Engineering glycoside hydrolase stability by the introduction of zinc binding
Abstract
The development of robust enzymes, in particular cellulases, is a key step in the success of biological routes to `second-generation' biofuels. The typical sources of the enzymes used to degrade biomass include mesophilic and thermophilic organisms. The endoglucanase J30 from glycoside hydrolase family 9 was originally identified through metagenomic analyses of compost-derived bacterial consortia. These studies, which were tailored to favor growth on targeted feedstocks, have already been shown to identify cellulases with considerable thermal tolerance. The amino-acid sequence of J30 shows comparably low identity to those of previously analyzed enzymes. As an enzyme that combines a well measurable activity with a relatively low optimal temperature (50°C) and a modest thermal tolerance, it offers the potential for structural optimization aimed at increased stability. Here, the crystal structure of wild-type J30 is presented along with that of a designed triple-mutant variant with improved characteristics for industrial applications. Through the introduction of a structural Zn2+site, the thermal tolerance was increased by more than 10°C and was paralleled by an increase in the catalytic optimum temperature by more than 5°C.
- Authors:
- Publication Date:
- Research Org.:
- Sandia National Lab. (SNL-CA), Livermore, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1457487
- Alternate Identifier(s):
- OSTI ID: 1476933; OSTI ID: 1506325
- Report Number(s):
- SAND-2018-9901J
Journal ID: ISSN 2059-7983; ACSDAD; PII: S2059798318006678
- Grant/Contract Number:
- AC02-76SF00515; AC04-94AL85000; AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Acta Crystallographica. Section D. Structural Biology
- Additional Journal Information:
- Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Volume: 74 Journal Issue: 7; Journal ID: ISSN 2059-7983
- Publisher:
- IUCr
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; glycoside hydrolases; protein engineering; thermal stability; X-ray crystallography
Citation Formats
Ellinghaus, Thomas L., Pereira, Jose H., McAndrew, Ryan P., Welner, Ditte H., DeGiovanni, Andy M., Guenther, Joel M., Tran, Huu M., Feldman, Taya, Simmons, Blake A., Sale, Kenneth L., and Adams, Paul D. Engineering glycoside hydrolase stability by the introduction of zinc binding. United Kingdom: N. p., 2018.
Web. doi:10.1107/S2059798318006678.
Ellinghaus, Thomas L., Pereira, Jose H., McAndrew, Ryan P., Welner, Ditte H., DeGiovanni, Andy M., Guenther, Joel M., Tran, Huu M., Feldman, Taya, Simmons, Blake A., Sale, Kenneth L., & Adams, Paul D. Engineering glycoside hydrolase stability by the introduction of zinc binding. United Kingdom. https://doi.org/10.1107/S2059798318006678
Ellinghaus, Thomas L., Pereira, Jose H., McAndrew, Ryan P., Welner, Ditte H., DeGiovanni, Andy M., Guenther, Joel M., Tran, Huu M., Feldman, Taya, Simmons, Blake A., Sale, Kenneth L., and Adams, Paul D. Wed .
"Engineering glycoside hydrolase stability by the introduction of zinc binding". United Kingdom. https://doi.org/10.1107/S2059798318006678.
@article{osti_1457487,
title = {Engineering glycoside hydrolase stability by the introduction of zinc binding},
author = {Ellinghaus, Thomas L. and Pereira, Jose H. and McAndrew, Ryan P. and Welner, Ditte H. and DeGiovanni, Andy M. and Guenther, Joel M. and Tran, Huu M. and Feldman, Taya and Simmons, Blake A. and Sale, Kenneth L. and Adams, Paul D.},
abstractNote = {The development of robust enzymes, in particular cellulases, is a key step in the success of biological routes to `second-generation' biofuels. The typical sources of the enzymes used to degrade biomass include mesophilic and thermophilic organisms. The endoglucanase J30 from glycoside hydrolase family 9 was originally identified through metagenomic analyses of compost-derived bacterial consortia. These studies, which were tailored to favor growth on targeted feedstocks, have already been shown to identify cellulases with considerable thermal tolerance. The amino-acid sequence of J30 shows comparably low identity to those of previously analyzed enzymes. As an enzyme that combines a well measurable activity with a relatively low optimal temperature (50°C) and a modest thermal tolerance, it offers the potential for structural optimization aimed at increased stability. Here, the crystal structure of wild-type J30 is presented along with that of a designed triple-mutant variant with improved characteristics for industrial applications. Through the introduction of a structural Zn2+site, the thermal tolerance was increased by more than 10°C and was paralleled by an increase in the catalytic optimum temperature by more than 5°C.},
doi = {10.1107/S2059798318006678},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 7,
volume = 74,
place = {United Kingdom},
year = {Wed Jun 27 00:00:00 EDT 2018},
month = {Wed Jun 27 00:00:00 EDT 2018}
}
https://doi.org/10.1107/S2059798318006678
Web of Science
Figures / Tables:
Works referenced in this record:
Calcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D
journal, January 1990
- Chauvaux, S.; Beguin, P.; Aubert, J. P.
- Biochemical Journal, Vol. 265, Issue 1
Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca
journal, October 1997
- Sakon, Joshua; Irwin, Diana; Wilson, David B.
- Nature Structural Biology, Vol. 4, Issue 10
Crystal Structures of A. acidocaldarius Endoglucanase Cel9A in Complex with Cello-Oligosaccharides: Strong −1 and −2 Subsites Mimic Cellobiohydrolase Activity
journal, November 2009
- Eckert, Kelvin; Vigouroux, Armelle; Lo Leggio, Leila
- Journal of Molecular Biology, Vol. 394, Issue 1
Relationship between the architecture of zinc coordination and zinc binding affinity in proteins – insights into zinc regulation
journal, January 2015
- Kochańczyk, Tomasz; Drozd, Agnieszka; Krężel, Artur
- Metallomics, Vol. 7, Issue 2
Biomass deconstruction to sugars
journal, August 2011
- Blanch, Harvey W.; Simmons, Blake A.; Klein-Marcuschamer, Daniel
- Biotechnology Journal, Vol. 6, Issue 9
xia2 : an expert system for macromolecular crystallography data reduction
journal, December 2009
- Winter, G.
- Journal of Applied Crystallography, Vol. 43, Issue 1
Apoprotein Structure and Metal Binding Characterization of a de Novo Designed Peptide, α 3 D IV , that Sequesters Toxic Heavy Metals
journal, April 2015
- Plegaria, Jefferson S.; Dzul, Stephen P.; Zuiderweg, Erik R. P.
- Biochemistry, Vol. 54, Issue 18
Structural and Functional Analysis of the Metal-binding Sites of Clostridium thermocellum Endoglucanase CelD
journal, April 1995
- Chauvaux, Sylvie; Souchon, Hélène; Alzari, Pedro M.
- Journal of Biological Chemistry, Vol. 270, Issue 17
Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement
journal, June 2014
- Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.
- FEBS Journal, Vol. 281, Issue 18
Structures and mechanisms of glycosyl hydrolases
journal, September 1995
- Davies, Gideon; Henrissat, Bernard
- Structure, Vol. 3, Issue 9
Identification of the molecular trigger for allosteric activation in glycogen phosphorylase
journal, May 1994
- Browner, Michelle F.; Hackos, David; Fletterick, Robert
- Nature Structural & Molecular Biology, Vol. 1, Issue 5
Probing the minimal determinants of zinc binding with computational protein design
journal, June 2016
- Guffy, Sharon L.; Der, Bryan S.; Kuhlman, Brian
- Protein Engineering Design and Selection, Vol. 29, Issue 8
Gene cloning, sequencing, and characterization of a family 9 endoglucanase (CelA) with an unusual pattern of activity from the thermoacidophile Alicyclobacillus acidocaldarius ATCC27009
journal, December 2002
- K., Eckert; F., Zielinski; Leggio, L. Lo
- Applied Microbiology and Biotechnology, Vol. 60, Issue 4, p. 428-436
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
De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy
journal, November 2015
- Huang, Po-Ssu; Feldmeier, Kaspar; Parmeggiani, Fabio
- Nature Chemical Biology, Vol. 12, Issue 1
A new default restraint library for the protein backbone in Phenix : a conformation-dependent geometry goes mainstream
journal, January 2016
- Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.
- Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 1
Revealing Nature's Cellulase Diversity The Digestion Mechanism of Caldicellulosiruptor bescii CelA
journal, December 2013
- Brunecky, R.; Alahuhta, M.; Xu, Q.
- Science, Vol. 342, Issue 6165, p. 1513-1516
Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012
- Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
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
The crystal structure of an inverting glycoside hydrolase family 9 exo-β-D-glucosaminidase and the design of glycosynthase
journal, February 2016
- Honda, Yuji; Arai, Sachiko; Suzuki, Kentaro
- Biochemical Journal, Vol. 473, Issue 4
TLSMD web server for the generation of multi-group TLS models
journal, January 2006
- Painter, Jay; Merritt, Ethan A.
- Journal of Applied Crystallography, Vol. 39, Issue 1
Three-dimensional structure of a thermostable bacterial cellulase
journal, May 1992
- Juy, Michel; Amrt, Adolfo G.; Alzari, Pedro M.
- Nature, Vol. 357, Issue 6373
Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius
journal, July 2009
- Pereira, Jose Henrique; Sapra, Rajat; Volponi, Joanne V.
- Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 8, p. 744-750
Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community
journal, January 2014
- Gladden, John M.; Park, Joshua I.; Bergmann, Jessica
- Biotechnology for Biofuels, Vol. 7, Issue 1
Reassembly and co-crystallization of a family 9 processive endoglucanase from its component parts: structural and functional significance of the intermodular linker
journal, January 2015
- Petkun, Svetlana; Rozman Grinberg, Inna; Lamed, Raphael
- PeerJ, Vol. 3
Zinc-Binding Cysteines: Diverse Functions and Structural Motifs
journal, April 2014
- Pace, Nicholas; Weerapana, Eranthie
- Biomolecules, Vol. 4, Issue 2
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
journal, March 2006
- Painter, Jay; Merritt, Ethan A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 4
Scaling and assessment of data quality
journal, December 2005
- Evans, Philip
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82
Structure of an endoglucanase from termite, Nasutitermes takasagoensis
journal, March 2002
- Khademi, Shahram; Guarino, Linda A.; Watanabe, Hirofumi
- Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 4
Sparse matrix sampling: a screening method for crystallization of proteins
journal, August 1991
- Jancarik, J.; Kim, S. H.
- Journal of Applied Crystallography, Vol. 24, Issue 4
Structural Basis for the Exocellulase Activity of the Cellobiohydrolase CbhA from Clostridium thermocellum †
journal, February 2004
- Schubot, Florian D.; Kataeva, Irina A.; Chang, Jessie
- Biochemistry, Vol. 43, Issue 5
Integration, scaling, space-group assignment and post-refinement
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144
Structure of the catalytic domain of the Clostridium thermocellum cellulase CelT
journal, February 2012
- Kesavulu, Muppuru M.; Tsai, Jia-Yin; Lee, Hsiao-Lin
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 3
Ab initio protein structure prediction of CASP III targets using ROSETTA
journal, January 1999
- Simons, Kim T.; Bonneau, Rich; Ruczinski, Ingo
- Proteins: Structure, Function, and Genetics, Vol. 37, Issue S3
Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
journal, July 2013
- D'haeseleer, Patrik; Gladden, John M.; Allgaier, Martin
- PLoS ONE, Vol. 8, Issue 7, Article No. e68465
Berkeley Screen: a set of 96 solutions for general macromolecular crystallization
journal, September 2017
- Pereira, Jose H.; McAndrew, Ryan P.; Tomaleri, Giovani P.
- Journal of Applied Crystallography, Vol. 50, Issue 5
Crystal structure of endo-1,4-β-glucanase from Eisenia fetida
journal, October 2013
- Arimori, Takao; Ito, Akihiro; Nakazawa, Masami
- Journal of Synchrotron Radiation, Vol. 20, Issue 6
X-Ray Crystal Structure of the Multidomain Endoglucanase Cel9G from Clostridium cellulolyticum Complexed with Natural and Synthetic Cello-Oligosaccharides
journal, July 2003
- Mandelman, D.; Belaich, A.; Belaich, J. P.
- Journal of Bacteriology, Vol. 185, Issue 14
Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community
journal, January 2010
- Allgaier, Martin; Reddy, Amitha; Park, Joshua I.
- PLoS ONE, Vol. 5, Issue 1
The crystal structure of the processive endocellulase CelF of Clostridium cellulolyticum in complex with a thiooligosaccharide inhibitor at 2.0Aresolution
journal, October 1998
- Parsiegla, G.
- The EMBO Journal, Vol. 17, Issue 19
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Crystal Structure of the Cellulase Cel9M Enlightens Structure/Function Relationships of the Variable Catalytic Modules in Glycoside Hydrolases
journal, September 2002
- Parsiegla, G.; Belaïch, A.; Belaïch, J. P.
- Biochemistry, Vol. 41, Issue 37
Structure, activity, and stability of metagenome-derived glycoside hydrolase family 9 endoglucanase with an N-terminal Ig-like domain: Structure of Metagenome-Derived Cellulase
journal, January 2015
- Okano, Hiroyuki; Kanaya, Eiko; Ozaki, Masashi
- Protein Science, Vol. 24, Issue 3
Figures / Tables found in this record: