Determination of the solution structure of malonyl-CoA by two-dimensional nuclear magnetic resonance spectroscopy and dynamical simulated annealing calculations

In order to understand the initial interaction of the substrates malonate, ATP, and CoA with malonyl-CoA synthetase, the catalytic product malonyl-CoA was characterized by NR IR spectroscopy and molecular modeling. To assign proton and carbon chemical shifts two-dimensional H-1-H-1 DQF-COSY and H-1-C-13 HMBC experiments were used. The structure of malonyl-CoA in the solution phase was determined based on distance constraints from NOESY and ROESY spectra, The structures were well-converged around the pantetheine region with the pairwise RMSD value of 0.08 nm. The solution structure exhibited a compact folded conformation with intramolecular hydrogen bonds among its carbonyl and hydroxyl groups. These findings will help us to understand the initial interaction of malonate and CoA with malonyl-CoA synthetase.