Structures of ligand-bound SAM-II riboswitch and its ligands. (A) Secondary structure representation of SAM-II riboswitch showing the helices P1, P2a/b, and the loop L1. The standard base-pairing interactions seen in the crystal structure (Gilbert et al. 2008) of the 52-nt SAM-II are shown here using the Leontis-Westhof notation (Leontis and Westhof 2001). (Orange) The sequence of the expression platform; (blue) the adenine moiety of SAM. (B) Three-dimensional (3D) structure of the SAM-II riboswitch bound to its cognate metabolite SAM, which is seen in an extended configuration and perpendicular to the bases U11 and U21 of the riboswitch that closely interacts with the sulfur (yellow) moiety of SAM. The expression platform (orange) that contains the Shine-Dalgarno sequence is part of the P2a/b helix and follows its curvature. Chemical structures of (C) SAM and (D) SAH ligands. SAM contains a methyl group attached to the sulfur giving the ligand a +1 overall charge, while SAH is neutral. SAM is shown in the S configuration at both the sulfur atom and the Cα of the methionyl moiety.
