Solid-State Nuclear Magnetic Resonance Analysis Reveals a Possible Calcium Binding Site of Pradimicin A.

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.