The structural basis of ribosome activity in peptide bond synthesis
The structural basis of ribosome activity in peptide bond synthesis
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DOI：
10.1126/science.289.5481.920
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发表时间：
2000-08-11
期刊：
影响因子：
56.9
通讯作者：
Steitz, TA
中科院分区：
文献类型：
--
作者：
Nissen, P;Hansen, J;Steitz, TA
使用原子结构的大核糖体亚基Haloarcula marismortui和它的复合物与两个底物类似物，我们建立的核糖体是一个核酶，并解决其所有的RNA活性位点的催化性能。这两种底物类似物仅与23 S rRNA结构域V的保守核糖体RNA（rRNA）残基接触;没有蛋白质侧链原子距离合成的肽键小于约18埃。肽链合成的机制似乎类似于丝氨酸蛋白酶中酰化步骤的逆转，A2486（大肠杆菌中的A2451）的碱基在胰凝乳蛋白酶中扮演着与组氨酸-57相同的一般碱基角色。A2486执行该功能所需的不寻常的pK（a）（其中K-a是酸解离常数）可能部分来自其与G2482（E.大肠杆菌），它也与一个埋藏的磷酸，可以稳定这两个碱基的不寻常的互变异构体相互作用。多肽出口通道主要由RNA形成，但蛋白质L4、L22和L39 e也有重要贡献，其出口被蛋白质L19、L22、L23、L24、L29和L31 e包围。
Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized. The mechanism of peptide band synthesis appears to resemble the reverse of the acylation step in serine proteases, with the base of A2486 (A2451 in Escherichia coti) playing the same general base role as histidine-57 in chymotrypsin. The unusual pK(a) (where K-a is the acid dissociation constant) required for A2486 to perform this function may derive in part from its hydrogen bonding to G2482 (G2447 in E. coli), which also interacts with a buried phosphate that could stabilize unusual tautomers of these two bases. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e.