Dadireddy Venkatareddy, Kumar Amrendra, Kumar Sumith, Sarma Siddhartha P, Mahanta Pranjal, Ramakumar Suryanarayanarao, Desirazu Rao N
Department of Physics, Indian Institute of Science, Bangalore, India.
Department of Biochemistry, Indian Institute of Science, Bangalore, India.
J Biol Chem. 2025 Jun 10;301(7):110356. doi: 10.1016/j.jbc.2025.110356.
Helicobacter pylori (H. pylori), a gastric pathogen with high genetic variability and a unique niche, causes peptic ulcers and gastric cancer. Natural transformation contributes to the genetic variability of H. pylori. To date, protein acetylation and the associated acetyltransferase(s) have not been reported in this bacterium. Here, we report protein acetylation in H. pylori and identify a putative protein acetyltransferase, HP0935, capable of acetylating amino acids and proteins, including DNA processing protein A (DprA), which is involved in natural transformation. HP0935 acetylates residue K133 in DprA, which is important for DNA binding, thus is likely to regulate natural transformation. We determined the crystal structures of HP0935 in its apo form and in complex with acetyl-coenzyme A (ACO) to 2.00 Å and 2.40 Å resolution, respectively. Structural analysis revealed a conformational change in the substrate-binding loops, α1-α2 and β6-β7, upon ACO binding. The structural comparison showed that HP0935 differs from other protein acetyltransferases in the length and orientation of these loops. Molecular dynamics simulation data suggest that these loops are highly dynamic, and ACO binding could affect their dynamics. Given that several proteins may undergo acetylation in H. pylori and the fact that HP0935 is the only known protein acetyltransferase, the loop dynamics are likely to facilitate the acceptance of multiple substrates by HP0935. Structure-based mutational analysis showed that no general base is required for the enzymatic activity. However, a conserved catalytic water molecule at the active site is likely to serve the purpose. Furthermore, the general acid Y127 is essential for enzymatic activity.
幽门螺杆菌（H. pylori）是一种具有高度遗传变异性且生存环境独特的胃部病原体，可引发消化性溃疡和胃癌。自然转化有助于幽门螺杆菌的遗传变异。迄今为止，尚未有关于该细菌中蛋白质乙酰化及相关乙酰转移酶的报道。在此，我们报道了幽门螺杆菌中的蛋白质乙酰化现象，并鉴定出一种推定的蛋白质乙酰转移酶HP0935，它能够使氨基酸和蛋白质乙酰化，包括参与自然转化的DNA加工蛋白A（DprA）。HP0935使DprA中的K133残基乙酰化，该残基对DNA结合很重要，因此可能调控自然转化。我们分别以2.00 Å和2.40 Å的分辨率测定了HP0935的无配体形式及其与乙酰辅酶A（ACO）复合物的晶体结构。结构分析显示，ACO结合后，底物结合环α1-α2和β6-β7发生了构象变化。结构比较表明，HP0935在这些环的长度和方向上与其他蛋白质乙酰转移酶不同。分子动力学模拟数据表明，这些环具有高度动态性，ACO结合可能会影响它们的动态性。鉴于幽门螺杆菌中可能有多种蛋白质会发生乙酰化，且HP0935是唯一已知的蛋白质乙酰转移酶，环的动态性可能有助于HP0935接受多种底物。基于结构的突变分析表明，酶活性不需要通用碱基。然而，活性位点处一个保守的催化水分子可能起到这个作用。此外，通用酸Y127对酶活性至关重要。
