mechanics calculations and biochemical studies elucidates
how the enzyme and the modified substrate mutually modulate their conformations
without compromising the enzyme's activity significantly. The study highlights
the plasticity of the system as origin of the broad substrate properties of DNA
polymerases and facilitates the design of improved systems.
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