Klebsiella pneumoniae is a member of the ESKAPE panel of pathogens that are top priority to tackle AMR. Bacterial peptidyl tRNA hydrolase (Pth), an essential, ubiquitous enzyme, hydrolyzes the peptidyl-tRNAs that accumulate in the cytoplasm because of premature termination of translation. Pth cleaves the ester bond between 2′ or 3′ hydroxyl of the ribose in the tRNA and C-terminal carboxylate of the peptide, thereby making free tRNA available for repeated cycles of protein synthesis and preventing cell death by alleviating tRNA starvation. Pth structures have been determined in peptide-bound or peptide-free states. In peptide-bound state, highly conserved residues F67, N69 and N115 adopt a conformation that is conducive to their interaction with peptide moiety of the substrate. While, in peptide-free state, these residues move away from the catalytic center, perhaps, in order to facilitate release of hydrolysed peptide. Here, we present a novel X-ray crystal structure of Pth from Klebsiella pneumoniae (KpPth), at 1.89 Å resolution, in which out of the two molecules in the asymmetric unit, one reflects the peptide-bound while the other reflects peptide-free conformation of the conserved catalytic site residues. Each molecule of the protein has canonical structure with seven stranded β-sheet structure surrounded by six α-helices. MD simulations indicate that both the forms converge over 500 ns simulation to structures with wider opening of the crevice at peptide-binding end. In solution, KpPth is monomeric and its 2D-HSQC spectrum displays a single set of well dispersed peaks. Further, KpPth was demonstrated to be enzymatically active on BODIPY-Lys-tRNA^Lys3.

肺炎克雷伯菌是ESKAPE病原体研究小组的成员，是应对AMR的重中之重。细菌肽基tRNA水解酶（Pth）是一种必需的普遍存在的酶，可水解由于翻译的过早终止而积聚在细胞质中的肽基tRNA。Pth裂解tRNA中核糖的2'或3'羟基与肽的C末端羧酸酯之间的酯键，从而使游离tRNA可用于蛋白质合成的重复循环并通过减轻tRNA饥饿来防止细胞死亡。已确定Pth结构处于肽结合状态或无肽状态。在肽结合状态下，高度保守的残基F67，N69和N115具有有利于它们与底物的肽部分相互作用的构象。而在无肽状态下，这些残基可能会离开催化中心，为了促进水解肽的释放。在这里，我们提出了一种新颖的Pth的X射线晶体结构肺炎克雷伯菌（KpPth），分辨率为1.89Å，其中不对称单元的两个分子中，一个反映肽结合的，另一个反映保守催化位点残基的无肽构象。蛋白质的每个分子均具有标准结构，具有七个链状的β-折叠结构，被六个α-螺旋包围。MD模拟表明，这两种形式在500 ns模拟中都收敛到在肽结合端裂隙更宽的结构。在溶液中，KpPth是单体的，其2D-HSQC光谱显示了一组分散良好的峰。此外，已证明KpPth对BODIPY-Lys-tRNA ^Lys3具有酶促活性。