Doi Takashi, Nakagawa Yu, Takegoshi K
Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
Biochemistry. 2017 Jan 24;56(3):468-472. doi: 10.1021/acs.biochem.6b01300. Epub 2017 Jan 12.
Pradimicin A (PRM-A) is a unique natural product that recognizes d-mannopyranoside (Man) in the presence of Ca ion. Although the Man binding geometry of PRM-A is largely understood, the molecular basis of Man recognition has yet to be established because of the lack of information regarding Ca binding geometry. In this work, to examine the Ca binding site of PRM-A, we performed a solid-state nuclear magnetic resonance experiment using Cd as a surrogate probe for Ca. Evaluation of C-Cd distances in the [PRM-A/Cd] complexes by rotational-echo double resonance (REDOR) and Cd frequency selective REDOR (FSR) revealed that PRM-A binds Cd at the anthraquinone moiety, which contradicts the previous hypothesis of the alanine moiety being the Ca and Cd binding sites of PRM-A. The distances between Cd and the carbon atoms at the binding site of PRM-A were found to be 3.5 ± 0.2 Å. Importantly, Man binding was shown not to alter the distances, indicating that [PRM-A/Ca] and [PRM-A/Ca/Man] complexes have similar Ca binding geometries. This study provides an important clue to understanding the molecular basis of Man recognition of PRM-A.
普拉地霉素A（PRM-A）是一种独特的天然产物，在钙离子存在的情况下能识别D-甘露吡喃糖苷（Man）。尽管PRM-A与Man的结合几何结构已基本明确，但由于缺乏有关钙结合几何结构的信息，Man识别的分子基础尚未确立。在这项工作中，为了研究PRM-A的钙结合位点，我们使用镉作为钙的替代探针进行了固态核磁共振实验。通过旋转回波双共振（REDOR）和镉频率选择性REDOR（FSR）对[PRM-A/镉]配合物中的碳-镉距离进行评估，结果表明PRM-A在蒽醌部分结合镉，这与之前认为丙氨酸部分是PRM-A的钙和镉结合位点的假设相矛盾。发现镉与PRM-A结合位点的碳原子之间的距离为3.5±0.2埃。重要的是，研究表明Man的结合不会改变这些距离，这表明[PRM-A/钙]和[PRM-A/钙/Man]配合物具有相似的钙结合几何结构。这项研究为理解PRM-A识别Man的分子基础提供了重要线索。
