The SNM1 nucleases which help maintain genome integrity are members of the metallo-β-lactamase (MBL) structural superfamily. Their conserved MBL-β-CASP-fold SNM1 core provides a molecular scaffold forming an active site which coordinates the metal ions required for catalysis. The features that determine SNM1 endo- versus exonuclease activity, and which control substrate selectivity and binding are poorly understood. We describe a structure of SNM1B/Apollo with two nucleotides bound to its active site, resembling the product state of its exonuclease reaction. The structure enables definition of key SNM1B residues that form contacts with DNA and identifies a 5′ phosphate binding pocket, which we demonstrate is important in catalysis and which has a key role in determining endo- versus exonucleolytic activity across the SNM1 family. We probed the capacity of SNM1B to digest past sites of common endogenous DNA lesions and find that base modifications planar to the nucleobase can be accommodated due to the open architecture of the active site, but lesions axial to the plane of the nucleobase are not well tolerated due to constriction around the altered base. We propose that SNM1B/Apollo might employ its activity to help remove common oxidative lesions from telomeres.

中文翻译：

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磷酸盐结合袋是 SNM1 核酸酶家族中外切和内切核酸酶活性的关键决定因素


有助于维持基因组完整性的 SNM1 核酸酶是金属-β-内酰胺酶 (MBL) 结构超家族的成员。它们保守的 MBL-β-CASP 折叠 SNM1 核心提供了一个分子支架，形成一个活性位点，协调催化所需的金属离子。决定 SNM1 内切核酸酶与外切核酸酶活性的特征以及控制底物选择性和结合的特征尚不清楚。我们描述了 SNM1B/Apollo 的结构，其活性位点结合有两个核苷酸，类似于其核酸外切酶反应的产物状态。该结构能够定义与 DNA 形成接触的关键 SNM1B 残基，并识别 5' 磷酸结合袋，我们证明这在催化中很重要，并且在确定 SNM1 家族的核酸内切与核酸外切活性方面具有关键作用。我们探讨了 SNM1B 消化常见内源性 DNA 损伤的过去位点的能力，发现由于活性位点的开放结构，可以适应核碱基平面上的碱基修饰，但核碱基平面轴向的损伤不能很好地耐受由于改变的底座周围的收缩。我们认为 SNM1B/Apollo 可能利用其活性来帮助消除端粒中常见的氧化损伤。