Structures of LIG1 engaging with mutagenic mismatches inserted by polβ in base excision repair
Structures of LIG1 engaging with mutagenic mismatches inserted by polβ in base excision repair
复制标题
DOI：
10.1101/2022.01.14.473406
复制
发表时间：
2022-01
期刊：
影响因子：
--
通讯作者：
Melike Çağlayan;Qun Tang;R. McKenna
中科院分区：
文献类型：
--
作者：
Melike Çağlayan;Qun Tang;R. McKenna
DNA 连接酶 I (LIG1) 催化 DNA 聚合酶 (pol) β 间隙填充后的最终连接步骤，polβ 错误的核苷酸插入会在碱基切除修复 (BER) 途径的下游步骤中产生末端不匹配的切口修复中间体。然而，LIG1 如何在原子分辨率下区分诱变 3' 错配仍不清楚。在这里，我们确定了具有 G:T 和 A:C 错配的 LIG1/切口 DNA 复合物的 X 射线结构，并发现了有利于或阻止碱基替换错误连接的连接酶策略。我们的结构表明，LIG1 活性位点可以以与 A:T 碱基配对相似的构象容纳 G:T 错配，而在 3' 链上存在 A:C 错配的情况下，在连接反应的初始步骤中，它保留在 LIG1-腺苷酸中间体中。此外，我们还分别展示了 3' 预插入 dG:T 和 dA:C 错配的切口 DNA 底物的诱变连接和异常切口密封。最后，我们证明了 AP-核酸内切酶 1 (APE1) 作为一种补偿性校对酶，在错配去除和 DNA 连接过程中与 LIG1 相互作用和协调。我们的总体发现和连接酶/切口 DNA 结构提供了最终 BER 步骤中准确与诱变结果的特征，其中包括 polβ、LIG1 和 APE1 的多蛋白复合物可以保持准确的修复。
DNA ligase I (LIG1) catalyzes final ligation step following DNA polymerase (pol) β gap filling and an incorrect nucleotide insertion by polβ creates a nick repair intermediate with mismatched end at the downstream steps of base excision repair (BER) pathway. Yet, how LIG1 discriminates against the mutagenic 3′-mismatches at atomic resolution remains undefined. Here, we determined X-ray structures of LIG1/nick DNA complexes with G:T and A:C mismatches and uncovered the ligase strategies that favor or deter ligation of base substitution errors. Our structures revealed that LIG1 active site can accommodate G:T mismatch in a similar conformation with A:T base pairing, while it stays in the LIG1-adenylate intermediate during initial step of ligation reaction in the presence of A:C mismatch at 3′-strand. Moreover, we showed mutagenic ligation and aberrant nick sealing of the nick DNA substrates with 3′-preinserted dG:T and dA:C mismatches, respectively. Finally, we demonstrated that AP-Endonuclease 1 (APE1), as a compensatory proofreading enzyme, interacts and coordinates with LIG1 during mismatch removal and DNA ligation. Our overall findings and ligase/nick DNA structures provide the features of accurate versus mutagenic outcomes at the final BER steps where a multi-protein complex including polβ, LIG1, and APE1 can maintain accurate repair.