Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA
Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA
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胞苷脱氨酶人 APOBEC3F 嵌合催化结构域与 DNA 复合物的晶体结构
DOI：
10.1002/cjoc.201800508
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发表时间：
2018-12-01
影响因子：
5.4
通讯作者：
Cao, Chunyang
中科院分区：
文献类型：
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作者：
Cheng, Chao;Zhang, Tianlong;Cao, Chunyang
APOBEC 3F（A3 F）通过其A3 F-CD 2结构域在逆转录过程中催化病毒cDNA中靶基序5 '-TC中的胞苷脱氨基而显示出抗病毒活性。但结构基础尚不明确。以前，嵌合A3 F-CD 2（即，A3 Fc-CD 2，其中A3 F-CD 2的残基195-217被A3 G-CD 2的残基197-221替换）被发现可溶，具有脱氨基活性。在这里，我们报告了A3 Fc-CD 2与单链DNA复合物（5 '-ATTTT（5）C（6）A（7）A（8）T（9）T-3'和5 '-ATTTT（5）C（6）A（7）A（8）C（9）T-3'）的晶体结构，分辨率分别为1.98埃和2.30埃。他们证明，一个分子DNA在两个位点结合两个A3 Fc-CD 2分子（单体A和B），这与报道的人A3 F-CD 2与10-dT DNA的复合物结构不同。第一个位点由单体A中远离Zn ~（2+）结合基序的Tyr（333）、Lys（358）和Tyr（359）残基通过π-π堆积和氢键与碱基dT（5）、dC（6）和dA（7）相互作用形成。第二个位点由Trp（277）、Y307、YFW 310组成，位于单体B的Zn ~（2+）结合区附近，主要通过π-π堆积和疏水作用与碱基dA（8）相互作用，决定DNA序列的脱氨偏好性。随后的生物化学研究进一步证实了这些残基对DNA结合和脱氨活性的贡献。这些研究有助于理解A3 F-CD 2催化胞苷脱氨的机制。
APOBEC3F (A3F) demonstrates antivirus activity through its A3F-CD2 domain catalyzing deamination of cytidine in target motif 5'-TC in viral cDNA during reverse transcription. But structural basis is unclear. Previously, chimeric A3F-CD2 (i.e., A3Fc-CD2, where residues 195-217 of A3F-CD2 were replaced with residues 197-221 of A3G-CD2) was found soluble with deamination activity. Here, we report crystal structures of A3Fc-CD2 in complexes with single-stranded DNA (5'-ATTTT(5)C(6)A(7)A(8)T(9)T-3' and 5'-ATTTT(5)C(6)A(7)A(8)C(9)T-3') at resolutions of 1.98 angstrom and 2.30 angstrom, respectively. They demonstrate that one molecular DNA binds two A3Fc-CD2 molecules (monomers A and B) at two sites, distinct from the reported complex structure of human A3F-CD2 with a 10-dT DNA. The first site is formed by residues Tyr(333), Lys(358) and Tyr(359) in monomer A, far away from Zn2+ binding motif, interacting with bases dT(5), dC(6) and dA(7) through pi-pi stacking and hydrogen bonds. The second site is composed of Trp(277), Y307YFW310 near to Zn2+ binding region in monomer B, interacting with base dA(8), mainly through pi-pi stacking and hydrophobic interactions, determining deamination preference of DNA sequence. Subsequent biochemical investigations further confirm the contribution of these residues to DNA binding and deamination activities. These studies are helpful to understand the mechanism how A3F-CD2 catalyzes cytidine deamination.