The C2′- and C3′-endo equilibrium for AMP molecules bound in the cystathionine-beta-synthase domain

The equilibrium between C2′- and C3′-endo conformations of nucleotides in solution, as well as their polymers DNA and RNA, has been well studied in previous work. However, this equilibrium of nucleotides in their binding state remains unclear. We observed two AMP molecules, in C3′- and C2′-endo conformations respectively, simultaneously bound to a cystathionine-beta-synthase (CBS) domain dimer of the magnesium and cobalt efflux protein CorC in the crystallographic study. The C2′-endo AMP molecule assumes the higher sugar pucker energy and one more hydrogen bond with the protein than the C3′-endo molecule does. The balance between the high sugar pucker energy and the low binding energy suggests an equilibrium or switch between C2′- and C3′-endo conformations of the bound nucleotides. Our work challenge the previous hypothesis that the ribose of the bound nucleotides would be locked in a fixed conformation.