DNA apurinic-apyrimidinic site binding and excision by endonuclease IV
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV
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DOI：
10.1038/nsmb.1414
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发表时间：
2008-05-01
影响因子：
16.8
通讯作者：
Tainer, John A.
中科院分区：
文献类型：
--
作者：
Garcin, Elsa D.;Hosfield, David J.;Tainer, John A.
大肠杆菌核酸内切酶IV是对DNA碱基切除修复至关重要的无碱基或无嘌呤-无嘧啶核酸内切酶超家族的原型。在这里，生物化学，突变和晶体学表征揭示了三种金属离子损伤结合和切割机制。1.10埃分辨率的无DNA和2.45埃分辨率的DNA-底物复合物结构通过Arg 37捕获底物稳定，并揭示了扭曲的Zn 3-配体排列，其在催化后恢复到适合于保持而不是释放切割的DNA产物的理想几何形状。1.45埃分辨率的DNA产物复合物结构显示了Tyr 72如何覆盖活性位点，调节其介电环境，并通过Glu 261激活的氢氧化物促进催化，在整个催化过程中与两个Zn 2+离子结合。这些结构，诱变和生物化学结果表明，一般要求脱碱基位点的去除，在不同的核酸内切酶IV α-β磷酸丙糖异构酶（TIM）桶和APE 1四层α-β折叠的脱嘌呤-脱嘧啶核酸内切酶家族的特定功能相反。
Escherichia coli endonuclease IV is an archetype for an abasic or apurinic-apyrimidinic endonuclease superfamily crucial for DNA base excision repair. Here biochemical, mutational and crystallographic characterizations reveal a three-metal ion mechanism for damage binding and incision. The 1.10-angstrom resolution DNA-free and the 2.45-angstrom resolution DNA-substrate complex structures capture substrate stabilization by Arg37 and reveal a distorted Zn3-ligand arrangement that reverts, after catalysis, to an ideal geometry suitable to hold rather than release cleaved DNA product. The 1.45-angstrom resolution DNA-product complex structure shows how Tyr72 caps the active site, tunes its dielectric environment and promotes catalysis by Glu261-activated hydroxide, bound to two Zn2+ ions throughout catalysis. These structural, mutagenesis and biochemical results suggest general requirements for abasic site removal in contrast to features specific to the distinct endonuclease IV alpha-beta triose phosphate isomerase (TIM) barrel and APE1 four-layer alpha-beta folds of the apurinic-apyrimidinic endonuclease families.