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Title: Active site and laminarin binding in glycoside hydrolase family 55

Abstract

The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium. Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ~30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Furthermore, application of thismore » experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [4];  [4]
  1. Univ. of Wisconsin, Madison, WI (United States); Univ. of Wisconsin, Oshkosh, WI (United States)
  2. Univ. of Wisconsin, Madison, WI (United States); Hokkaido Univ., Sapporo (Japan)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. of Wisconsin, Madison, WI (United States)
  5. California State Univ., Fullerton, CA (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1182778
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 290; 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; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; genomics; glycoside hydrolase; hydrolase; proteomics; x-ray crystallography; β-1,3-glucanase; GH55; cell-free translation; exo-glucanase

Citation Formats

Bianchetti, Christopher M., Takasuka, Taichi E., Deutsch, Sam, Udell, Hannah S., Yik, Eric J., Bergeman, Lai F., and Fox, Brian G. Active site and laminarin binding in glycoside hydrolase family 55. United States: N. p., 2015. Web. doi:10.1074/jbc.M114.623579.
Bianchetti, Christopher M., Takasuka, Taichi E., Deutsch, Sam, Udell, Hannah S., Yik, Eric J., Bergeman, Lai F., & Fox, Brian G. Active site and laminarin binding in glycoside hydrolase family 55. United States. https://doi.org/10.1074/jbc.M114.623579
Bianchetti, Christopher M., Takasuka, Taichi E., Deutsch, Sam, Udell, Hannah S., Yik, Eric J., Bergeman, Lai F., and Fox, Brian G. Mon . "Active site and laminarin binding in glycoside hydrolase family 55". United States. https://doi.org/10.1074/jbc.M114.623579. https://www.osti.gov/servlets/purl/1182778.
@article{osti_1182778,
title = {Active site and laminarin binding in glycoside hydrolase family 55},
author = {Bianchetti, Christopher M. and Takasuka, Taichi E. and Deutsch, Sam and Udell, Hannah S. and Yik, Eric J. and Bergeman, Lai F. and Fox, Brian G.},
abstractNote = {The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium. Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ~30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Furthermore, application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.},
doi = {10.1074/jbc.M114.623579},
journal = {Journal of Biological Chemistry},
number = 19,
volume = 290,
place = {United States},
year = {Mon Mar 09 00:00:00 EDT 2015},
month = {Mon Mar 09 00:00:00 EDT 2015}
}

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Works referenced in this record:

Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases
journal, January 2014

  • Book, Adam J.; Yennamalli, Ragothaman M.; Takasuka, Taichi E.
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/1754-6834-7-109

Cloning and characterization of multiple glycosyl hydrolase genes from Trichoderma virens
journal, March 2002


Glycosidase mechanisms
journal, October 2000


Purification and Characterization of Laminaran Hydrolases from Trichoderma viride
journal, January 2003

  • Nobe, Rika; Sakakibara, Yoichi; Fukuda, Nobuhiro
  • Bioscience, Biotechnology, and Biochemistry, Vol. 67, Issue 6
  • DOI: 10.1271/bbb.67.1349

Molecular characterization of a novel β-1,3-exoglucanase related to mycoparasitism of Trichoderma harzianum
journal, January 1999


Fusion of Dioxygenase and Lignin-binding Domains in a Novel Secreted Enzyme from Cellulolytic Streptomyces sp. SirexAA-E
journal, May 2013

  • Bianchetti, Christopher M.; Harmann, Connor H.; Takasuka, Taichi E.
  • Journal of Biological Chemistry, Vol. 288, Issue 25
  • DOI: 10.1074/jbc.M113.475848

Binding Site Dynamics and Aromatic–Carbohydrate Interactions in Processive and Non-Processive Family 7 Glycoside Hydrolases
journal, April 2013

  • Taylor, Courtney B.; Payne, Christina M.; Himmel, Michael E.
  • The Journal of Physical Chemistry B, Vol. 117, Issue 17
  • DOI: 10.1021/jp401410h

Ensemble Refinement of Protein Crystal Structures: Validation and Application
journal, September 2007


The Active Site of Cellobiohydrolase Cel6A from Trichoderma r eesei :  The Roles of Aspartic Acids D221 and D175
journal, August 2002

  • Koivula, Anu; Ruohonen, Laura; Wohlfahrt, Gerd
  • Journal of the American Chemical Society, Vol. 124, Issue 34
  • DOI: 10.1021/ja012659q

Structures of an active-site mutant of a plant 1,3-β-glucanase in complex with oligosaccharide products of hydrolysis
journal, December 2012

  • Wojtkowiak, Agnieszka; Witek, Kamil; Hennig, Jacek
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 1
  • DOI: 10.1107/S0907444912042175

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
journal, December 2007

  • Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S090744490705024X

Substructure search procedures for macromolecular structures
journal, October 2003

  • Grosse-Kunstleve, R. W.; Adams, P. D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 11
  • DOI: 10.1107/S0907444903018043

Wounding in the plant tissue: the defense of a dangerous passage
journal, September 2014

  • Savatin, Daniel V.; Gramegna, Giovanna; Modesti, Vanessa
  • Frontiers in Plant Science, Vol. 5
  • DOI: 10.3389/fpls.2014.00470

Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts
journal, January 2008

  • Klock, Heath E.; Koesema, Eric J.; Knuth, Mark W.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 71, Issue 2
  • DOI: 10.1002/prot.21786

Autoinduction of Protein Expression
journal, April 2009


Acquisition of Digestive Enzymes by Siricid Woodwasps from Their Fungal Symbiont
journal, June 1983


Site-Directed Mutation of the Putative Catalytic Residues of Endoglucanase CenA from Cellulomonas fimi
journal, February 1995

  • Damude, Howard Glenn; Withers, Stephen G.; Kilburn, Douglas G.
  • Biochemistry, Vol. 34, Issue 7
  • DOI: 10.1021/bi00007a016

SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces
journal, January 2013

  • Takasuka, Taichi E.; Book, Adam J.; Lewin, Gina R.
  • Scientific Reports, Vol. 3, Issue 1
  • DOI: 10.1038/srep01030

Callose synthesis in higher plants
journal, June 2009

  • Chen, Xiong-Yan; Kim, Jae-Yean
  • Plant Signaling & Behavior, Vol. 4, Issue 6
  • DOI: 10.4161/psb.4.6.8359

Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio
journal, March 2011

  • Adams, Aaron S.; Jordan, Michelle S.; Adams, Sandye M.
  • The ISME Journal, Vol. 5, Issue 8
  • DOI: 10.1038/ismej.2011.14

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
journal, May 2009

  • Terwilliger, Thomas C.; Adams, Paul D.; Read, Randy J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6
  • DOI: 10.1107/S0907444909012098

Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77 — a mini-review
journal, January 2014


The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009

  • Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn663

Cloning and Characterization of the Gene Encoding Endo-β-1,3-glucanase from Arthrobacter sp. NHB-10
journal, June 2007

  • Okazaki, Katsuichiro; Nishimura, Naohito; Matsuoka, Fumiyoshi
  • Bioscience, Biotechnology, and Biochemistry, Vol. 71, Issue 6
  • DOI: 10.1271/bbb.70030

Modelling dynamics in protein crystal structures by ensemble refinement
journal, December 2012


Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007


Crystal Structure of Glycoside Hydrolase Family 55 β-1,3-Glucanase from the Basidiomycete Phanerochaete chrysosporium
journal, February 2009

  • Ishida, Takuya; Fushinobu, Shinya; Kawai, Rie
  • Journal of Biological Chemistry, Vol. 284, Issue 15
  • DOI: 10.1074/jbc.M808122200

Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation
journal, September 2011

  • Payne, Christina M.; Bomble, Yannick J.; Taylor, Courtney B.
  • Journal of Biological Chemistry, Vol. 286, Issue 47
  • DOI: 10.1074/jbc.M111.297713

Predicting the potential distribution of Sirex noctilio (Hymenoptera: Siricidae), a significant exotic pest of Pinus plantations
journal, March 2006

  • Carnegie, Angus J.; Matsuki, Mamoru; Haugen, Dennis A.
  • Annals of Forest Science, Vol. 63, Issue 2
  • DOI: 10.1051/forest:2005104

ExPASy: the proteomics server for in-depth protein knowledge and analysis
journal, July 2003


The Tryptophan Residue at the Active Site Tunnel Entrance of Trichoderma reesei Cellobiohydrolase Cel7A Is Important for Initiation of Degradation of Crystalline Cellulose
journal, March 2013

  • Nakamura, Akihiko; Tsukada, Takeshi; Auer, Sanna
  • Journal of Biological Chemistry, Vol. 288, Issue 19
  • DOI: 10.1074/jbc.M113.452623

Structure, Mechanistic Action, and Essential Residues of a GH-64 Enzyme, Laminaripentaose-producing β-1,3-Glucanase
journal, July 2009

  • Wu, Hsin-Mao; Liu, Sheng-Wen; Hsu, Ming-Tsung
  • Journal of Biological Chemistry, Vol. 284, Issue 39
  • DOI: 10.1074/jbc.M109.010983

A novel endo-beta-1,3-glucanase, BGN13.1, involved in the mycoparasitism of Trichoderma harzianum.
journal, January 1995


Cloning, sequence and structure of a gene encoding an antifungal glucan 1,3-β-glucosidase from Trichoderma atroviride (T. harzianum)
journal, October 2001


A Secondary Xylan-binding Site Enhances the Catalytic Activity of a Single-domain Family 11 Glycoside Hydrolase
journal, October 2007

  • Ludwiczek, Martin L.; Heller, Markus; Kantner, Terrence
  • Journal of Molecular Biology, Vol. 373, Issue 2
  • DOI: 10.1016/j.jmb.2007.07.057

142. The structure of laminarin. Part II. The minor structural features
journal, January 1958

  • Peat, Stanley; Whelan, W. J.; Lawley, H. G.
  • Journal of the Chemical Society (Resumed)
  • DOI: 10.1039/jr9580000729

The β-Glucanase Zg LamA from Zobellia galactanivorans Evolved a Bent Active Site Adapted for Efficient Degradation of Algal Laminarin
journal, December 2013

  • Labourel, Aurore; Jam, Murielle; Jeudy, Alexandra
  • Journal of Biological Chemistry, Vol. 289, Issue 4
  • DOI: 10.1074/jbc.M113.538843

Glycoside hydrolases: Catalytic base/nucleophile diversity
journal, June 2010

  • Vuong, Thu V.; Wilson, David B.
  • Biotechnology and Bioengineering, Vol. 107, Issue 2, p. 195-205
  • DOI: 10.1002/bit.22838

Arthrobacter phenanthrenivorans sp. nov., to accommodate the phenanthrene-degrading bacterium Arthrobacter sp. strain Sphe3
journal, February 2009

  • Kallimanis, A.; Kavakiotis, K.; Perisynakis, A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 2
  • DOI: 10.1099/ijs.0.000984-0

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
  • DOI: 10.1107/S0907444909042073

Use of Dinitrosalicylic Acid Reagent for Determination of Reducing Sugar
journal, March 1959


Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

GeneDesign 3.0 is an updated synthetic biology toolkit
journal, March 2010

  • Richardson, Sarah M.; Nunley, Paul W.; Yarrington, Robert M.
  • Nucleic Acids Research, Vol. 38, Issue 8
  • DOI: 10.1093/nar/gkq143

Carbohydrate-binding modules: fine-tuning polysaccharide recognition
journal, September 2004

  • Boraston, Alisdair B.; Bolam, David N.; Gilbert, Harry J.
  • Biochemical Journal, Vol. 382, Issue 3
  • DOI: 10.1042/BJ20040892

Biochemical Properties and Atomic Resolution Structure of a Proteolytically Processed β-Mannanase from Cellulolytic Streptomyces sp. SirexAA-E
journal, April 2014


The architecture of parallel β-helices and related folds
journal, October 2001


Analysis of the structural heterogeneity of laminarin by electrospray-ionisation-mass spectrometry
journal, February 1996


Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
journal, November 2007

  • Warnecke, Falk; Luginbühl, Peter; Ivanova, Natalia
  • Nature, Vol. 450, Issue 7169
  • DOI: 10.1038/nature06269

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
  • DOI: 10.1107/S0907444909052925

A combined approach to improving large-scale production of tobacco etch virus protease
journal, September 2007

  • Blommel, Paul G.; Fox, Brian G.
  • Protein Expression and Purification, Vol. 55, Issue 1, p. 53-68
  • DOI: 10.1016/j.pep.2007.04.013

Enzymatic Assembly of Overlapping DNA Fragments
book, May 2011


Enhanced Bacterial Protein Expression During Auto-Induction Obtained by Alteration of Lac Repressor Dosage and Medium Composition
journal, January 2007

  • Blommel, Paul G.; Becker, Katie J.; Duvnjak, Petar
  • Biotechnology Progress, Vol. 23, Issue 3
  • DOI: 10.1021/bp070011x

Mechanisms of enzymatic glycoside hydrolysis
journal, January 1994


Cloning and Expression of a Novel Trichoderma viride Laminarinase AI Gene ( lamAI )
journal, January 2004

  • Nobe, Rika; Sakakibara, Yoichi; Ogawa, Kihachiro
  • Bioscience, Biotechnology, and Biochemistry, Vol. 68, Issue 10
  • DOI: 10.1271/bbb.68.2111

NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995

  • Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW.
  • Journal of Biomolecular NMR, Vol. 6, Issue 3
  • DOI: 10.1007/BF00197809

Expression of cmg1, an Exo-β-1,3-Glucanase Gene from Coniothyrium minitans, Increases during Sclerotial Parasitism
journal, February 2001

  • Giczey, Gábor; Kerényi, Zoltán; Fülöp, László
  • Applied and Environmental Microbiology, Vol. 67, Issue 2
  • DOI: 10.1128/AEM.67.2.865-871.2001

Gene Cloning and Heterologous Expression of Glycoside Hydrolase Family 55 β-1,3-Glucanase from the Basidiomycete Phanerochaete Chrysosporium
journal, March 2006


Cloning and targeted gene disruption of EXG1, encoding exo-beta 1, 3-glucanase, in the phytopathogenic fungus Cochliobolus carbonum.
journal, January 1994


Nomenclature for sugar-binding subsites in glycosyl hydrolases
journal, January 1997

  • Davies, Gideon J.; Wilson, Keith S.; Henrissat, Bernard
  • Biochemical Journal, Vol. 321, Issue 2
  • DOI: 10.1042/bj3210557

The absence of an identifiable single catalytic base residue in Thermobifida fusca exocellulase Cel6B
journal, July 2009


The cell wall: a carbohydrate armour for the fungal cell
journal, October 2007


The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation: Metabolomics of leaf-cutter ant fungus gardens
journal, April 2014

  • Huang, Eric L.; Aylward, Frank O.; Kim, Young-Mo
  • Environmental Microbiology Reports, Vol. 6, Issue 4
  • DOI: 10.1111/1758-2229.12163

Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences
book, January 2013


Antitumor anthraquinones from an endophytic actinomycete Micromonospora lupini sp. nov.
journal, July 2007

  • Igarashi, Yasuhiro; Trujillo, Martha E.; Martínez-Molina, Eustoquio
  • Bioorganic & Medicinal Chemistry Letters, Vol. 17, Issue 13
  • DOI: 10.1016/j.bmcl.2007.04.039

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens
journal, March 2012

  • Aylward, Frank O.; Burnum, Kristin E.; Scott, Jarrod J.
  • The ISME Journal, Vol. 6, Issue 9
  • DOI: 10.1038/ismej.2012.10

Bacterial symbionts in agricultural systems provide a strategic source for antibiotic discovery
journal, August 2013

  • Ramadhar, Timothy R.; Beemelmanns, Christine; Currie, Cameron R.
  • The Journal of Antibiotics, Vol. 67, Issue 1
  • DOI: 10.1038/ja.2013.77

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997


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  • Garfoot, Andrew L.; Dearing, Kacey L.; VanSchoiack, Andrew D.
  • Journal of Biological Chemistry, Vol. 292, Issue 12
  • DOI: 10.1074/jbc.m116.762104