X-ray Crystallographic Studies of Family 11 Xylanase Michaelis and Product Complexes: Implications for the Catalytic Mechanism of Retaining Glycoside Hydrolases

Wan, Qun; Zhang, Qiu; Hamilton-Brehm, Scott D.; Weiss, Kevin L.; Mustyakimov, Marat; Coates, Leighton; Langan, Paul; Graham, David E.; Kovalevskyi, Andrii Y.

doi:10.1107/S1399004713023626

Title: X-ray Crystallographic Studies of Family 11 Xylanase Michaelis and Product Complexes: Implications for the Catalytic Mechanism of Retaining Glycoside Hydrolases

Journal Article · Wed Jan 01 00:00:00 EST 2014 · Acta Crystallographica. Section D: Biological Crystallography (Online)

DOI:https://doi.org/10.1107/S1399004713023626· OSTI ID:1117460

Wan, Qun ^[1];

^[1]; Hamilton-Brehm, Scott D. ^[2];

^[1]; Mustyakimov, Marat ^[1];

^[1];

^[1]

ORNL
Desert Research Institute (DRI), Reno

Cite

Export

Save

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-00OR22725

OSTI ID:: 1117460

Journal Information:: Acta Crystallographica. Section D: Biological Crystallography (Online), Vol. 70, Issue 1; ISSN 1399-0047

Country of Publication:: United States

Language:: English

References (57)

Hemicelluloses Scheller, Henrik Vibe; Ulvskov, Peter Annual Review of Plant Biology, Vol. 61, Issue 1 https://doi.org/10.1146/annurev-arplant-042809-112315	journal	June 2010
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
The Two Major Xylanases from Trichoderma Reesei: Characterization of Both Enzymes and Genes Törrönen, Anneli; Mach, Robert L.; Messner, Robert Nature Biotechnology, Vol. 10, Issue 11 https://doi.org/10.1038/nbt1192-1461	journal	November 1992
Xylanases, xylanase families and extremophilic xylanases Collins, Tony; Gerday, Charles; Feller, Georges FEMS Microbiology Reviews, Vol. 29, Issue 1, p. 3-23 https://doi.org/10.1016/j.femsre.2004.06.005	journal	January 2005
Substrate conformational changes in glycoside hydrolase catalysis. A first-principles molecular dynamics study Biarnés, Xevi; Ardèvol, Albert; Planas, Antoni Biocatalysis and Biotransformation, Vol. 28, Issue 1 https://doi.org/10.3109/10242420903408252	journal	December 2009
Oligosaccharide Binding in Family 8 Glycosidases: Crystal Structures of Active-Site Mutants of the β-1,4-Xylanase pXyl from Pseudoaltermonas haloplanktis TAH3a in Complex with Substrate and Product ^† ^, ^‡ De Vos, D.; Collins, T.; Nerinckx, W. Biochemistry, Vol. 45, Issue 15 https://doi.org/10.1021/bi052193e	journal	April 2006
Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement Watanabe, Nobuhiko; Akiba, Toshihiko; Kanai, Ryuta Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 7 https://doi.org/10.1107/S0907444906017379	journal	June 2006
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Identification of Glutamic Acid 78 as the Active Site Nucleophile in Bacillus subtilis Xylanase Using Electrospray Tandem Mass Spectrometry Miao, Shichang; Ziser, Lothar; Aebersold, Ruedi Biochemistry, Vol. 33, Issue 23 https://doi.org/10.1021/bi00189a002	journal	June 1994
Cooperativity in monomeric enzymes with single ligand-binding sites Porter, Carol M.; Miller, Brian G. Bioorganic Chemistry, Vol. 43 https://doi.org/10.1016/j.bioorg.2011.11.001	journal	August 2012
Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the ph optimum of a glycosidase 1 1Edited by M. F. Summers Joshi, Manish D.; Sidhu, Gary; Pot, Isabelle Journal of Molecular Biology, Vol. 299, Issue 1 https://doi.org/10.1006/jmbi.2000.3722	journal	May 2000
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Krissinel, E.; Henrick, K. Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12 https://doi.org/10.1107/S0907444904026460	journal	November 2004
Structural Basis for Allosteric Regulation of the Monomeric Allosteric Enzyme Human Glucokinase Kamata, Kenji; Mitsuya, Morihiro; Nishimura, Teruyuki Structure, Vol. 12, Issue 3 https://doi.org/10.1016/j.str.2004.02.005	journal	March 2004
Stereographic representation of the cremer-pople ring-puckering parameters for pyranoid rings Jeffrey, George A.; Yates, John H. Carbohydrate Research, Vol. 74, Issue 1 https://doi.org/10.1016/S0008-6215(00)84786-2	journal	September 1979
Protein release and foaming in Escherichia coli cultures grown in minimal medium Törnkvist, M.; Larsson, G.; Enfors, S. -O. Bioprocess Engineering, Vol. 15, Issue 5 https://doi.org/10.1007/BF02391583	journal	October 1996
Stable adducts of nerve agents sarin, soman and cyclosarin with TRIS, TES and related buffer compounds—Characterization by LC-ESI-MS/MS and NMR and implications for analytical chemistry Gäb, Jürgen; John, Harald; Melzer, Marco Journal of Chromatography B, Vol. 878, Issue 17-18 https://doi.org/10.1016/j.jchromb.2010.01.043	journal	May 2010
Optimizing harvest of corn stover fractions based on overall sugar yields following ammonia fiber expansion pretreatment and enzymatic hydrolysis Garlock, Rebecca J.; Chundawat, Shishir PS; Balan, Venkatesh Biotechnology for Biofuels, Vol. 2, Issue 1 https://doi.org/10.1186/1754-6834-2-29	journal	January 2009
Site-directed mutagenesis at aspartate and glutamate residues of xylanase from Bacillus pumilus Ko, E. P.; Akatsuka, H.; Moriyama, H. Biochemical Journal, Vol. 288, Issue 1 https://doi.org/10.1042/bj2880117	journal	November 1992
Substrate Dependency and Effect of Xylanase Supplementation on Enzymatic Hydrolysis of Ammonia-Treated Biomass Gupta, Rajesh; Kim, Tae Hyun; Lee, Yoon Y. Applied Biochemistry and Biotechnology, Vol. 148, Issue 1-3 https://doi.org/10.1007/s12010-007-8071-5	journal	October 2007
Glycosidase mechanisms Vasella, Andrea; Davies, Gideon J.; Böhm, Matthias Current Opinion in Chemical Biology, Vol. 6, Issue 5 https://doi.org/10.1016/S1367-5931(02)00380-0	journal	October 2002
Itineraries of enzymatically and non-enzymatically catalyzed substitutions at O-glycopyranosidic bonds Nerinckx, Wim; Desmet, Tom; Claeyssens, Marc Arkivoc, Vol. 2006, Issue 13, p. 90-116 https://doi.org/10.3998/ark.5550190.0007.d10	journal	August 2006
Mutational and crystallographic analyses of the active site residues of the bacillus circulans xylanase Wakarchuk, Warren W.; Campbell, Robert L.; Sung, Wing L. Protein Science, Vol. 3, Issue 3 https://doi.org/10.1002/pro.5560030312	journal	March 1994
Sugar Ring Distortion in the Glycosyl-Enzyme Intermediate of a Family G/11 Xylanase ^† ^, ^‡ Sidhu, Gary; Withers, Stephen G.; Nguyen, Nham T. Biochemistry, Vol. 38, Issue 17 https://doi.org/10.1021/bi982946f	journal	April 1999
The p K _a of the General Acid/Base Carboxyl Group of a Glycosidase Cycles during Catalysis: A ¹³ C-NMR Study of Bacillus circulans Xylanase ^† McIntosh, Lawrence P.; Hand, Greg; Johnson, Philip E. Biochemistry, Vol. 35, Issue 31 https://doi.org/10.1021/bi9613234	journal	January 1996
Structural Comparison of Two Major endo-1,4-Xylanases from Trichoderma reesei Torronen, Anneli; Rouvinen, Juha Biochemistry, Vol. 34, Issue 3 https://doi.org/10.1021/bi00003a019	journal	January 1995
A Secondary Xylan-binding Site Enhances the Catalytic Activity of a Single-domain Family 11 Glycoside Hydrolase Ludwiczek, Martin L.; Heller, Markus; Kantner, Terrence Journal of Molecular Biology, Vol. 373, Issue 2 https://doi.org/10.1016/j.jmb.2007.07.057	journal	October 2007
Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants Wan, Qun; Kovalevsky, Andrey; Zhang, Qiu Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 69, Issue 3 https://doi.org/10.1107/S1744309113001164	journal	February 2013
Crystallographic Snapshots of an Entire Reaction Cycle for a Retaining Xylanase from Streptomyces olivaceoviridis E-86 Suzuki, Ryuichiro; Fujimoto, Zui; Ito, Shigeyasu The Journal of Biochemistry, Vol. 146, Issue 1 https://doi.org/10.1093/jb/mvp047	journal	March 2009
Covalent Binding of Three Epoxyalkyl Xylosides to the Active Site of endo -1,4-Xylanase II from Trichoderma reesei ^† ^, ^‡ Havukainen, Riikka; Törrönen, Anneli; Laitinen, Tuomo Biochemistry, Vol. 35, Issue 29 https://doi.org/10.1021/bi953052n	journal	January 1996
Strategies for Modulating the pH-Dependent Activity of a Family 11 Glycoside Hydrolase Ludwiczek, Martin L.; D’Angelo, Igor; Yalloway, Gary N. Biochemistry, Vol. 52, Issue 18 https://doi.org/10.1021/bi400034m	journal	April 2013
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Structures and mechanisms of glycosyl hydrolases Davies, Gideon; Henrissat, Bernard Structure, Vol. 3, Issue 9 https://doi.org/10.1016/S0969-2126(01)00220-9	journal	September 1995
Exploring the Cellulose/Xylan Specificity of the β-1,4-Glycanase Cex from Cellulomonas fimi through Crystallography and Mutation ^† ^, ^‡ Notenboom, Valerie; Birsan, Camelia; Warren, R. Antony J. Biochemistry, Vol. 37, Issue 14 https://doi.org/10.1021/bi9729211	journal	April 1998
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
QM/MM study of catalytic mechanism of Xylanase Cex from Cellulomonas fimi Liu, Jingli; Zhang, Chunchun; Xu, Dingguo Journal of Molecular Graphics and Modelling, Vol. 37 https://doi.org/10.1016/j.jmgm.2012.04.005	journal	July 2012
Distributing many points on a sphere Saff, E. B.; Kuijlaars, A. B. J. The Mathematical Intelligencer, Vol. 19, Issue 1 https://doi.org/10.1007/BF03024331	journal	December 1997
Enzymatic deconstruction of xylan for biofuel production Dodd, Dylan; Cann, Isaac K. O. GCB Bioenergy, Vol. 1, Issue 1 https://doi.org/10.1111/j.1757-1707.2009.01004.x	journal	February 2009
Glycosidase-catalysed synthesis of alkyl glycosides van Rantwijk, F.; Woudenberg-van Oosterom, M.; Sheldon, R. A. Journal of Molecular Catalysis B: Enzymatic, Vol. 6, Issue 6 https://doi.org/10.1016/S1381-1177(99)00042-9	journal	June 1999
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Interlaboratory testing of methods for assay of xylanase activity Bailey, Michael J.; Biely, Peter; Poutanen, Kaisa Journal of Biotechnology, Vol. 23, Issue 3, p. 257-270 https://doi.org/10.1016/0168-1656(92)90074-J	journal	May 1992
Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH Fushinobu, S.; Ito, K.; Konno, M. Protein Engineering Design and Selection, Vol. 11, Issue 12, p. 1121-1128 https://doi.org/10.1093/protein/11.12.1121	journal	December 1998
Mechanisms of enzymatic glycoside hydrolysis McCarter, John D.; Stephen Withers, G. Current Opinion in Structural Biology, Vol. 4, Issue 6 https://doi.org/10.1016/0959-440X(94)90271-2	journal	January 1994
Determination of steady-state kinetic parameters for a xylanase-catalyzed hydrolysis of neutral underivatized xylooligosaccharides by mass spectrometry Jänis, Janne; Pulkkinen, Petri; Rouvinen, Juha Analytical Biochemistry, Vol. 365, Issue 2 https://doi.org/10.1016/j.ab.2007.03.034	journal	June 2007
The activity of family 11 xylanases at alkaline pH Gibbs, M. D.; Reeves, R. A.; Hardiman, E. M. New Biotechnology, Vol. 27, Issue 6 https://doi.org/10.1016/j.nbt.2010.06.004	journal	December 2010
Conformational Analyses of the Reaction Coordinate of Glycosidases Davies, Gideon J.; Planas, Antoni; Rovira, Carme Accounts of Chemical Research, Vol. 45, Issue 2 https://doi.org/10.1021/ar2001765	journal	August 2011
Structural and functional properties of low molecular weight endo-1,4-β -xylanases Törrönen, Anneli; Rouvinen, Juha Journal of Biotechnology, Vol. 57, Issue 1-3 https://doi.org/10.1016/S0168-1656(97)00095-3	journal	September 1997
A Simple Assay for Xylanase Using o -Nitrophenyl- β - D -xylobioside Taguchi, Hisataka; Hamasaki, Tohru; Akamatsu, Takashi Bioscience, Biotechnology, and Biochemistry, Vol. 60, Issue 6 https://doi.org/10.1271/bbb.60.983	journal	January 1996
Understanding the Structural Basis for Substrate and Inhibitor Recognition in Eukaryotic GH11 Xylanases Vardakou, Maria; Dumon, Claire; Murray, James W. Journal of Molecular Biology, Vol. 375, Issue 5 https://doi.org/10.1016/j.jmb.2007.11.007	journal	February 2008
Insights into transition state stabilization of the β-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants Notenboom, Valerie; Birsan, Camelia; Nitz, Mark Nature Structural Biology, Vol. 5, Issue 9 https://doi.org/10.1038/1852	journal	September 1998
Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry Zolotnitsky, G.; Cogan, U.; Adir, N. Proceedings of the National Academy of Sciences, Vol. 101, Issue 31 https://doi.org/10.1073/pnas.0404311101	journal	July 2004
Nomenclature for sugar-binding subsites in glycosyl hydrolases Davies, Gideon J.; Wilson, Keith S.; Henrissat, Bernard Biochemical Journal, Vol. 321, Issue 2 https://doi.org/10.1042/bj3210557	journal	January 1997
Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display ^2,5 B conformations at the active centre Sabini, Elisabetta; Wilson, Keith S.; Danielsen, Steffen Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 9 https://doi.org/10.1107/S0907444901010873	journal	August 2001
Enzymology and Evolution of the Pyruvate Pathway to 2-Oxobutyrate in Methanocaldococcus jannaschii Drevland, R. M.; Waheed, A.; Graham, D. E. Journal of Bacteriology, Vol. 189, Issue 12 https://doi.org/10.1128/JB.00166-07	journal	April 2007
Crystallographic analysis shows substrate binding at the −3 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-β-xylanases Vandermarliere, Elien; Bourgois, Tine M.; Rombouts, Sigrid Biochemical Journal, Vol. 410, Issue 1 https://doi.org/10.1042/BJ20071128	journal	January 2008
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Mapping the conformational itinerary of β-glycosidases by X-ray crystallography Davies, G. J.; Ducros, V. M. -A.; Varrot, A. Biochemical Society Transactions, Vol. 31, Issue 3 https://doi.org/10.1042/bst0310523	journal	June 2003

Similar Records

X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism

Journal Article · Tue Dec 23 00:00:00 EST 2014 · Acta Crystallogr. D · OSTI ID:1117460

Wan, Qun; Zhang, Qiu; Hamilton-Brehm, Scott; +6 more

Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography

Journal Article · Sat Oct 31 00:00:00 EDT 2020 · The Protein Journal · OSTI ID:1117460

Li, Zhihong; Zhang, Xiaoshuai; Li, Chunran; +2 more

Cloning, recombinant production, crystallization and preliminary X-ray diffraction studies of a family 84 glycoside hydrolase from Clostridium perfringens

Journal Article · Thu Sep 01 00:00:00 EDT 2005 · Acta Crystallographica. Section F · OSTI ID:1117460

Ficko-Blean, Elizabeth

Title: X-ray Crystallographic Studies of Family 11 Xylanase Michaelis and Product Complexes: Implications for the Catalytic Mechanism of Retaining Glycoside Hydrolases

Citation Formats

References (57)

Similar Records

Related Subjects