6FBD

KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the second primer nucleotide.

6FBD の概要

• エントリーDOI: 10.2210/pdb6fbd/pdb
• 分子名称: DNA polymerase I, thermostable, DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*AP*(OH3)P*C)-3'), DNA (5'-D(P*AP*AP*AP*CP*GP*GP*TP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), ... (8 entities in total)
• 機能のキーワード: dna polymerase, modified nucleotides, klentaq, klentaq dna polymerase, dna binding protein
• 由来する生物種: Thermus aquaticus; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 70505.65

構造登録者

Kropp, H.M.,Diederichs, K.,Marx, A. (登録日: 2017-12-19, 公開日: 2018-09-26, 最終更新日: 2024-05-08)

主引用文献

Kropp, H.M.,Durr, S.L.,Peter, C.,Diederichs, K.,Marx, A.
Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Proc. Natl. Acad. Sci. U.S.A., 115:9992-9997, 2018

PubMed Abstract: 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.

PubMed: 30224478
DOI: 10.1073/pnas.1811518115

実験手法

X-RAY DIFFRACTION (2.099 Å)