Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG

Author(s)

Prates, Erica Teixeira ^{[1, 2, 3, 4]} ; Crowley, Michael F. ^[5] ; Skaf, Munir S. ^{[1, 3]} ; Beckham, Gregg T. ^[2]

Affiliation

^[1] Univ Estadual Campinas, Inst Chem, BR-13084862 Campinas, SP - Brazil

^[2] Natl Renewable Energy Lab, Natl Bioenergy Ctr, Golden, CO 80403 - USA

^[3] Univ Estadual Campinas, Ctr Comp Engn & Sci, BR-13084862 Campinas, SP - Brazil

^[4] Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37830 - USA

^[5] Natl Renewable Energy Lab, Biosci Ctr, Golden, CO 80403 - USA

• Document type: Journal article
• Source: Journal of Physical Chemistry B; v. 123, n. 48, p. 10142-10151, DEC 5 2019.
• Web of Science Citations: 0

Abstract

Given the abundance of lignin in nature, multiple enzyme systems have been discovered to cleave the beta-O-4 bonds, the most prevalent intermonomer linkage. In particular, stereo specific 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 beta-aryl ether catabolic pathway of Sphingomonas sp. SYK-6, namely, LigF, a beta-etherase, and LigG, a lyase. For LigF, the free-energy landscape supports a S(N)2 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 S(N)2-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 beta-aryl ether cleavage pathway and reveals key structural features underpinning the ligninolytic activity detected in several sphingomonad GSTs. (AU)

• FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
• Grantee: Munir Salomao Skaf
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 16/04775-5 - Multiscale simulations of enzymes and enzymatic complexes to lignocellulosic biomass degradation
• Grantee: Érica Teixeira Prates
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor