Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase

Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate transfer ribonucleic acids (tRNAs), an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the “prokaryotic-like” ProRSs are distinguished from “eukaryotic-like” ProRSs by the presence of an editing insertion domain (INS) inserted between motifs 2 and 3 of the main catalytic domain. Earlier studies suggested that the presence of coupled-domain dynamics could contribute to catalysis; however, the role that the distal and highly mobile INS domain plays in catalysis at the synthetic active site is not completely understood. In the present study, a combination of theoretical and experimental approaches has been used to elucidate the precise role of INS domain dynamics. Quantum mechanical/molecular mechanical simulations were carried out to model catalytic prolyl-adenylate formation by Enterococcus faecalis ProRS. The energetics of the adenylate formation by the wild-type enzyme was computed and contrasted with variants containing active site mutations as well as a deletion mutant lacking the INS domain. The combined results revealed that two distinct types of dynamics contribute to the enzyme’s catalytic power. One set of motions is intrinsic to the INS domain and leads to conformational preorganization that is essential for catalysis. A second type of motion, stemming from the electrostatic reorganization of active site residues, impacts the height and width of the energy profile and has a critical role in fine-tuning the substrate orientation to facilitate reactive collisions. Thus, motions in a distal domain can preorganize the active site of an enzyme to optimize catalysis.