Mitochondrial genome maintenance exonuclease 1 (MGME1) helps to ensure mitochondrial DNA (mtDNA) integrity by serving as an ancillary 5′-exonuclease for DNA polymerase γ. Curiously, MGME1 exhibits unique bidirectionality in vitro, being capable of degrading DNA from either the 5′ or 3′ end. The structural basis of this bidirectionally and, particularly, how it processes DNA from the 5′ end to assist in mtDNA maintenance remain unclear. Here, we present a crystal structure of human MGME1 in complex with a 5′-overhang DNA, revealing that MGME1 functions as a rigid DNA clamp equipped with a single-strand (ss)-selective arch, allowing it to slide on single-stranded DNA in either the 5′-to-3′ or 3′-to-5′ direction. Using a nuclease activity assay, we have dissected the structural basis of MGME1-derived DNA cleavage patterns in which the arch serves as a ruler to determine the cleavage site. We also reveal that MGME1 displays partial DNA-unwinding ability that helps it to better resolve 5′-DNA flaps, providing insights into MGME1-mediated 5′-end processing of nascent mtDNA. Our study builds on previously solved MGME1–DNA complex structures, finally providing the comprehensive functional mechanism of this bidirectional, ss-specific exonuclease.

中文翻译：

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MGME1 如何处理 DNA 5' 末端以维持线粒体基因组完整性的结构基础

线粒体基因组维护核酸外切酶 1 (MGME1) 作为 DNA 聚合酶 γ 的辅助 5'-核酸外切酶，有助于确保线粒体 DNA (mtDNA) 的完整性。奇怪的是，MGME1 在体外表现出独特的双向性，能够从 5' 或 3' 端降解 DNA。这种双向的结构基础，特别是它如何从 5' 端加工 DNA 以协助 mtDNA 维护，目前仍不清楚。在这里，我们展示了人类 MGME1 与 5' 突出 DNA 复合物的晶体结构，揭示了 MGME1 作为配备有单链 (ss) 选择性拱的刚性 DNA 夹发挥作用，使其能够在单链上滑动DNA 为 5' 至 3' 或 3' 至 5' 方向。使用核酸酶活性测定，我们剖析了 MGME1 衍生的 DNA 切割模式的结构基础，其中拱形作为标尺来确定切割位点。我们还发现 MGME1 显示出部分 DNA 解旋能力，有助于其更好地解析 5'-DNA 瓣，从而深入了解 MGME1 介导的新生 mtDNA 5' 端加工。我们的研究建立在先前解决的 MGME1-DNA 复合物结构的基础上，最终提供了这种双向、ss 特异性核酸外切酶的综合功能机制。