Fig. 3: Conformational changes of Mtb-RNase J upon RNA binding.

a Overall structure of the Mtb-RNase J/ssRNA complex. The ssRNA was shown in a stick model. The metal ions were shown in gray spheres. Chains A and B were colored blue and orange, respectively. b The electrostatic potential surface of the Mtb-RNase J/ssRNA complex. Red: negative potential; blue: positive potential. c Superimposition of the Tth-RNase J and Mtb-RNase J structures. Mtb-RNase J and Tth-RNase J were shown in cyan and gray, respectively. The significant differences in RNA binding were highlighted in blue color. The red arrows show the shifts. A black box represented the RNA binding region. d–f The electrostatic potential surfaces of Tth-RNase J (d, PDB: 3BK2), apo-Mtb-RNase J (e, PDB: 7WNT), and chain B of Mtb-RNase J/ssRNA complex (f, PDB: 7WNU) were shown, respectively. The red arrows denoted the different conformations of RNase J. g Details of the RNA binding sites in the Mtb-RNase J/ssRNA complex. RNase J was shown in a cartoon model, whereas ssRNA was in a stick model with an electron density map contoured to 1.0 σ at the 2Fo-Fc map. The slice of the structure was viewed from the inside of the protein looking outwards. h The schematic representation of the RNA binding sites. Residues involved in RNA-binding on the β-lactamases, the β-CASP, and the loop were shown in yellow, black, and gray, respectively. Blue and red arrows indicated interactions through the main and the side chains of different residues, respectively. The scissile phosphate was highlighted in red.