Structure of the trans-acting glmS catalytic riboswitch from Bacillus subtilis as derived by homology modeling based on the crystal structure of the glmS riboswitch from Thermoanaerobacter tengcongensis (Klein and Ferre-D'Amare 2006). (A) Modeled secondary structure of the catalytic core ribozyme used in this study, color coded by structure element. The outlined nucleotides of the closing loop of helix P1 were removed to obtain a trans-acting ribozyme, the small “c” at the 3′ terminus was added to stabilize P1. The substrate strand is shown in red with the cleavage site indicated by an open arrow. For FRET studies “(G)” on the 5′ end was removed and a donor (“D,” fluorescein) and an acceptor (“A,” tetramethylrhodamine) fluorophore were attached to the substrate 5′ and 3′ termini, respectively, as indicated. To obtain a noncleavable substrate analog (ncS3) for structural studies of the precursor form, the 2′-hydroxyl of the underlined A-1 nucleotide was modified to 2′-methoxy. (B) Stick and ribbon depiction of the glmS precursor crystal structure from Thermoanaerobacter tengcongensis bound to glucose-6-phosphate (PDB ID 2H0Z; Klein and Ferre-D'Amare 2006) that shows only the elements contained in the trans-acting ribozyme studied here, using the same color code as in panel A. The Glc6P ligand is represented in space filling, a chelated Mg2+ ion is shown as a green sphere. Rendered using PyMol (DeLano 2002).
