Solution structure of ribosomal protein L16 from Thermus thermophilus HB8
Solution structure of ribosomal protein L16 from Thermus thermophilus HB8
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DOI：
10.1016/j.jmb.2004.10.011
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发表时间：
2004-12-10
影响因子：
5.6
通讯作者：
Kobayashi, Y
中科院分区：
文献类型：
--
作者：
Nishimura, M;Yoshida, T;Kobayashi, Y
核糖体蛋白L16是细菌核糖体的重要组成部分。它组织核糖体50 S亚基中氨酰tRNA结合位点的结构。用核磁共振法测定了嗜热栖热菌HB 8 L16的三维结构。在溶液中，L16形成与位于连接两层的环区域处的两个额外的β片层组合的α + β夹层结构。末端区域和中心环区域未显示任何特定的二级结构。L16的结构部分可以很好地叠加在核糖体50 S亚基的晶体结构中确定的L16的C-α模型上。通过将L16溶液结构叠加到核糖体晶体结构的坐标上，我们构建了在详细结构中代表L16的核糖体结合状态的组合模型。该模型表明L16具有与23 SrRNA的螺旋38、39、42、43和89以及5SrRNA的螺旋4接触的残基。这表明它对核糖体结构的广泛影响。L16与L10 e蛋白（古细菌的对应物）的比较表明，它们共享一个共同的折叠，但在某些功能重要性区域，特别是在N-末端区域，存在差异。L16中所有已知的对阿维拉霉素和依维米星产生耐药性的突变位点都被定位，使得它们的侧链暴露于核糖体内腔中的溶剂。这表明L16作为抗生素结合位点的一部分直接参与。(C)2004爱思唯尔有限公司保留所有权利。
Ribosomal protein L16 is an essential component of the bacterial ribosome. It organizes the architecture of aminoacyl tRNA binding site in the ribosome 50 S subunit. The three-dimensional structure of L16 from Thermus thermophilus HB8 was determined by NMR. In solution, L16 forms an alpha + beta sandwich structure combined with two additional beta sheets located at the loop regions connecting the two layers. The terminal regions and a central loop region did not show any specific secondary structure. The structured part of L16 could be superimposed well on the C-alpha, model of L16 determined in the crystal structure of the ribosome 50 S subunit. By overlaying the L16 solution structure onto the coordinates of the ribosome crystal structure, we constructed the combined model that represents the ribosome-bound state of L16 in the detailed structure. The model showed that L16 possesses residues in contact with helices 38, 39, 42, 43 and 89 of 23 S rRNA and helix 4 of 5 S rRNA. This suggests its broad effect on the ribosome architecture. Comparison of L16 with the L10e protein, which is the archaeal counterpart, showed that they share a common fold, but differ in some regions of functional importance, especially in the N-terminal region. All known mutation sites in L16 that confer resistance to avilamycin and evernimicin were positioned so that their side-chains were exposed to solvent in the internal cavity of the ribosome. This suggests the direct participation of L16 as a part of the binding site for antibiotics. (C) 2004 Elsevier Ltd. All rights reserved.