Characterizing the Structural Basis of Stereospecificity in Enzymatic Cleavage of Lignin Bonds

Understanding how bacteria digest plant lignin informs engineering efforts to extract value from lignin.

The Science

To determine the structural basis for stereospecificity of bacterial enzymes involved in lignin bond cleavage, researchers solved the crystal structures of the enzymes involved. The detailed structural and biochemical characterization of the lignin degradation pathway members reveals important new aspects of the enzyme mechanisms and determinants of substrate specificity.


The Impact

Lignin is a combinatorial polymer comprised of monoaromatic units and is a potential source of valuable aromatic chemicals. However, its recalcitrance to chemical or biological digestion presents a major obstacle to the production of second-generation biofuels and other valuable bioproducts. These collaborative studies elucidating mechanisms of lignin degradation may enable the development of efficient pathways for converting lignin into components of advanced biofuels and other bioproducts.


Lignin’s recalcitrance to chemical or biological digestion presents a major obstacle to the production of second-generation biofuels and valuable coproducts from lignin’s monoaromatic units. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin was reported in the bacterium Sphingobium sp. SYK-6. In a collaborative effort, researchers from the Department of Energy’s (DOE) Great Lakes Bioenergy Research Center (GLBRC) and Joint BioEnergy Institute (JBEI) determined the X-ray crystal structures and biochemical characterizations of several glutathione-dependent β-etherases that participate in the cleavage of lignin. Results from these studies reveal important new aspects of the enzyme mechanisms and the determinants of substrate specificity. As β-aryl ether bonds account for 50 percent to 70 percent of all inter-unit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on lignin valorization.

Principal Investigator

George N. Phillips Jr.
Rice University
[email protected]

BER Program Manager

Shing Kwok

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


This work was funded by GLBRC and JBEI (DOE Office of Science, Office of Biological and Environmental Research DE-FC02-07ER64494 and DE-AC02-05CH11231, respectively), additional grants from DOE (Office of Science, Office of Basic Energy Sciences, Contract No. DE-AC02-05CH11231 and DE-AC02-06CH11357), grants from the National Institutes of Health (AGM-12006, GM109456, GM098248, P41GM103399, and S10RR027000), the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor (Grant 085P1000817), National Cancer Institute (ACB-12002), and University of Wisconsin-Madison.


Helmich, K. E., J. H. Pereira, D. L. Gall, R. A. Heins, R. P. McAndrew, C. Bingman, K. Deng, K. C. Holland, D. R. Noguera, B. A. Simmons, K. L. Sale, J. Ralph, T. J. Donohue, P. D. Adams and G. N. Phillips Jr. 2015.  “Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-aryl Ether Bonds in Lignin,” The Journal of Biological Chemistry. DOI: 10.1074/jbc.M115.694307.

Pereira, J. H., R. A. Heins, D. L. Gall, R. P. McAndrew, K. Deng, K. C. Holland, T. J. Donohue, D. R. Noguera, B. A. Simmons, K. L. Sale, J. R. Ralph and P. D. Adams. 2016. “Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-aryl Ether Cleavage Pathway from Sphingobium sp SYK-6,” The Journal of Biological Chemistry. DOI: 10.1074/jbc.M115.700427.