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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 insightmore » 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.« less

Authors:
 [1];  [2];  [3];  [1];  [2];  [2];  [3];  [3];  [2];  [2];  [3];  [4]
+ Show Author Affiliations
  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)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1379331
Grant/Contract Number:  
AC02-05CH11231; FC02-07ER64494
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 291; Journal Issue: 19; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; biodegradation; biofuel; crystal structure; enzyme kinetics; lignin degradation

Citation Formats

Pereira, Jose Henrique, Heins, Richard A., Gall, Daniel L., McAndrew, Ryan P., Deng, Kai, Holland, Keefe C., Donohue, Timothy J., Noguera, Daniel R., Simmons, Blake A., Sale, Kenneth L., Ralph, John, and Adams, Paul D. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. United States: N. p., 2016. Web. doi:10.1074/jbc.M115.700427.
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Pereira, Jose Henrique, Heins, Richard A., Gall, Daniel L., McAndrew, Ryan P., Deng, Kai, Holland, Keefe C., Donohue, Timothy J., Noguera, Daniel R., Simmons, Blake A., Sale, Kenneth L., Ralph, John, & Adams, Paul D. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. United States. https://doi.org/10.1074/jbc.M115.700427
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Pereira, Jose Henrique, Heins, Richard A., Gall, Daniel L., McAndrew, Ryan P., Deng, Kai, Holland, Keefe C., Donohue, Timothy J., Noguera, Daniel R., Simmons, Blake A., Sale, Kenneth L., Ralph, John, and Adams, Paul D. Thu . "Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6". United States. https://doi.org/10.1074/jbc.M115.700427. https://www.osti.gov/servlets/purl/1379331.
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@article{osti_1379331,
title = {Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6},
author = {Pereira, Jose Henrique and Heins, Richard A. and Gall, Daniel L. and McAndrew, Ryan P. and Deng, Kai and Holland, Keefe C. and Donohue, Timothy J. and Noguera, Daniel R. and Simmons, Blake A. and Sale, Kenneth L. and Ralph, John and Adams, Paul D.},
abstractNote = {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.},
doi = {10.1074/jbc.M115.700427},
journal = {Journal of Biological Chemistry},
number = 19,
volume = 291,
place = {United States},
year = {Thu Mar 03 00:00:00 EST 2016},
month = {Thu Mar 03 00:00:00 EST 2016}
}
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Publisher's Version of Record
https://doi.org/10.1074/jbc.M115.700427
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