Department of Microbiology and Virology, Kerman University of Medical Sciences, Kerman, Iran.
Research Center for Tropical and Infectious Diseases Kerman University of Medical Sciences, Kerman, Iran.
Iran Biomed J. 2021 May 1;25(3):193-201. doi: 10.29252/ibj.25.3.157.
There is limited information on the three-dimensional (3D) prediction and modeling of the colistin resistance-associated proteins PmrA/B TCS in Acinetobacter baumannii. We aimed to evaluate the stereochemical structure and domain characterization of phosphotransferase membrane receptor A/B (PmrA/B) in an A. baumannii isolate resistant to high-level colistin, using bioinformatics tools.
The species of the isolate and its susceptibility to colistin were confirmed by PCR-sequencing and minimum inhibitory concentration assay, respectively. For 3D prediction of the PmrA/B, we used 16 template models with the highest quality (e-value <1 × 10−50).
Prediction of the PmrA structure revealed a monomeric non-redundant protein consisting of 28 α-helices and 22 β-sheets. The PmrA DNA-binding motif displayed three antiparallel α-helices, followed by three β-sheets, and was bond to the major groove of DNA by intermolecular van der Waals bonds through amino acids Lys, Asp, His, and Arg, respectively. Superimposition of the deduced PmrA 3D structure with the closely related PmrA protein model (GenBank no. WP_071210493.1) revealed no distortion in conformation, due to Glu→Lys substitution at position 218. Similarly, the PmrB protein structure displayed 24 α-helices and 13 β-sheets. In our case, His251 acted as a phosphate receptor in the HisKA domain. The amino acid substitutions were mainly observed at the putative N-terminus region of the protein. Furthermore, two substitutions (Lys21→Ser and Ser28→Arg) in the transmembrane domain were detected.
The DNA-binding motif of PmrA is highly conserved, though the N-terminal fragment of PmrB showed a high rate of base substitutions. This research provides valuable insights into the mechanism of colistin resistance in A. baumannii.
目前关于鲍曼不动杆菌中多粘菌素耐药相关蛋白 PmrA/B TCS 的三维（3D）预测和建模的信息有限。我们旨在使用生物信息学工具评估对高水平多粘菌素耐药的鲍曼不动杆菌分离株中磷酸转移酶膜受体 A/B（PmrA/B）的立体化学结构和结构域特征。
通过 PCR 测序和最小抑菌浓度测定分别确认分离株的物种及其对多粘菌素的敏感性。对于 PmrA/B 的 3D 预测，我们使用了 16 个质量最高（e 值 <1 × 10−50）的模板模型。
PmrA 结构的预测揭示了一种由 28 个α-螺旋和 22 个β-折叠组成的单体非冗余蛋白。PmrA DNA 结合基序显示出三个反平行的α-螺旋，其后是三个β-折叠，并通过赖氨酸、天冬氨酸、组氨酸和精氨酸分别的氨基酸之间的分子间范德华键与 DNA 的大沟结合。推导出的 PmrA 3D 结构与密切相关的 PmrA 蛋白模型（GenBank 编号 WP_071210493.1）的叠加没有由于位置 218 的Glu→Lys 取代而导致构象变形。同样，PmrB 蛋白结构显示 24 个α-螺旋和 13 个β-折叠。在我们的案例中，His251 在 HisKA 结构域中充当磷酸受体。氨基酸取代主要观察到在蛋白质的假定 N 端区域。此外，在跨膜结构域中检测到两个取代（Lys21→Ser 和 Ser28→Arg）。
PmrA 的 DNA 结合基序高度保守，尽管 PmrB 的 N 端片段显示出高碱基取代率。这项研究为鲍曼不动杆菌中多粘菌素耐药机制提供了有价值的见解。
