Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.
Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.
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DOI：
10.1038/ncomms15024
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发表时间：
2017-04-28
影响因子：
16.6
通讯作者：
Schiffer CA
中科院分区：
文献类型：
--
作者：
Kouno T;Silvas TV;Hilbert BJ;Shandilya SMD;Bohn MF;Kelch BA;Royer WE;Somasundaran M;Kurt Yilmaz N;Matsuo H;Schiffer CA
核酸编辑酶是免疫系统的重要组成部分，其致命地突变病毒病原体和体细胞地突变免疫球蛋白，并且有助于癌症的多样化和致命性。在这些酶中，有7种人APOBEC 3脱氧胞苷脱氨酶，每种酶都具有独特的靶序列特异性和亚细胞定位。虽然酶学和生物学后果已被广泛研究，但APOBEC 3识别和编辑DNA的机制仍然难以捉摸。在这里，我们提出了一个复杂的胞苷脱氨酶与ssDNA结合在2.2 π活性位点的晶体结构。该结构不仅可视化了准备用于催化APOBEC 3A的活性位点，而且精确定位了赋予CC/TC基序特异性的残基。APOBEC 3A-ssDNA复合物定义了5′-3′方向性和微妙的构象变化，这些变化将ssDNA夹紧在结合沟内，揭示了ssDNA识别的结构和机制，这些结构和机制可能在所有多核苷酸脱氨酶中是保守的，从而为基于机制的治疗方法的设计打开了大门。胞苷脱氨酶是进化上保守的酶，其通过将胞苷脱氨为尿苷来编辑基因组。在本文中，作者展示了APOBEC 3A的晶体结构，其中活性位点结合了单链DNA底物，以阐明底物识别的机制和特异性。
Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A–ssDNA complex defines the 5′–3′ directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics. Cytidine deaminases are evolutionarily conserved enzymes that edit genomes by deaminating cytidine to uridine. Here the authors present the crystal structure of APOBEC3A with a single-stranded DNA substrate bound in the active site to shed light on the mechanism and specificity of substrate recognition.