skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6

Journal Article · · Journal of Biological Chemistry
 [1];  [2];  [3];  [1];  [2];  [2];  [3];  [3];  [2];  [2];  [3];  [4]
  1. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  3. Univ. of Wisconsin, Madison, WI (United States). United States Dept. of Energy Great Lakes Bioenergy Research Center
  4. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
+ Show Author Affiliations

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.

Research Organization:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231; FC02-07ER64494
OSTI ID:
1379331
Journal Information:
Journal of Biological Chemistry, Vol. 291, Issue 19; ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular BiologyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 32 works
Citation information provided by
Web of Science

References (36)

Molecular Characterization of Microbial Alcohol Dehydrogenases journal January 1994
Short-chain dehydrogenases/reductases (SDR): the 2002 update journal February 2003
Sphingobium sp. SYK-6 LigG involved in lignin degradation is structurally and biochemically related to the glutathione transferase omega class journal October 2012
Protocols for production of selenomethionine-labeled proteins in 2-L polyethylene terephthalate bottles using auto-induction medium journal April 2005
Pathways for degradation of lignin in bacteria and fungi journal January 2011
Exploring glutathione lyases as biocatalysts: paving the way for enzymatic lignin depolymerization and future stereoselective applications journal January 2015
The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative journal March 2009
A Group of Sequence-Related Sphingomonad Enzymes Catalyzes Cleavage of β-Aryl Ether Linkages in Lignin β-Guaiacyl and β-Syringyl Ether Dimers journal October 2014
Atomic Resolution Structures of R-specific Alcohol Dehydrogenase from Lactobacillus brevis Provide the Structural Bases of its Substrate and Cosubstrate Specificity journal June 2005
An overview of second generation biofuel technologies journal March 2010
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard journal December 2007
Structures of Ternary Complexes of BphK, a Bacterial Glutathione S -Transferase That Reductively Dechlorinates Polychlorinated Biphenyl Metabolites journal August 2006
Coot model-building tools for molecular graphics journal November 2004
Glutathione transferases in bacteria: Bacterial GSTs journal November 2008
Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions journal November 2013
Towards automated crystallographic structure refinement with phenix.refine journal March 2012
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Enzymatic cleavage of lignin β-O-4 aryl ether bonds via net internal hydrogen transfer journal January 2013
Determination of macromolecular structures from anomalous diffraction of synchrotron radiation journal October 1991
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids journal May 2007
The GSH- and GSSG-bound structures of glutaredoxin from Clostridium oremlandii journal December 2014
Identification of Three Alcohol Dehydrogenase Genes Involved in the Stereospecific Catabolism of Arylglycerol- -Aryl Ether by Sphingobium sp. Strain SYK-6 journal June 2009
An aspartate residue in yeast alcohol dehydrogenase I determines the specificity for coenzyme journal July 1991
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard journal May 2009
Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1 journal April 2014
NMRPipe: A multidimensional spectral processing system based on UNIX pipes journal November 1995
Convenient synthesis of chiral lignin model compounds via optical resolution: four stereoisomers of guaiacylglycerol-β-guaiacyl ether and both enantiomers of 3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)-propan-1-one (erone) journal February 2012
FEM: feature-enhanced map journal February 2015
Genetic and Biochemical Investigations on Bacterial Catabolic Pathways for Lignin-Derived Aromatic Compounds journal January 2007
Genome Sequence of Benzo(a)pyrene-Degrading Bacterium Novosphingobium pentaromativorans US6-1 journal January 2012
Roles of the Enantioselective Glutathione S-Transferases in Cleavage of  -Aryl Ether journal March 2003
The emerging role for bacteria in lignin degradation and bio-product formation journal June 2011
Critical Residues for Structure and Catalysis in Short-chain Dehydrogenases/Reductases journal April 2002
Stereochemical Features of Glutathione-dependent Enzymes in the Sphingobium sp. Strain SYK-6 β-Aryl Etherase Pathway journal February 2014
Phaser crystallographic software journal July 2007
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997

Cited By (10)

Database Mining for Novel Bacterial β-Etherases, Glutathione-Dependent Lignin-Degrading Enzymes journal November 2019
Bacterial Catabolism of β-Hydroxypropiovanillone and β-Hydroxypropiosyringone Produced in the Reductive Cleavage of Arylglycerol-β-Aryl Ether in Lignin journal January 2018
Microbial β-etherases and glutathione lyases for lignin valorisation in biorefineries: current state and future perspectives journal May 2018
Biomimetic Reductive Cleavage of Keto Aryl Ether Bonds by Small‐Molecule Thiols journal September 2019
Effect of Novel Pretreatment of Steam Explosion Associated with Ammonium Sulfite Process on Enzymatic Hydrolysis of Corn Straw journal May 2019
Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35 journal December 2018
Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism: Bacterial catabolism of lignin-derived aromatics journal November 2017
Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB journal June 2018
Biotransformation of lignin: Mechanisms, applications and future work journal October 2019
Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS) journal September 2018

Similar Records

Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG
Journal Article · Tue Nov 05 00:00:00 EST 2019 · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry · OSTI ID:1379331
+1 more
Stereochemical Features of Glutathione-dependent Enzymes in the Sphingobium sp. Strain SYK-6 β-Aryl Etherase Pathway
Journal Article · Fri Feb 07 00:00:00 EST 2014 · Journal of Biological Chemistry · OSTI ID:1379331
+3 more
In vitro methods for processing lignin and other aromatic compounds
Patent · Tue Nov 10 00:00:00 EST 2020 · OSTI ID:1379331
+5 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
biodegradation
biofuel
crystal structure
enzyme kinetics
lignin degradation