Structural and functional characterization of archaeal DIMT1 unveils distinct protein dynamics essential for efficient catalysis

IF 4.4 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Structure Pub Date : 2024-08-14 DOI:10.1016/j.str.2024.07.013

引用次数: 0

Abstract

Dimethyladenosine transferase 1 (DIMT1), an ortholog of bacterial KsgA is a conserved protein that assists in ribosome biogenesis by modifying two successive adenosine bases near the 3′ end of small subunit (SSU) rRNA. Although KsgA/DIMT1 proteins have been characterized in bacteria and eukaryotes, they are yet unexplored in archaea. Also, their dynamics are not well understood. Here, we structurally and functionally characterized the apo and holo forms of archaeal DIMT1 from Pyrococcus horikoshii. Wild-type protein and mutants were analyzed to capture different transition states, including open, closed, and intermediate states. This study reports a unique inter-domain movement that is needed for substrate (RNA) positioning in the catalytic pocket, and is only observed in the presence of the cognate cofactors S-adenosyl-L-methionine (SAM) or S-adenosyl-L-homocysteine (SAH). The binding of the inhibitor sinefungine, an analog of SAM or SAH, to archaeal DIMT1 blocks the catalytic pocket and renders the enzyme inactive.

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古菌 DIMT1 的结构和功能特征揭示了高效催化所必需的独特蛋白质动力学特性

二甲基腺苷转移酶 1（DIMT1）是细菌 KsgA 的同源物，它是一种保守蛋白，通过修饰小亚基（SSU）rRNA 3′末端附近的两个连续腺苷碱基来协助核糖体的生物发生。虽然 KsgA/DIMT1 蛋白在细菌和真核生物中已被定性，但在古细菌中尚未被研究。此外，它们的动态变化也不甚了解。在这里，我们从结构和功能上鉴定了来自角越火球菌的古生 DIMT1 的 apo 和 holo 形式。我们分析了野生型蛋白质和突变体，以捕捉不同的过渡状态，包括开放、封闭和中间状态。本研究报告了底物（RNA）在催化袋中定位所需的一种独特的结构域间运动，这种运动只有在存在同源辅助因子 S-腺苷-L-蛋氨酸（SAM）或 S-腺苷-L-高半胱氨酸（SAH）时才能观察到。SAM 或 SAH 的类似物抑制剂正鱼藤碱（sinefungine）与古蘑菇 DIMT1 结合后会阻塞催化袋，使酶失去活性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Structure 生物-生化与分子生物学

CiteScore

8.90

自引率

1.80%

发文量

155

审稿时长

3-8 weeks

期刊介绍： Structure aims to publish papers of exceptional interest in the field of structural biology. The journal strives to be essential reading for structural biologists, as well as biologists and biochemists that are interested in macromolecular structure and function. Structure strongly encourages the submission of manuscripts that present structural and molecular insights into biological function and mechanism. Other reports that address fundamental questions in structural biology, such as structure-based examinations of protein evolution, folding, and/or design, will also be considered. We will consider the application of any method, experimental or computational, at high or low resolution, to conduct structural investigations, as long as the method is appropriate for the biological, functional, and mechanistic question(s) being addressed. Likewise, reports describing single-molecule analysis of biological mechanisms are welcome. In general, the editors encourage submission of experimental structural studies that are enriched by an analysis of structure-activity relationships and will not consider studies that solely report structural information unless the structure or analysis is of exceptional and broad interest. Studies reporting only homology models, de novo models, or molecular dynamics simulations are also discouraged unless the models are informed by or validated by novel experimental data; rationalization of a large body of existing experimental evidence and making testable predictions based on a model or simulation is often not considered sufficient.