An active site water broadens substrate specificity in S-ribosylhomocysteinase (LuxS): a docking, MD, and QM/MM study

Abstract

Type-2 quorum sensing (QS-2) is a cell-cell signaling process known to be used by a number of pathogenic bacteria and to play important roles in their population growth and virulence. S-ribosyl homocysteinase (LuxS) is a key enzyme in the formation of the signaling molecule of QS-2, autoinducer II (AI-2). In this study, substrate (S-ribosylhomocysteine: SRH) binding and possible initial reaction steps of its catalytic mechanism leading to formation of a putative 2-keto-SRH intermediate have been examined. Specifically, docking and MD simulations were used to gain insights into the structure of the active-site-bound substrate complex. An ONIOM QM/MM hybrid method was then used to elucidate the mechanism of the first stage of the enzyme catalytic process. It is shown that the substrate may bind within the active site when its ribosyl moiety is in the α- (α-SRH) or β-furanose (β-SRH) configuration or as a linear aldose (linear-SRH). The α-SRH complex is preferred, lying 47.5 kJ mol(-1) lower in energy than the next lowest energy initial complex β-SRH. However, the MD and QM/MM calculations indicate that an active site water stably locates within the active site and that it can facilitate ring-opening of either α-SRH or β-furanose, leading to formation of a common active-site-bound 2-keto-SRH intermediate, without the need to pass through a linear aldose SRH configuration. Hence, regardless of the ribose's configuration within the bound SRH substrate, LuxS is able to catalyze the conversion of SRH to a common 2-keto-SRH intermediate.