An uncommon [K⁺(Mg²⁺)₂] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch

Structural analysis of the metal-ion triad. (A) Metal ion network in Burkholderia Guanidine-I riboswitch. |F_o|–|F_c| electron density map, prior to ion modeling, contoured at 3.2σ (gray mesh). Modeled Mg²⁺ (green, M_A and M_B) and K⁺ (yellow, M_C). Orange dashed lines denote metal ion coordination. (B) 160° rotation of A. (C) Structural superposition of D. dadantii Mg²⁺ cluster (RNA, orange; ion, gray). (D) Structural superposition of S. acidophilus Mg²⁺ cluster (RNA and ions, gray). (E) Structural superposition of the Burkholderia Guanidine-I riboswitch ion core and binding pocket with the S. acidophilus ppGpp riboswitch binding pocket and ion core (PDB ID:6DMC; [Peselis and Serganov 2018]). Ions from Burkholderia Guanidine-I riboswitch are shown as gray transparent spheres. (F) Structural superposition of the Burkholderia Guanidine-I riboswitch ion-core and binding pocket with the S. lipocalidus PRPP riboswitch binding pocket and ion core (PDB ID: 6DLT [Peselis and Serganov 2018]). Ions from Burkholderia Guanidine-I riboswitch are shown as gray transparent spheres. (G) Ion cluster of the closed DNA polymerase β product complex. Mg²⁺ and Na⁺ are shown in green and yellow spheres, respectively (PDB ID: 4KLL [Freudenthal et al. 2013]). (H) Structural superposition of the DNA polymerase β product complex with the Burkholderia Guanidine-I metal-ion triad (translucent purple and gray). For RNAs superpositions between ykkC-I riboswitches, structural superpositions were performed for all non-hydrogen atoms with residues 20–41 and 63–102 of the Burkholderia ykkC-I riboswitch deleted from the search. Structural superposition of Burkholderia ykkC-I and DNA polymerase β product complex is centered on the three metal ions.