Fig. 5: Structural comparison of SAM-using SAMURI and natural SAM riboswitches.
From: Structure and catalytic activity of the SAM-utilizing ribozyme SAMURI
a, The SAMURI-catalyzed methylation of A52 and the alignment of SAM-reacted SAMURI (blue) and ProSeDMA-reacted SAMURI (green). Overall structure and excerpt of the modified adenosine and reacted cofactor are shown on the right. b, Detailed structure of SAH-bound and m3A-containing SAMURI with the electron density map from front and top views. The σA-weighted 2Fo − Fc map contoured at 1σ is presented as a blue mesh, while the position of SAH and the methyl group is confirmed by the Fo − Fc omit map (green, contoured at 3σ). c, SAM-binding pocket of SAMURI shown in surface representation (blue) with SAH (yellow) and methylated A52 (red). d,e, SAM binding by natural riboswitches. Characteristic interactions between the methionine tail and the SAM-binding pocket of Thermoanaerobacter tengcongensis SAM I riboswitch (Protein Data bank (PDB) 2GIS), metX SAM II riboswitch (PDB 2QWY), Enterococcus faecalis SAM III riboswitch (PDB 3E5C) and the SAM–SAH riboswitch (PDB 6YL5).
