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结构可塑性与酶作用:结核分枝杆菌肽基-tRNA水解酶的晶体结构

Structural plasticity and enzyme action: crystal structures of mycobacterium tuberculosis peptidyl-tRNA hydrolase.

作者信息

Selvaraj M, Roy Siddhartha, Singh N S, Sangeetha R, Varshney Umesh, Vijayan M

机构信息

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

出版信息

J Mol Biol. 2007 Sep 7;372(1):186-93. doi: 10.1016/j.jmb.2007.06.053. Epub 2007 Jun 27.

Abstract

Peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis. The structure of the enzyme from Mycobacterium tuberculosis has been determined in three crystal forms. This structure and the structure of the enzyme from Escherichia coli in its crystal differ substantially on account of the binding of the C terminus of the E. coli enzyme to the peptide-binding site of a neighboring molecule in the crystal. A detailed examination of this difference led to an elucidation of the plasticity of the binding site of the enzyme. The peptide-binding site of the enzyme is a cleft between the body of the molecule and a polypeptide stretch involving a loop and a helix. This stretch is in the open conformation when the enzyme is in the free state as in the crystals of M. tuberculosis peptidyl-tRNA hydrolase. Furthermore, there is no physical continuity between the tRNA and the peptide-binding sites. The molecule in the E. coli crystal mimics the peptide-bound enzyme molecule. The peptide stretch referred to earlier now closes on the bound peptide. Concurrently, a channel connecting the tRNA and the peptide-binding site opens primarily through the concerted movement of two residues. Thus, the crystal structure of M. tuberculosis peptidyl-tRNA hydrolase when compared with the crystal structure of the E. coli enzyme, leads to a model of structural changes associated with enzyme action on the basis of the plasticity of the molecule.

摘要

肽基 - tRNA水解酶切割肽基 - tRNA中tRNA与连接的肽之间的酯键,以避免其积累产生的毒性,并释放tRNA以便在蛋白质合成中进行进一步循环。结核分枝杆菌中该酶的结构已通过三种晶体形式确定。由于大肠杆菌酶的C末端与晶体中相邻分子的肽结合位点结合,该结构与大肠杆菌中该酶的晶体结构有很大不同。对这种差异的详细研究导致了对该酶结合位点可塑性的阐明。该酶的肽结合位点是分子主体与涉及一个环和一个螺旋的多肽片段之间的裂隙。当酶处于游离状态时,如在结核分枝杆菌肽基 - tRNA水解酶的晶体中,该片段处于开放构象。此外,tRNA和肽结合位点之间没有物理连续性。大肠杆菌晶体中的分子模拟了肽结合的酶分子。前面提到的多肽片段现在围绕结合的肽闭合。同时,连接tRNA和肽结合位点的通道主要通过两个残基的协同运动打开。因此,与大肠杆菌酶的晶体结构相比,结核分枝杆菌肽基 - tRNA水解酶的晶体结构基于分子的可塑性,得出了与酶作用相关的结构变化模型。

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