title: Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.
abstract: There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50-70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.
authors.affiliation: From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
authors.forename: Jose Henrique
authors.initials: JH
authors.lastname: Pereira
authors.affiliation: From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Heins
authors.affiliation: the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Gall
authors.affiliation: From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
authors.forename: Ryan P
authors.initials: RP
authors.lastname: McAndrew
authors.affiliation: From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551.
authors.forename: Kai
authors.initials: K
authors.lastname: Deng
authors.affiliation: From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551.
authors.forename: Keefe C
authors.initials: KC
authors.lastname: Holland
authors.affiliation: the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Donohue
authors.affiliation: the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Noguera
authors.affiliation: From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551.
authors.forename: Blake A
authors.initials: BA
authors.lastname: Simmons
authors.affiliation: From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: Sale
authors.affiliation: the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and.
authors.forename: John
authors.initials: J
authors.lastname: Ralph
authors.affiliation: From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the Department of Bioengineering, University of California, Berkeley, California 94720 pdadams@lbl.gov.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D002384:Catalysis; D018360:Crystallography, X-Ray; D004987:Ethers / Q000378:metabolism; D008031:Lignin / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D008958:Models, Molecular; D010088:Oxidoreductases / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D042301:Sphingomonadaceae / Q000201:enzymology*; D013237:Stereoisomerism; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D004987:Ethers; D008031:Lignin; D010088:Oxidoreductases
keywords: biodegradation; biofuel; crystal structure; enzyme kinetics; lignin degradation