7WW8

Crystal structure of MutT-8-oxo-dGTP complex: Reaction for 5 hr in 5 mM Mn2+

7WW8 の概要

• エントリーDOI: 10.2210/pdb7ww8/pdb
• 関連するBIRD辞書のPRD_ID: PRD_900003
• 分子名称: 7,8-dihydro-8-oxoguanine-triphosphatase, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, SULFATE ION, ... (7 entities in total)
• 機能のキーワード: nudix hydrolase, hydrolase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 16094.37

構造登録者

Nakamura, T.,Yamagata, Y. (登録日: 2022-02-12, 公開日: 2022-06-01, 最終更新日: 2023-11-29)

主引用文献

Nakamura, T.,Yamagata, Y.
Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase.
Proc.Natl.Acad.Sci.USA, 119:e2203118119-e2203118119, 2022

PubMed Abstract: Escherichia coli MutT prevents mutations by hydrolyzing mutagenic 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP) in the presence of Mg2+ or Mn2+ ions. MutT is one of the most studied enzymes in the nucleoside diphosphate-linked moiety X (Nudix) hydrolase superfamily, which is widely distributed in living organisms. However, the catalytic mechanisms of most Nudix hydrolases, including two- or three-metal-ion mechanisms, are still unclear because these mechanisms are proposed using the structures mimicking the reaction states, such as substrate analog complexes. Here, we visualized the hydrolytic reaction process of MutT by time-resolved X-ray crystallography using a biological substrate, 8-oxo-dGTP, and an active metal ion, Mn2+. The reaction was initiated by soaking MutT crystals in a MnCl2 solution and stopped by freezing the crystals at various time points. In total, five types of intermediate structures were refined by investigating the time course of the electron densities in the active site as well as the anomalous signal intensities of Mn2+ ions. The structures and electron densities show that three Mn2+ ions bind to the Nudix motif of MutT and align the substrate 8-oxo-dGTP for catalysis. Accompanied by the coordination of the three Mn2+ ions, a water molecule, bound to a catalytic base, forms a binuclear Mn2+ center for nucleophilic substitution at the β-phosphorus of 8-oxo-dGTP. The reaction condition using Mg2+ also captured a structure in complex with three Mg2+ ions. This study provides the structural details essential for understanding the three-metal-ion mechanism of Nudix hydrolases and proposes that some of the Nudix hydrolases share this mechanism.

PubMed: 35594391
DOI: 10.1073/pnas.2203118119

実験手法

X-RAY DIFFRACTION (1.64 Å)