Substrate binding proteins (SBPs) bind to specific ligands in the periplasmic regions of cells and then bind to membrane proteins to participate in transport or signal transduction. Typically, SBPs consist of two α/β domains and recognize the substrate by a flexible hinge region between the two domains. Conversely, the short-length SBPs are often observed in protein databases, which are located around methyl-accepting chemotaxis protein genes. We previously determined the crystal structure of Rhodothermus marinus SBP (named as RmSBP), consisting of a single α/β domain; however, the substrate recognition mechanism is still unclear. To better understand the functions of short length RmSBP, we performed a comprehensive study, involving comparative structure analysis, computational substrate docking, and X-ray crystallographic data. RmSBP shares a high level of similarity in the α/β domain region with other SBPs, but it has a distinct topology in the C-terminal domain. The substrate binding model suggested that conformational changes in the peripheral region of RmSBP was required to recognize the substrate. We determined the crystal structures of RmSBP at pH 5.5, 6.0, and 7.5. RmSBP showed structural flexibility in the β1–α2 loop, β5–β6 loop, and extended C-terminal domains, based on the electron density map and temperature B-factor analysis. These results provide information that will further our understanding on the functions of the short length SBP.

底物结合蛋白 (SBP) 与细胞周质区域中的特定配体结合，然后与膜蛋白结合，参与转运或信号转导。通常，SBP 由两个 α/β 结构域组成，并通过两个结构域之间的柔性铰链区识别底物。相反，在蛋白质数据库中经常观察到短长度的 SBP，这些数据库位于接受甲基的趋化蛋白基因周围。我们之前确定了海红藻的晶体结构SBP（命名为 RmSBP），由单个 α/β 结构域组成；然而，底物识别机制仍不清楚。为了更好地理解短长度 RmSBP 的功能，我们进行了综合研究，包括比较结构分析、计算基板对接和 X 射线晶体学数据。RmSBP 在 α/β 域区域与其他 SBP 具有高度相似性，但它在 C 端域具有不同的拓扑结构。底物结合模型表明，RmSBP 外围区域的构象变化是识别底物所必需的。我们确定了 RmSBP 在 pH 5.5、6.0 和 7.5 下的晶体结构。基于电子密度图和温度 B 因子分析，RmSBP 在 β1-α2 环、β5-β6 环和扩展的 C 端结构域中显示出结构灵活性。