Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
Sci Rep. 2021 Dec 27;11(1):24457. doi: 10.1038/s41598-021-03969-3.
Synthesis of bacterial proteins on the ribosome starts with a formylated methionine. Removal of the N-terminal formyl group is essential and is carried out by peptide deformylase (PDF). Deformylation occurs co-translationally, shortly after the nascent-chain emerges from the ribosomal exit tunnel, and is necessary to allow for further N-terminal processing. Here we describe the kinetic mechanism of deformylation by PDF of ribosome-bound nascent-chains and show that PDF binding to and dissociation from ribosomes is rapid, allowing for efficient scanning of formylated substrates in the cell. The rate-limiting step in the PDF mechanism is a conformational rearrangement of the nascent-chain that takes place after cleavage of the formyl group. Under conditions of ongoing translation, the nascent-chain is deformylated rapidly as soon as it becomes accessible to PDF. Following deformylation, the enzyme is slow in releasing the deformylated nascent-chain, thereby delaying further processing and potentially acting as an early chaperone that protects short nascent chains before they reach a length sufficient to recruit other protein biogenesis factors.
核糖体上细菌蛋白的合成始于甲硫氨酸的甲酰化。去除 N 端甲酰基是必不可少的，由肽脱甲酰基酶（PDF）完成。脱甲酰化发生在翻译共延伸过程中，新生肽链刚从核糖体出口隧道中出来不久，这对于允许进一步的 N 端加工是必要的。在这里，我们描述了 PDF 对核糖体结合的新生肽链的脱甲酰基作用的动力学机制，并表明 PDF 与核糖体的结合和解离速度很快，这使得在细胞中有效地扫描甲酰化底物成为可能。PDF 机制的限速步骤是新生肽链在甲酰基团被切割后发生的构象重排。在持续翻译的条件下，新生肽链一旦可被 PDF 作用，就会迅速被脱甲酰化。脱甲酰化后，酶缓慢释放脱甲酰化的新生肽链，从而延迟进一步的加工，并可能作为一种早期伴侣，在短新生肽链达到足以招募其他蛋白质生物发生因子的长度之前保护它们。
