LeuRS synthetase: a first-principles investigation of the water-mediated editing reaction

Abstract

Starting from the crystallographic structure of the Thermus thermophilus leucyl-tRNA (LeuRS) synthethase system and recent theoretical findings, our combined hybrid QM/MM and free energy metadynamics sampling approach shows that in the editing domain the enzymatic activity is initiated by the dissociation of a specific water molecule in proximity of the chemical bonds (-C*-O*-) constituting the nucleotide binding of the tRNA to the leucyl protein. A crucial promoter of the reaction is the 3'-OH group of the cognate tRNA bound to the editing site of leucyl, which forms a stable hydrogen bond with this peculiar catalytic water molecule. We could identify two possible reaction mechanisms for the initial stage of the editing reaction: In one case the 3'-OH group of the cognate tRNA acts as a Lewis acid, and one of the protons of the catalytic water molecule becomes a temporarily shared proton between 3'-OH and this specific H(2)O, thus helping its dissociation. The dissociation products OH(-) and H(+) attack the C* and O* atoms, respectively, thus promoting the C-O bond cleavage. In the second case, the 3'-OH group of the cognate tRNA drives, via its hydrogen bond, the catalytic water molecule toward the -C*-O*- bond, and the unoccupied LUMO state, located on top of this bond, becomes the electron acceptor for the dissociating water molecule. This promotes the reaction toward the same final product found in the former pathway, but without involving temporary proton transfers to 3'-OH.