Abstract
Given the abundance of lignin in nature, multiple enzyme systems have been discovered to cleave the β-O-4 bonds, the most prevalent intermonomer linkage. In particular, stereospecific cleavage of lignin oligomers by glutathione S-transferases (GSTs) has been reported in several sphingomonads. Here, we apply quantum mechanics/molecular mechanics simulations to study the mechanism of two glutathione-dependent enzymes in the β-aryl ether catabolic pathway of Sphingomonas sp. SYK-6, namely, LigF, a β-etherase, and LigG, a lyase. For LigF, the free-energy landscape supports a SN2 reaction mechanism, with the monoaromatic leaving group being promptly neutralized upon release. Specific interactions with conserved residues are responsible for stereoselectivity and for activation of the cofactor as a nucleophile. A glutathione conjugate is also released by LigF and serves the substrate of LigG, undergoing a SN2-like reaction, in which Cys15 acts as the nucleophile, to yield the second monoaromatic product. The simulations suggest that the electron-donating substituent at the para-position found in lignin-derived aromatics and the interaction with Tyr217 are essential for reactivity in LigG. Overall, this work deepens the understanding of the stereospecific enzymatic mechanisms in the β-aryl ether cleavage pathway and reveals key structural features underpinning the ligninolytic activity detected in several sphingomonad GSTs.
| Original language | English |
|---|---|
| Pages (from-to) | 10142-10151 |
| Number of pages | 10 |
| Journal | Journal of Physical Chemistry B |
| Volume | 123 |
| Issue number | 48 |
| DOIs | |
| State | Published - Dec 5 2019 |
Funding
This work was partially authored by Alliance for Sustainable Energy, LLC, the manager and operator of the National Renewable Energy Laboratory for the U.S. Department of Energy under contract no. DE-AC36-08GO28308. M.F.C. and G.T.B. acknowledge funding for the MD simulations from the U.S. Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy, Bioenergy Technologies Office. G.T.B. also acknowledges funding from the Center for Bioenergy Innovation, a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. E.T.P. and M.S.S. thank funding from the São Paulo Research Foundation (grant nos. 2016/04775-5 and 2013/08293-7). We thank Andreas W. Goetz (San Diego Supercomputer Center, University of California San Diego) who provided DFTB3 implementation in Amber16 for our purposes and for his valuable advices on the adopted methodology. We thank Luiz Carlos Dias (Institute of Chemistry, University of Campinas) for discussions. We acknowledge computer time from the NREL Computational Science Center, which is supported by the DOE Office of Energy Efficiency and Renewable Energy under contract no. DE-AC36-08GO28308.