A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing
A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing
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DOI：
10.1038/nature06683
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发表时间：
2008-03-06
期刊：
影响因子：
64.8
通讯作者：
Ban, Nenad
中科院分区：
文献类型：
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作者：
Bingel-Erlenmeyer, Rouven;Kohler, Rebecca;Ban, Nenad
信使RNA导向的蛋白质合成是由核糖体完成的（1-3）。在真细菌中，这个复杂的过程是由一种携带甲酰蛋氨酸（tRNA(fMet)）的特殊转移RNA启动的（4-6）。所有细菌新生多肽的氨基末端甲酰化蛋氨酸阻断活性氨基以防止不利的副反应并提高翻译起始的效率（7,8）。处理新生链的第一个酶因子是肽去甲酰基酶（PDF）（5,9-11）；当多肽从核糖体通道（12,13）中出现时，在新合成的蛋白质采用其天然折叠之前，它会去除这个甲酰基，这可能会掩埋N端。接下来，n端蛋氨酸被蛋氨酸氨基肽酶切除（14）。细菌pdf是金属蛋白酶共享一个保守的N端催化结构域。所有革兰氏阴性菌，包括大肠杆菌，都具有以羧基末端α -螺旋延伸为特征的- 1类pdf（15）。关注PDF作为抗菌药物靶点的研究（14,16）并没有揭示其协同翻译作用模式的机制，尽管早期的研究表明它与核糖体共同纯化（17）。在这里，我们提供了生化证据，证明大肠杆菌PDF通过其C端延伸直接与核糖体相互作用。在3.7埃分辨率下对PDF核糖体相互作用螺旋和核糖体之间复合物的晶体学分析表明，该酶将其活性位点定位于核糖体隧道出口，以有效地处理新生链。此外，我们发现PDF与核糖体的相互作用增强了细胞活力。这些结果为理解蛋白质合成和新生链酶处理之间的耦合提供了结构基础，并为PDF与核糖体相关伴侣触发因子的相互作用提供了见解。
Messenger- RNA- directed protein synthesis is accomplished by the ribosome(1-3). In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine ( tRNA(fMet))(4-6). The amino- terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side- reactions and to enhance the efficiency of translation initiation(7,8). The first enzymatic factor that processes nascent chains is peptide deformylase ( PDF)(5,9-11); it removes this formyl group as polypeptides emerge from the ribosomal tunnel(12,13) and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase(14). Bacterial PDFs are metalloproteases sharing a conserved N- terminal catalytic domain. All Gram- negative bacteria, including Escherichia coli, possess class- 1 PDFs characterized by a carboxy- terminal alpha- helical extension(15). Studies focusing on PDF as a target for antibacterial drugs(14,16) have not revealed the mechanism of its co- translational mode of action despite indications in early work that it co- purifies with ribosomes(17). Here we provide biochemical evidence that E. coli PDF interacts directly with the ribosome via its C- terminal extension. Crystallographic analysis of the complex between the ribosome- interacting helix of PDF and the ribosome at 3.7 angstrom resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co- translational processing of emerging nascent chains. Furthermore, we have found that the interaction of PDF with the ribosome enhances cell viability. These results provide the structural basis for understanding the coupling between protein synthesis and enzymatic processing of nascent chains, and offer insights into the interplay of PDF with the ribosome- associated chaperone trigger factor.