Wang Qiang, Su Haibin
Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China.
Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China.
Biochemistry. 2022 Oct 18;61(20):2241-2247. doi: 10.1021/acs.biochem.2c00098. Epub 2022 Sep 30.
The peptidyl transferase center (PTC) in the large subunit of the ribosome plays a critical role in protein synthesis by catalyzing the formation of peptide bonds with an astounding speed of about 15 to 20 peptide bonds per second. The ribosome coordinates the nucleophilic attack and deprotonation in the rate-limiting step at the PTC. However, the details of peptide bond formation within the ribosome, particularly the precise role of the two water molecules in the PTC, remain unclear. Here, we propose a novel stepwise "proton shuttle" mechanism which corroborates all the reported experimental measurements so far. In this mechanism, a water molecule close to A76 of peptidyl-tRNA 2'- and 3'-O stabilizes the transition state. The other one adjacent to the carbonyl oxygen of peptidyl-tRNA actively participates in the proton shuttle, playing the catalytic role of ribosome-catalyzed peptide bond formation.
核糖体大亚基中的肽基转移酶中心（PTC）在蛋白质合成中起着关键作用，它以每秒约15至20个肽键的惊人速度催化肽键的形成。核糖体在PTC的限速步骤中协调亲核攻击和去质子化。然而，核糖体内部肽键形成的细节，特别是PTC中两个水分子的确切作用，仍不清楚。在此，我们提出了一种新颖的逐步“质子穿梭”机制，该机制证实了迄今为止所有已报道的实验测量结果。在这种机制中，靠近肽基 - tRNA 2'-和3'-O的A76的一个水分子稳定过渡态。另一个与肽基 - tRNA的羰基氧相邻的水分子积极参与质子穿梭，发挥核糖体催化肽键形成的催化作用。
