Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain
Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain
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DOI：
10.1074/jbc.m115.679951
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发表时间：
2015-11-20
影响因子：
4.8
通讯作者：
Aihara, Hideki
中科院分区：
文献类型：
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作者：
Shi, Ke;Carpenter, Michael A.;Aihara, Hideki
功能和深度测序研究已经联合证明APOBEC3B参与癌症突变。APOBEC3B是一种单链DNA胞嘧啶脱氨酶，通常作为基于DNA的病原体的核定位限制因子。然而，它在癌细胞中过度表达，并在单链DNA中引发对5'-Tc基序的内在偏好，这是乳腺癌、头颈、肺、膀胱、宫颈和其他几种肿瘤类型中最常见的突变二核苷酸。在许多情况下，APOBEC3B突变占分散和聚集（kataegis）胞嘧啶突变的大部分。在这里，我们报道了APOBEC3B催化结构域多晶体形式的第一个结构。这些结构揭示了一个紧密封闭的活性位点构象，表明底物的可及性是由相邻的柔性环调节的。对催化重要的残基是通过突变分析确定的，结果提供了对目标位点选择机制的见解。我们还报道了核苷酸（dCMP）结合的晶体结构，该结构通知了结合单链DNA的多步骤模型。总的来说，这些高分辨率的晶体结构为进一步的机制研究和开发新的抗癌药物提供了框架，以抑制该酶，抑制肿瘤的进化，并最大限度地减少耐药性和转移等不良后果。
Functional and deep sequencing studies have combined to demonstrate the involvement of APOBEC3B in cancer mutagenesis. APOBEC3B is a single-stranded DNA cytosine deaminase that functions normally as a nuclear-localized restriction factor of DNA-based pathogens. However, it is overexpressed in cancer cells and elicits an intrinsic preference for 5'-Tc motifs in single-stranded DNA, which is the most frequently mutated dinucleotide in breast, head/neck, lung, bladder, cervical, and several other tumor types. In many cases, APOBEC3B mutagenesis accounts for the majority of both dispersed and clustered (kataegis) cytosine mutations. Here, we report the first structures of the APOBEC3B catalytic domain in multiple crystal forms. These structures reveal a tightly closed active site conformation and suggest that substrate accessibility is regulated by adjacent flexible loops. Residues important for catalysis are identified by mutation analyses, and the results provide insights into the mechanism of target site selection. We also report a nucleotide (dCMP)-bound crystal structure that informs a multistep model for binding single-stranded DNA. Overall, these high resolution crystal structures provide a framework for further mechanistic studies and the development of novel anti-cancer drugs to inhibit this enzyme, dampen tumor evolution, and minimize adverse outcomes such as drug resistance and metastasis.