Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor
Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor
复制标题
DOI：
10.1107/s0907444913027042
复制
发表时间：
2013-12-01
影响因子：
2.2
通讯作者：
Drohat, Alexander C.
中科院分区：
文献类型：
--
作者：
Manvilla, Brittney A.;Pozharski, Edwin;Drohat, Alexander C.
脱嘌呤/脱嘧啶核酸内切酶1（APE 1）介导脱碱基位点和其他DNA损伤的修复，并且对于碱基切除修复和链断裂修复途径是必需的。APE 1在脱碱基位点水解磷酸二酯键，产生5 '-脱氧核糖磷酸和修复合成所需的3'-OH引物。它还具有额外的修复活动，包括删除3 '阻断基团。APE 1是一种强大的酶，绝对需要Mg 2+，但对于APE 1和DNA酶I超家族中的其他酶，二价阳离子的化学计量和催化功能仍然没有解决。先前报道的无DNA APE 1的结构在活性位点中含有Sm 3+或Pb 2+。然而，这些是Mg 2+的不良替代物，因为Sm 3+不是辅因子，Pb 2+抑制APE 1，并且它们的配位几何形状预计与Mg 2+不同。在1.92埃分辨率下解析了人APE 1的晶体结构，其中活性位点中具有单个Mg 2+离子。结构揭示了Mg 2+通过两个羧酸基团和四个水分子的理想八面体配位。在DNA酶I超家族中，一个直接与Mg 2+配位的残基和两个与内球水分子结合的残基是严格保守的。这种结构，连同最近的酶-产物复合物的结构，告知在APE 1催化反应的化学计量和Mg 2+的作用。
Apurinic/apyrimidinic endonuclease 1 (APE1) mediates the repair of abasic sites and other DNA lesions and is essential for base-excision repair and strand-break repair pathways. APE1 hydrolyzes the phosphodiester bond at abasic sites, producing 5'-deoxyribose phosphate and the 3'-OH primer needed for repair synthesis. It also has additional repair activities, including the removal of 3'-blocking groups. APE1 is a powerful enzyme that absolutely requires Mg2+, but the stoichiometry and catalytic function of the divalent cation remain unresolved for APE1 and for other enzymes in the DNase I superfamily. Previously reported structures of DNA-free APE1 contained either Sm3+ or Pb2+ in the active site. However, these are poor surrogates for Mg2+ because Sm3+ is not a cofactor and Pb2+ inhibits APE1, and their coordination geometry is expected to differ from that of Mg2+. A crystal structure of human APE1 was solved at 1.92 angstrom resolution with a single Mg2+ ion in the active site. The structure reveals ideal octahedral coordination of Mg2+ via two carboxylate groups and four water molecules. One residue that coordinates Mg2+ directly and two that bind inner-sphere water molecules are strictly conserved in the DNase I superfamily. This structure, together with a recent structure of the enzyme-product complex, inform on the stoichiometry and the role of Mg2+ in APE1-catalyzed reactions.