Role of Mg2+ Ions in DNA Hydrolysis by EcoRV, Studied by the 3D-Reference Interaction Site Model and Molecular Dynamics

Itaru Onishi, Shunya Sunaba, Norio Yoshida, Fumio Hirata, Masayuki Irisa

研究成果: ジャーナルへの寄稿学術誌査読

4 被引用数 (Scopus)

抄録

The role of Mg2+ ions during precursor formation in DNA hydrolysis by the homodimeric restriction enzyme EcoRV was elucidated based on the 3D-reference interaction site model (RISM) theory and the molecular dynamics (MD) simulation. From an analysis of the spatial distribution of Mg2+ in an active site using 3D-RISM, we identified a new position for Mg2+ in the X-ray EcoRV-DNA complex structure (1rvb). We refer to the position as site IV. Site IV is almost at the same position as that of a Ca2+ ion in the superimposed X-ray crystallographic active-site structure of the PvuII-DNA complex (1f0o). 3D-RISM was also used to locate the position of water molecules, including the water nucleophile at the active site. MD simulations were carried out with the initial structure having two Mg2+ ions at site IV and at site I∗, experimentally identified by Horton et al., to find a stable complex structure in which the DNA fragment was rearranged to orient the scissile bond direction toward the water nucleophile. The equilibrium active-site structure of the EcoRV-DNA complex obtained from the MD simulation was similar to the superimposed X-ray crystallographic structure of the BamHI-DNA complex (2bam). In the active-site structure, two metal ions have almost the same position (≤1.0 Å) as that of 2bam, and the scissile phosphate is twisted to orient the scissile bond toward the water nucleophile, as is the case in 2bam. We propose the equilibrium active-site structure obtained in this study as a precursor for the hydrolysis reaction of EcoRV.

本文言語英語
ページ(範囲)9061-9075
ページ数15
ジャーナルJournal of Physical Chemistry B
122
39
DOI
出版ステータス出版済み - 10月 4 2018

!!!All Science Journal Classification (ASJC) codes

  • 物理化学および理論化学
  • 表面、皮膜および薄膜
  • 材料化学

フィンガープリント

「Role of Mg2+ Ions in DNA Hydrolysis by EcoRV, Studied by the 3D-Reference Interaction Site Model and Molecular Dynamics」の研究トピックを掘り下げます。これらがまとまってユニークなフィンガープリントを構成します。

引用スタイル