Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD:: archaeon specificity and catalytic mechanism of adenylate formation
Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD:: archaeon specificity and catalytic mechanism of adenylate formation
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DOI：
10.1093/emboj/17.17.5227
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发表时间：
1998-09-01
期刊：
影响因子：
11.4
通讯作者：
Moras, D
中科院分区：
文献类型：
--
作者：
Schmitt, E;Moulinier, L;Moras, D
对kodakaraensis焦球菌（Pyrococcus kodakaraensis）的天冬氨酸-tRNA合成酶（AspRS）晶体结构在1.9埃分辨率下进行了解析，其催化结构域的序列和三维结构与真核生物的AspRS高度同源，而结合tRNA反密码子的n端结构域则与真细菌酶的结构域更为相似。它的结构解释了古细菌asprs的独特特性，即同时容纳tRNA（Asp）和tRNA（Asn）。用ATP和天冬氨酸分别或一起浸泡载脂蛋白酶晶体可以使腺苷酸形成。由于二聚体酶在晶体状态下的不对称性，在同一个晶体中可以看到反应的不同步骤。从而表征了天冬氨酸活化反应的四种不同状态，揭示了所观察到的构象变化的功能相关性。氨基酸底物的结合诱导了两个不变环的运动，这两个不变环确保了肽基部分形成腺苷酸的位置。一个明确的空间和功能分配的三个镁离子辅因子可以作出。这项研究表明，残基在古细菌和真核生物的asprs中都存在，但在真核细菌的酶中不存在。
The crystal structure of aspartyl-tRNA synthetase (AspRS) from Pyrococcus kodakaraensis was solved at 1.9 Angstrom resolution, The sequence and three-dimensional structure of the catalytic domain are highly homologous to those of eukaryotic AspRSs, In contrast, the N-terminal domain, whose function is to bind the tRNA anticodon, is more similar to that of eubacterial enzymes. Its structure explains the unique property of archaeal AspRSs of accommodating both tRNA(Asp) and tRNA(Asn). Soaking the apo-enzyme crystals with ATP and aspartic acid both separately and together allows the adenylate formation to be followed. Due to the asymmetry of the dimeric enzyme in the crystalline state, different steps of the reaction could be visualized within the same crystal. Four different states of the aspartic acid activation reaction could thus be characterized, revealing the functional correlation of the observed conformational changes. The binding of the amino acid substrate induces movement of two invariant loops which secure the position of the peptidyl moiety for adenylate formation. An unambiguous spatial and functional assignment of three magnesium ion cofactors can be made. This study shows the important role of residues present in both archaeal and eukaryotic AspRSs, but absent from the eubacterial enzymes.