Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA.
J Mol Biol. 2012 Feb 17;416(2):208-20. doi: 10.1016/j.jmb.2011.12.030. Epub 2011 Dec 21.
Mycobacterium tuberculosis ArfA (Rv0899) is a membrane protein encoded by an operon that is required for supporting bacterial growth in acidic environments. Its C-terminal domain (C domain) shares significant sequence homology with the OmpA-like family of peptidoglycan-binding domains, suggesting that its physiological function in acid stress protection may be related to its interaction with the mycobacterial cell wall. Previously, we showed that ArfA forms three independently structured modules, and we reported the structure of its central domain (B domain). Here, we describe the high-resolution structure and dynamics of the C domain, we identify ArfA as a peptidoglycan-binding protein and we elucidate the molecular basis for its specific recognition of diaminopimelate-type peptidoglycan. The C domain of ArfA adopts the characteristic fold of the OmpA-like family. It exhibits pH-dependent conformational dynamics (with significant heterogeneity at neutral pH and a more ordered structure at acidic pH), which could be related to its acid stress response. The C domain associates tightly with polymeric peptidoglycan isolated from M. tuberculosis and also associates with a soluble peptide intermediate of peptidoglycan biosynthesis. This enabled us to characterize the peptidoglycan binding site where five highly conserved ArfA residues, including two key arginines, establish the specificity for diaminopimelate- but not Lys-type peptidoglycan. ArfA is the first peptidoglycan-binding protein to be identified in M. tuberculosis. Its functions in acid stress protection and peptidoglycan binding suggest a link between the acid stress response and the physicochemical properties of the mycobacterial cell wall.
结核分枝杆菌 ArfA（Rv0899）是一种膜蛋白，由一个操纵子编码，该操纵子对于在酸性环境中支持细菌生长是必需的。其 C 端结构域（C 结构域）与 OmpA 样肽聚糖结合结构域家族具有显著的序列同源性，这表明其在酸应激保护中的生理功能可能与其与分枝杆菌细胞壁的相互作用有关。以前，我们发现 ArfA 形成三个独立结构的模块，并报道了其中心结构域（B 结构域）的结构。在这里，我们描述了 C 结构域的高分辨率结构和动力学，确定了 ArfA 是一种肽聚糖结合蛋白，并阐明了其对二氨基庚二酸型肽聚糖特异性识别的分子基础。ArfA 的 C 结构域采用 OmpA 样家族的特征折叠。它表现出 pH 依赖性构象动力学（在中性 pH 时具有显著的异质性，在酸性 pH 时具有更有序的结构），这可能与其酸应激反应有关。C 结构域与从结核分枝杆菌中分离的聚合肽聚糖紧密结合，也与肽聚糖生物合成的可溶性肽中间产物结合。这使我们能够表征肽聚糖结合位点，其中五个高度保守的 ArfA 残基（包括两个关键精氨酸）建立了对二氨基庚二酸型但不是赖氨酸型肽聚糖的特异性。ArfA 是在结核分枝杆菌中鉴定的第一个肽聚糖结合蛋白。它在酸应激保护和肽聚糖结合中的功能表明酸应激反应与分枝杆菌细胞壁的物理化学性质之间存在联系。
