Model for ProQ–RNA interaction. (A) Alignment of AlphaFold model of FinO domain of ProQ (Jumper et al. 2021; Varadi et al. 2022) and Lp RocC/RocR cocrystal structure (PDB ID: 7RGU; Kim et al. 2022). (B) Summary of in vitro biochemical results. Residues which were modified for gel shift experiments are colored based on the size of the detrimental effects on RNA binding when modified: strong (R80, Y70, R58; magenta), moderate (K35, K54, R62; cyan), effects that varied across RNA ligands (K35, R69; green), and those with only weak effects (D41, T65; orange). (C,D) Surface representation of the concave-face binding pocket of ProQ, with residues colored as in (B). The terminal two pyrimidine nucleotides from RocR are shown in stick representation and are colored by atomic identity. The two panels compare (C) ProQ residues identified as important for RNA interactions in vitro in the current work and (D) residues found in previous B3H experiments to contribute to cspE-3′ and SibB binding in vivo (Pandey et al. 2020).
