Structural diversity and oligomerization of bacterial ubiquitin-like proteins

IF 4.4 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Structure Pub Date : 2025-04-17 DOI:10.1016/j.str.2025.03.011

Minheng Gong, Qiaozhen Ye, Yajie Gu, Lydia R. Chambers, Andrey A. Bobkov, Neal K. Arakawa, Mariusz Matyszewski, Kevin D. Corbett

引用次数: 0

Abstract

Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have recently been shown to function in anti-bacteriophage immunity, but the biological functions of others remain unknown. Here, we show that ubiquitin-like proteins in two bacterial operon families show surprising architectural diversity, possessing one to three β-grasp domains preceded by diverse N-terminal domains. We find that a large group of bacterial ubiquitin-like proteins possess three β-grasp domains and form homodimers and helical filaments mediated by conserved Ca²⁺ ion binding sites. Our findings highlight a distinctive mode of self-assembly for ubiquitin-like proteins and suggest that Ca²⁺-mediated ubiquitin-like protein filament assembly and/or disassembly enables cells to sense and respond to stress conditions that alter intracellular metal ion concentration.

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细菌泛素样蛋白的结构多样性和寡聚化

细菌拥有多种与真核泛素化途径同源的操纵子，编码预测的E1、E2、E3、去泛素酶和泛素样蛋白。其中一些途径最近被证明在抗噬菌体免疫中起作用，但其他途径的生物学功能尚不清楚。在这里，我们发现两个细菌操纵子家族中的泛素样蛋白表现出惊人的结构多样性，具有1到3个β-抓握结构域，前面是不同的n端结构域。我们发现一大群细菌泛素样蛋白具有三个β-把握结构域，并形成同源二聚体和螺旋细丝，由保守的Ca2+离子结合位点介导。我们的发现强调了泛素样蛋白的一种独特的自组装模式，并表明Ca2+介导的泛素样蛋白丝组装和/或拆卸使细胞能够感知和响应改变细胞内金属离子浓度的应激条件。

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.