Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism Aiming Ren, Kanagalaghatta R.

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Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism Aiming Ren, Kanagalaghatta R. Rajashankar, Dinshaw J. Patel Structure Volume 23, Issue 8, Pages 1375-1381 (August 2015) DOI: 10.1016/j.str.2015.05.016 Copyright © 2015 Elsevier Ltd Terms and Conditions

Structure 2015 23, 1375-1381DOI: (10.1016/j.str.2015.05.016) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 1 Chemical Formulas of ZMP and its Analogs, the Secondary Structure of the Sensing Domain of the Thermosinus carboxydivorans Nor1 ZMP Riboswitch, and the Impact of Mg2+ Cations on Complex Formation (A) Chemical formula of ZMP. (B) Chemical formula of Z (ZMP analog lacking phosphate). (C) Chemical formula of AICA (ZMP analog lacking sugar and phosphate groups). (D) Schematic of sequence and secondary structure of the sensing domain of the pfl motif of T. carboxydivorans (Thermosinus carboxydivorans Nor1). (E) ITC-based binding curves for binding of ZMP to its riboswitch as a function of Mg2+ concentration ranging from nothing added to 20 mM Mg2+ added. See also Figure S1. Structure 2015 23, 1375-1381DOI: (10.1016/j.str.2015.05.016) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 2 Tertiary Structure of the Sensing Domain of the ZMP-Bound Riboswitch (A and B) Two alternative views of the ZMP-bound sensing domain of the riboswitch. The color coding is similar to the schematic in Figure 1D. The bound ZMP is highlighted in a space-filling representation. (C) Schematic of secondary structure based on the crystal structure of the sensing domain of the Thermosinus carboxydivorans Nor1 riboswitch in the ZMP-bound state. The bound ZMP is indicated by the letter Z in red. (D and E) Two views of the ZMP-bound sensing domain of the riboswitch in a surface representation with the bound ZMP in a space-filling representation. Burial of the 5-aminoimidazole-4-carboxamide (Z) ring and sugar of bound ZMP is shown in (D), while (E) shows that the phosphate of bound ZMP is accessible to solvent. (F) A ribose-zipper formed between G37-G38-A39-C40 of the zippered-up segment of helix P1 and C57-C58-G59-A60 segment of helix P3. See also Figures S2–S4. Structure 2015 23, 1375-1381DOI: (10.1016/j.str.2015.05.016) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 3 Details of Intermolecular Interactions Between Bound ZMP and RNA in the Structure of the Complex (A) Interaction between the 5-aminoimidazole-4-carboxamide ring of ZMP and the Watson-Crick edge of U66. (B) Interaction of the sugar-phosphate backbone of ZMP and RNA residues lining the binding pocket. (C and D) Two views of the intercalative stacking of the 5-aminoimidazole-4-carboxamide ring of ZMP between bases of G14 and G67 of the RNA. (E) The coordination geometry of the bound Mg2+ ion. The divalent ion is coordinated to the carboxamide group of ZMP, two phosphate oxygens, and three water molecules. (F) ITC-based binding curves for complex formation between the sensing domain of the ZMP riboswitch and ZMP, Z (lacks phosphate of ZMP), AICA (lacks sugar and phosphate of ZMP), and AMP, under 5 mM Mg2+ conditions. (G) ITC-based binding curves for complex formation between the sensing domain of the ZMP riboswitch for wild-type RNA and its U66G, U66C, and C14-G65 substitutions, under 5 mM Mg2+ conditions. See also Figures S2–S4. Structure 2015 23, 1375-1381DOI: (10.1016/j.str.2015.05.016) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 4 Impact of Residue Substitutions Lining and Adjacent to the Ligand-Binding Pocket of the Sensing Domain of the Riboswitch in the ZMP-Bound State (A) Schematic outlining residue alignments above the ligand-binding pocket of the sensing domain of the riboswitch in the ZMP-bound state. (B) A-minor groove pairing alignment of A30 with the G14-C65 Watson-Crick pair. (C) Alignment of the sugar-phosphate of G15 relative to the major groove edge of the G26-C31 Watson-Crick pair. (D) ITC-based data of the impact of base substitutions on the thermodynamics of complex formation. Replacement of A30 by U30, and replacement of G26-C31 by A26-U31, for residues lining and adjacent to the ligand-binding pocket of the sensing domain of the ZMP riboswitch in the bound state. See also Figures S2–S4. Structure 2015 23, 1375-1381DOI: (10.1016/j.str.2015.05.016) Copyright © 2015 Elsevier Ltd Terms and Conditions