Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues
Abstract
Auxiliary activity (AA) enzymes are produced by numerous bacterial and fungal species to assist in the degradation of biomass. These enzymes are abundant but have yet to be fully characterized. Here, we report the X-ray structure of Thermobifida fusca AA10A (TfAA10A), investigate mutational characterization of key surface residues near its active site, and explore the importance of the various domains of Thermobifida fusca AA10B (TfAA10B). The structure of TfAA10A is similar to other bacterial LPMOs (lytic polysaccharide monooxygenases), including signs of photo-reduction and a distorted active site, with mixed features showing both type I and II copper coordination. The point mutation experiments of TfAA10A show that Trp82 and Asn83 are needed for binding, but only Trp82 affects activity. The TfAA10B domain truncation mutants reveal that CBM2 is crucial for the binding of substrate, but that the X1 module does not affect binding or activity. In TfAA10A, Trp82 and Asn83 are needed for binding, but only Trp82 affects activity. The TfAA10B domain truncation mutants reveal that CBM2 is crucial for substrate binding, but that the X1 module does not affect binding or activity. The structure of TfAA10A is similar to other bacterial lytic polysaccharide monooxygenases with mixed features showing both typemore »
- Publication Date:
- Research Org.:
- National Renewable Energy Lab. (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1618689
- Alternate Identifier(s):
- OSTI ID: 1415124
- Report Number(s):
- NREL/JA-2700-70439
Journal ID: ISSN 1754-6834; 243; PII: 925
- Grant/Contract Number:
- AC36-08GO28308
- Resource Type:
- Published Article
- Journal Name:
- Biotechnology for Biofuels
- Additional Journal Information:
- Journal Name: Biotechnology for Biofuels Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 1754-6834
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- Netherlands
- Language:
- English
- Subject:
- 09 BIOMASS FUELS; Thermobifida fusca; biofuels; biomass degrading enzymes; LPMO; cellulose; oxidative chemistry
Citation Formats
Kruer-Zerhusen, Nathan, Alahuhta, Markus, Lunin, Vladimir V., Himmel, Michael E., Bomble, Yannick J., and Wilson, David B. Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues. Netherlands: N. p., 2017.
Web. doi:10.1186/s13068-017-0925-7.
Kruer-Zerhusen, Nathan, Alahuhta, Markus, Lunin, Vladimir V., Himmel, Michael E., Bomble, Yannick J., & Wilson, David B. Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues. Netherlands. https://doi.org/10.1186/s13068-017-0925-7
Kruer-Zerhusen, Nathan, Alahuhta, Markus, Lunin, Vladimir V., Himmel, Michael E., Bomble, Yannick J., and Wilson, David B. Thu .
"Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues". Netherlands. https://doi.org/10.1186/s13068-017-0925-7.
@article{osti_1618689,
title = {Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues},
author = {Kruer-Zerhusen, Nathan and Alahuhta, Markus and Lunin, Vladimir V. and Himmel, Michael E. and Bomble, Yannick J. and Wilson, David B.},
abstractNote = {Auxiliary activity (AA) enzymes are produced by numerous bacterial and fungal species to assist in the degradation of biomass. These enzymes are abundant but have yet to be fully characterized. Here, we report the X-ray structure of Thermobifida fusca AA10A (TfAA10A), investigate mutational characterization of key surface residues near its active site, and explore the importance of the various domains of Thermobifida fusca AA10B (TfAA10B). The structure of TfAA10A is similar to other bacterial LPMOs (lytic polysaccharide monooxygenases), including signs of photo-reduction and a distorted active site, with mixed features showing both type I and II copper coordination. The point mutation experiments of TfAA10A show that Trp82 and Asn83 are needed for binding, but only Trp82 affects activity. The TfAA10B domain truncation mutants reveal that CBM2 is crucial for the binding of substrate, but that the X1 module does not affect binding or activity. In TfAA10A, Trp82 and Asn83 are needed for binding, but only Trp82 affects activity. The TfAA10B domain truncation mutants reveal that CBM2 is crucial for substrate binding, but that the X1 module does not affect binding or activity. The structure of TfAA10A is similar to other bacterial lytic polysaccharide monooxygenases with mixed features showing both type I and II copper coordination. The role of LPMOs and the variability of abundance in genomes are not fully explored. LPMOs likely perform initial attacks into crystalline cellulose to allow larger processive cellulases to bind and attack, but the precise nature of their synergistic behavior remains to be definitively characterized.},
doi = {10.1186/s13068-017-0925-7},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 10,
place = {Netherlands},
year = {Thu Nov 30 00:00:00 EST 2017},
month = {Thu Nov 30 00:00:00 EST 2017}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s13068-017-0925-7
https://doi.org/10.1186/s13068-017-0925-7
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 31 works
Citation information provided by
Web of Science
Web of Science
Figures / Tables:
Table 1: X-ray data collection and refinement statistics. Statistics for the highest resolution bin are in parenthesis
All figures and tables
(6 total)
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Do new cellulolytic enzyme preparations affect the industrial strategies for high solids lignocellulosic ethanol production?: SHF Gives Higher Cellulosic Ethanol Fermentation
journal, September 2013
- Cannella, David; Jørgensen, Henning
- Biotechnology and Bioengineering, Vol. 111, Issue 1
Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism
journal, December 2013
- Kim, S.; Stahlberg, J.; Sandgren, M.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 1
On the catalytic mechanisms of lytic polysaccharide monooxygenases
journal, April 2016
- Walton, Paul H.; Davies, Gideon J.
- Current Opinion in Chemical Biology, Vol. 31
Pre-calculated protein structure alignments at the RCSB PDB website: Fig. 1.
journal, October 2010
- Prlić, Andreas; Bliven, Spencer; Rose, Peter W.
- Bioinformatics, Vol. 26, Issue 23
Overview of the CCP 4 suite and current developments
journal, March 2011
- Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases
journal, February 2016
- Frandsen, Kristian E. H.; Simmons, Thomas J.; Dupree, Paul
- Nature Chemical Biology, Vol. 12, Issue 4
Applications of computational science for understanding enzymatic deconstruction of cellulose
journal, April 2011
- Beckham, Gregg T.; Bomble, Yannick J.; Bayer, Edward A.
- Current Opinion in Biotechnology, Vol. 22, Issue 2
Catalase improves saccharification of lignocellulose by reducing lytic polysaccharide monooxygenase-associated enzyme inactivation
journal, November 2015
- Scott, Brian R.; Huang, Hong Zhi; Frickman, Jesper
- Biotechnology Letters, Vol. 38, Issue 3
Stimulation of Lignocellulosic Biomass Hydrolysis by Proteins of Glycoside Hydrolase Family 61 Structure and Function of a Large, Enigmatic Family
journal, April 2010
- Harris, Paul; Welner, Ditte; McFarland, K.
- Biochemistry, Vol. 49, Issue 15, p. 3305-3316
Crystal Structure and Computational Characterization of the Lytic Polysaccharide Monooxygenase GH61D from the Basidiomycota Fungus Phanerochaete chrysosporium
journal, March 2013
- Wu, Miao; Beckham, Gregg T.; Larsson, Anna M.
- Journal of Biological Chemistry, Vol. 288, Issue 18
An Oxidative Enzyme Boosting the Enzymatic Conversion of Recalcitrant Polysaccharides
journal, October 2010
- Vaaje-Kolstad, Gustav; Westereng, Bjørge; Horn, Svein J.
- Science, Vol. 330, Issue 6001, p. 219-222
The Fibronectin Type 3-Like Repeat from the Clostridium thermocellum Cellobiohydrolase CbhA Promotes Hydrolysis of Cellulose by Modifying Its Surface
journal, September 2002
- Kataeva, I. A.; Seidel, R. D.; Shah, A.
- Applied and Environmental Microbiology, Vol. 68, Issue 9, p. 4292-4300
Localization of Glucose Oxidase and Catalase Activities in Aspergillus niger
journal, January 1992
- Witteveen, Cor F. B.; Veenhuis, Marten; Visser, Jaap
- Applied and Environmental Microbiology, Vol. 58, Issue 4
Integration of bacterial lytic polysaccharide monooxygenases into designer cellulosomes promotes enhanced cellulose degradation
journal, June 2014
- Arfi, Y.; Shamshoum, M.; Rogachev, I.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 25
Linearization of the Bradford Protein Assay Increases Its Sensitivity: Theoretical and Experimental Studies
journal, May 1996
- Zor, Tsaffrir; Selinger, Zvi
- Analytical Biochemistry, Vol. 236, Issue 2
Kinetic Studies of Thermobifida fusca Cel9A Active Site Mutant Enzymes
journal, August 2004
- Zhou, Weilin; Irwin, Diana C.; Escovar-Kousen, Jose
- Biochemistry, Vol. 43, Issue 30, p. 9655-9663
Extracellular electron transfer systems fuel cellulose oxidative degradation
journal, April 2016
- Kracher, D.; Scheiblbrandner, S.; Felice, A. K. G.
- Science, Vol. 352, Issue 6289
The Slowdown of the Endoglucanase Trichoderma reesei Cel5A-Catalyzed Cellulose Hydrolysis Is Related to Its Initial Activity
journal, November 2014
- Shu, Zhiyu; Wang, Yefei; An, Liaoyuan
- Biochemistry, Vol. 53, Issue 48
Regulation and characterization of Thermobifida fusca carbohydrate-binding module proteins E7 and E8
journal, January 2008
- Moser, Felix; Irwin, Diana; Chen, Shaolin
- Biotechnology and Bioengineering, Vol. 100, Issue 6, p. 1066-1077
A rapid quantitative activity assay shows that the Vibrio cholerae colonization factor GbpA is an active lytic polysaccharide monooxygenase
journal, August 2014
- Loose, Jennifer S. M.; Forsberg, Zarah; Fraaije, Marco W.
- FEBS Letters, Vol. 588, Issue 18
Lytic polysaccharide monooxygenases: a crystallographer's view on a new class of biomass-degrading enzymes
journal, October 2016
- Frandsen, Kristian E. H.; Lo Leggio, Leila
- IUCrJ, Vol. 3, Issue 6
Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose
journal, August 2013
- Payne, Christina M.; Resch, Michael G.; Chen, Liqun
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 36
Oxidative Cleavage of Cellulose by Fungal Copper-Dependent Polysaccharide Monooxygenases
journal, December 2011
- Beeson, William T.; Phillips, Christopher M.; Cate, Jamie H. D.
- Journal of the American Chemical Society, Vol. 134, Issue 2
Cel48A from Thermobifida fusca : Structure and site directed mutagenesis of key residues : Structure and Mutagenesis of
journal, November 2013
- Kostylev, Maxim; Alahuhta, Markus; Chen, Mo
- Biotechnology and Bioengineering, Vol. 111, Issue 4
Accurate bond and angle parameters for X-ray protein structure refinement
journal, July 1991
- Engh, R. A.; Huber, R.
- Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 4
Cleavage of cellulose by a CBM33 protein
journal, August 2011
- Forsberg, Zarah; Vaaje-Kolstad, Gustav; Westereng, Bjørge
- Protein Science, Vol. 20, Issue 9
The Buccaneer software for automated model building. 1. Tracing protein chains
journal, August 2006
- Cowtan, Kevin
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 9
Structural Basis for Substrate Targeting and Catalysis by Fungal Polysaccharide Monooxygenases
journal, June 2012
- Li, Xin; Beeson, William T.; Phillips, Christopher M.
- Structure, Vol. 20, Issue 6, p. 1051-1061
Novel approach to phasing proteins: derivatization by short cryo-soaking with halides
journal, February 2000
- Dauter, Zbigniew; Dauter, Miroslawa; Rajashankar, K. R.
- Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 2
Production and effect of aldonic acids during enzymatic hydrolysis of lignocellulose at high dry matter content
journal, January 2012
- Cannella, David; Hsieh, Chia-wen C.; Felby, Claus
- Biotechnology for Biofuels, Vol. 5, Issue 1
Microbial Cellulose Utilization: Fundamentals and Biotechnology
journal, September 2002
- Lynd, L. R.; Weimer, P. J.; van Zyl, W. H.
- Microbiology and Molecular Biology Reviews, Vol. 66, Issue 3, p. 506-577
MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009
- Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
Automatic protein structure solution from weak X-ray data
journal, November 2013
- Skubák, Pavol; Pannu, Navraj S.
- Nature Communications, Vol. 4, Issue 1
The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013
- Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
- Nucleic Acids Research, Vol. 42, Issue D1
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex
journal, February 2012
- Brunecky, Roman; Alahuhta, Markus; Bomble, Yannick J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 3
REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011
- Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Comparison of the early stages of forced unfolding for fibronectin type III modules
journal, May 2001
- Craig, D.; Krammer, A.; Schulten, K.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 10
Insights into Higher-Order Organization of the Cellulosome Revealed by a Dissect-and-Build Approach: Crystal Structure of Interacting Clostridium thermocellum Multimodular Components
journal, March 2010
- Adams, Jarrett J.; Currie, Mark A.; Ali, Sabrina
- Journal of Molecular Biology, Vol. 396, Issue 4
Lytic Polysaccharide Monooxygenases in Biomass Conversion
journal, December 2015
- Hemsworth, Glyn R.; Johnston, Esther M.; Davies, Gideon J.
- Trends in Biotechnology, Vol. 33, Issue 12
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Crystal Structure and Binding Properties of the Serratia marcescens Chitin-binding Protein CBP21
journal, December 2004
- Vaaje-Kolstad, G.; Houston, D. R.; Riemen, A. H. K.
- Journal of Biological Chemistry, Vol. 280, Issue 12
Spectroscopic and computational insight into the activation of O2 by the mononuclear Cu center in polysaccharide monooxygenases
journal, June 2014
- Kjaergaard, C. H.; Qayyum, M. F.; Wong, S. D.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 24
Production of four Neurospora crassa lytic polysaccharide monooxygenases in Pichia pastoris monitored by a fluorimetric assay
journal, January 2012
- Kittl, Roman; Kracher, Daniel; Burgstaller, Daniel
- Biotechnology for Biofuels, Vol. 5, Issue 1
Biochemical characterization of engineered amylopullulanase from Thermoanaerobacter ethanolicus 39E-implicating the non-necessity of its 100 C-terminal amino acid residues
journal, May 2008
- Lin, Hsu-Yang; Chuang, Hsu-Han; Lin, Fu-Pang
- Extremophiles, Vol. 12, Issue 5
Cellobiose Dehydrogenase and a Copper-Dependent Polysaccharide Monooxygenase Potentiate Cellulose Degradation by Neurospora crassa
journal, December 2011
- Phillips, Christopher M.; Beeson, William T.; Cate, Jamie H.
- ACS Chemical Biology, Vol. 6, Issue 12, p. 1399-1406
Two-Parameter Kinetic Model Based on a Time-Dependent Activity Coefficient Accurately Describes Enzymatic Cellulose Digestion
journal, July 2013
- Kostylev, Maxim; Wilson, David
- Biochemistry, Vol. 52, Issue 33
Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases
journal, May 2014
- Forsberg, Z.; Mackenzie, A. K.; Sorlie, M.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 23
The Copper Active Site of CBM33 Polysaccharide Oxygenases
journal, April 2013
- Hemsworth, Glyn R.; Taylor, Edward J.; Kim, Robbert Q.
- Journal of the American Chemical Society, Vol. 135, Issue 16
Recent insights into copper-containing lytic polysaccharide mono-oxygenases
journal, October 2013
- Hemsworth, Glyn R.; Davies, Gideon J.; Walton, Paul H.
- Current Opinion in Structural Biology, Vol. 23, Issue 5, p. 660-668
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
journal, January 2013
- Levasseur, Anthony; Drula, Elodie; Lombard, Vincent
- Biotechnology for Biofuels, Vol. 6, Issue 1, Article No. 41
Comparative Study of Two Chitin-Active and Two Cellulose-Active AA10-Type Lytic Polysaccharide Monooxygenases
journal, March 2014
- Forsberg, Zarah; Røhr, Åsmund Kjendseth; Mekasha, Sophanit
- Biochemistry, Vol. 53, Issue 10
Works referencing / citing this record:
Expression and secretion of a lytic polysaccharide monooxygenase by a fast-growing cyanobacterium
journal, April 2019
- Russo, D. A.; Zedler, J. A. Z.; Wittmann, D. N.
- Biotechnology for Biofuels, Vol. 12, Issue 1
An actinobacteria lytic polysaccharide monooxygenase acts on both cellulose and xylan to boost biomass saccharification
journal, May 2019
- Corrêa, Thamy Lívia Ribeiro; Júnior, Atílio Tomazini; Wolf, Lúcia Daniela
- Biotechnology for Biofuels, Vol. 12, Issue 1
Characterization and synergistic action of a tetra‐modular lytic polysaccharide monooxygenase from Bacillus cereus
journal, June 2018
- Mutahir, Zeeshan; Mekasha, Sophanit; Loose, Jennifer S. M.
- FEBS Letters, Vol. 592, Issue 15
Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in Streptomyces sp. CC0208
journal, December 2018
- Zhang, Hongyu; Dong, Shirui; Lou, Tingting
- Journal of Basic Microbiology, Vol. 59, Issue 3
Substrate selectivity in starch polysaccharide monooxygenases
journal, June 2019
- Vu, Van V.; Hangasky, John A.; Detomasi, Tyler C.
- Journal of Biological Chemistry, Vol. 294, Issue 32
Sequence and Structural Analysis of AA9 and AA10 LPMOs: An Insight into the Basis of Substrate Specificity and Regioselectivity
journal, September 2019
- Zhou, Xiaoli; Qi, Xiaohua; Huang, Hongxia
- International Journal of Molecular Sciences, Vol. 20, Issue 18
Figures / Tables found in this record:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.