Identification and structural analysis of a thermophilic β-1,3-glucanase from compost
Abstract
β-1,3-glucanase can specifically hydrolyze glucans to oligosaccharides and has potential applications in biotechnology. We used the metatranscriptomic technology to discover a thermophilic β-1,3-glucanase from compost. The phylogenetic study shows that it belongs to the family 16 glycoside hydrolase (GH16) and is most homologous with an enzyme from Streptomyces sioyaensis, an actinobacterium. It has the activity of 146.9 U/mg in the optimal reaction condition (75 °C and pH 5.5). Its catalytic domain was crystallized and diffracted to 1.14 Å resolution. The crystal structure shows a sandwich-like β-jelly-roll fold with two disulfide bonds. After analyzing the occurring frequencies of these cysteine residues, we designed two mutants (C160G and C180I) to study the role of these disulfide bonds. Both mutants have decreased their optimal temperature from 75 to 70 °C, which indicate that the disulfide bonds are important to maintain thermostability. Interestingly, the activity of C160G has increased ~ 17% to reach 171.4 U/mg. We speculate that the increased activity of C160G mutant is due to increased dynamics near the active site. Our studies give a good example of balancing the rigidity and flexibility for enzyme activity, which is helpful for protein engineering.
- Authors:
-
[3];
[1]
- Nanjing Agricultural University (China)
- Zhejiang Univ. of Technology, Hangzhou (China). Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Qingdao Vland Biotech Group Inc., Qingdao (China)
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1830100
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Bioresources and Bioprocessing
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2197-4365
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; β-1,3-glucanase; Crystal structure; Disulfde bond; Mutagenesis; Molecular dynamics
Citation Formats
Feng, Jianwei, Xu, Shenyuan, Feng, Ruirui, Kovalevsky, Andrey, Zhang, Xia, Liu, Dongyang, and Wan, Qun. Identification and structural analysis of a thermophilic β-1,3-glucanase from compost. United States: N. p., 2021.
Web. doi:10.1186/s40643-021-00449-4.
Feng, Jianwei, Xu, Shenyuan, Feng, Ruirui, Kovalevsky, Andrey, Zhang, Xia, Liu, Dongyang, & Wan, Qun. Identification and structural analysis of a thermophilic β-1,3-glucanase from compost. United States. https://doi.org/10.1186/s40643-021-00449-4
Feng, Jianwei, Xu, Shenyuan, Feng, Ruirui, Kovalevsky, Andrey, Zhang, Xia, Liu, Dongyang, and Wan, Qun. Sun .
"Identification and structural analysis of a thermophilic β-1,3-glucanase from compost". United States. https://doi.org/10.1186/s40643-021-00449-4. https://www.osti.gov/servlets/purl/1830100.
@article{osti_1830100,
title = {Identification and structural analysis of a thermophilic β-1,3-glucanase from compost},
author = {Feng, Jianwei and Xu, Shenyuan and Feng, Ruirui and Kovalevsky, Andrey and Zhang, Xia and Liu, Dongyang and Wan, Qun},
abstractNote = {β-1,3-glucanase can specifically hydrolyze glucans to oligosaccharides and has potential applications in biotechnology. We used the metatranscriptomic technology to discover a thermophilic β-1,3-glucanase from compost. The phylogenetic study shows that it belongs to the family 16 glycoside hydrolase (GH16) and is most homologous with an enzyme from Streptomyces sioyaensis, an actinobacterium. It has the activity of 146.9 U/mg in the optimal reaction condition (75 °C and pH 5.5). Its catalytic domain was crystallized and diffracted to 1.14 Å resolution. The crystal structure shows a sandwich-like β-jelly-roll fold with two disulfide bonds. After analyzing the occurring frequencies of these cysteine residues, we designed two mutants (C160G and C180I) to study the role of these disulfide bonds. Both mutants have decreased their optimal temperature from 75 to 70 °C, which indicate that the disulfide bonds are important to maintain thermostability. Interestingly, the activity of C160G has increased ~ 17% to reach 171.4 U/mg. We speculate that the increased activity of C160G mutant is due to increased dynamics near the active site. Our studies give a good example of balancing the rigidity and flexibility for enzyme activity, which is helpful for protein engineering.},
doi = {10.1186/s40643-021-00449-4},
journal = {Bioresources and Bioprocessing},
number = 1,
volume = 8,
place = {United States},
year = {Sun Oct 17 00:00:00 EDT 2021},
month = {Sun Oct 17 00:00:00 EDT 2021}
}
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Works referenced in this record:
Engineering disulfide bonds in Selenomonas ruminantium β-xylosidase by experimental and computational methods
journal, February 2017
- Dehnavi, Ehsan; Fathi-Roudsari, Mehrnoosh; Mirzaie, Sako
- International Journal of Biological Macromolecules, Vol. 95
Metagenome and Metatranscriptome Analyses Using Protein Family Profiles
journal, July 2016
- Zhong, Cuncong; Edlund, Anna; Yang, Youngik
- PLOS Computational Biology, Vol. 12, Issue 7
Crystal structural basis for Rv0315, an immunostimulatory antigen and inactive beta-1,3-glucanase of Mycobacterium tuberculosis
journal, October 2015
- Dong, Wanyu; Huang, Junhua; Li, Yanan
- Scientific Reports, Vol. 5, Issue 1
Gene finding in metatranscriptomic sequences
journal, September 2014
- Ismail, Wazim Mohammed; Ye, Yuzhen; Tang, Haixu
- BMC Bioinformatics, Vol. 15, Issue S9
SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection
journal, September 2020
- Jin, Xiaopeng; Liao, Qing; Wei, Hang
- Bioinformatics, Vol. 37, Issue 7
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997
- Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
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
Carbohydrate Binding Modules: Biochemical Properties and Novel Applications
journal, June 2006
- Shoseyov, O.; Shani, Z.; Levy, I.
- Microbiology and Molecular Biology Reviews, Vol. 70, Issue 2
The 1.3 Å crystal structure of a novel endo-β-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96
journal, August 2007
- Fibriansah, Guntur; Masuda, Sumiko; Koizumi, Naoya
- Proteins: Structure, Function, and Bioinformatics, Vol. 69, Issue 3
Comparative Protein Structure Modeling Using MODELLER
journal, June 2016
- Webb, Benjamin; Sali, Andrej
- Current Protocols in Bioinformatics, Vol. 54, Issue 1
Enzyme systems of thermophilic anaerobic bacteria for lignocellulosic biomass conversion
journal, January 2021
- Singh, Nisha; Mathur, Anshu S.; Gupta, Ravi P.
- International Journal of Biological Macromolecules, Vol. 168
Insights into the functionality of fungal community during the large scale aerobic co-composting process of swine manure and rice straw
journal, September 2020
- Wang, Xuanqing; Kong, Zhijian; Wang, Yonghong
- Journal of Environmental Management, Vol. 270
Protein release and foaming in Escherichia coli cultures grown in minimal medium
journal, October 1996
- Törnkvist, M.; Larsson, G.; Enfors, S. -O.
- Bioprocess Engineering, Vol. 15, Issue 5
Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011
- Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran
- Nature Biotechnology, Vol. 29, Issue 7
ESPript: analysis of multiple sequence alignments in PostScript
journal, April 1999
- Gouet, P.; Courcelle, E.; Stuart, D.
- Bioinformatics, Vol. 15, Issue 4
LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery
journal, October 2011
- Laskowski, Roman A.; Swindells, Mark B.
- Journal of Chemical Information and Modeling, Vol. 51, Issue 10
Dynamic allostery can drive cold adaptation in enzymes
journal, June 2018
- Saavedra, Harry G.; Wrabl, James O.; Anderson, Jeremy A.
- Nature, Vol. 558, Issue 7709
Improving the fermentable sugar yields of wheat straw by high-temperature pre-hydrolysis with thermophilic enzymes of Malbranchea cinnamomea
journal, July 2020
- Zhu, Ning; Jin, Hongmei; Kong, Xiangping
- Microbial Cell Factories, Vol. 19, Issue 1
Molecular identification of a novel β-1,3-glucanase from alkaliphilic Nocardiopsis sp. strain F96
journal, April 2006
- Masuda, Sumiko; Endo, Kimiko; Koizumi, Naoya
- Extremophiles, Vol. 10, Issue 3
Expression and purification of soluble and functional fusion protein DAB 389 IL‐2 into the E. coli strain Rosetta‐gami (DE3)
journal, November 2019
- Zarkar, Nasrin; Nasiri Khalili, Mohammad Ali; Khodadadi, Sirus
- Biotechnology and Applied Biochemistry, Vol. 67, Issue 2
Improved low-resolution crystallographic refinement with Phenix and Rosetta
journal, September 2013
- DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J.
- Nature Methods, Vol. 10, Issue 11
Composting To Inactivate Foodborne Pathogens for Crop Soil Application: A Review
journal, October 2018
- Gurtler, Joshua B.; Doyle, Michael P.; Erickson, Marilyn C.
- Journal of Food Protection, Vol. 81, Issue 11
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
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
Beta-glucans from edible and medicinal mushrooms: Characteristics, physicochemical and biological activities
journal, August 2015
- Zhu, Fengmei; Du, Bin; Bian, Zhaoxiang
- Journal of Food Composition and Analysis, Vol. 41
Isolation and biochemical characterization of an endo-1,3-β-glucanase from Streptomyces sioyaensis containing a C-terminal family 6 carbohydrate-binding module that binds to 1,3-β-glucan The GenBank accession number for the sequence reported in this paper is AF21741.
journal, April 2002
- Hong, Tang-Yao; Cheng, Chun-Wei; Huang, Jenn-Wen
- Microbiology, Vol. 148, Issue 4
Characterization of a Novel Endo-β-galactosidase Specific for Releasing the Disaccharide GlcNAcα1→4Gal from Glycoconjugates ,
journal, January 2002
- Ashida, Hisashi; Maskos, Karol; Li, Su-Chen
- Biochemistry, Vol. 41, Issue 7
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes
journal, July 2006
- Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8
Purification and characterization of four extracellular 1,3- -glucanases of Botrytis cinerea
journal, November 1993
- Stahmann, K. -P.; Schimz, K. -L.; Sahm, H.
- Journal of General Microbiology, Vol. 139, Issue 11
ExPASy: SIB bioinformatics resource portal
journal, May 2012
- Artimo, P.; Jonnalagedda, M.; Arnold, K.
- Nucleic Acids Research, Vol. 40, Issue W1
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
A systematic review on the composting of green waste: Feedstock quality and optimization strategies
journal, July 2018
- Reyes-Torres, M.; Oviedo-Ocaña, E. R.; Dominguez, I.
- Waste Management, Vol. 77
Use of Dinitrosalicylic Acid Reagent for Determination of Reducing Sugar
journal, March 1959
- Miller, G. L.
- Analytical Chemistry, Vol. 31, Issue 3
Ligand docking and binding site analysis with PyMOL and Autodock/Vina
journal, April 2010
- Seeliger, Daniel; de Groot, Bert L.
- Journal of Computer-Aided Molecular Design, Vol. 24, Issue 5
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
Crystal Structures of the Laminarinase Catalytic Domain from Thermotoga maritima MSB8 in Complex with Inhibitors : ESSENTIAL RESIDUES FOR β-1,3- and β-1,4-GLUCAN SELECTION
journal, November 2011
- Jeng, Wen-Yih; Wang, Nai-Chen; Lin, Cheng-Tse
- Journal of Biological Chemistry, Vol. 286, Issue 52
Contributions of the biochemical factors and bacterial community to the humification process of in situ large-scale aerobic composting
journal, March 2021
- Wang, Xuanqing; Wang, Mengmeng; Zhang, Juan
- Bioresource Technology, Vol. 323
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016
- Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
- Molecular Biology and Evolution, Vol. 33, Issue 7
Adaptations of protein structure and function to temperature: there is more than one way to 'skin a cat'
journal, June 2015
- Fields, P. A.; Dong, Y.; Meng, X.
- Journal of Experimental Biology, Vol. 218, Issue 12
Biochemical and genetic characterization of β-1,3 glucanase from a deep subseafloor Laceyella putida
journal, September 2015
- Kobayashi, Tohru; Uchimura, Kohsuke; Kubota, Takaaki
- Applied Microbiology and Biotechnology, Vol. 100, Issue 1
Hot spots in cold adaptation: Localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes
journal, September 1998
- Fields, P. A.; Somero, G. N.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 19
Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance
journal, June 2017
- Oda, Toshiyuki; Lim, Kyungtaek; Tomii, Kentaro
- BMC Bioinformatics, Vol. 18, Issue 1
Thermostability in endoglucanases is fold-specific
journal, January 2011
- Yennamalli, Ragothaman M.; Rader, Andrew J.; Wolt, Jeffrey D.
- BMC Structural Biology, Vol. 11, Issue 1
MOLREP an Automated Program for Molecular Replacement
journal, December 1997
- Vagin, A.; Teplyakov, A.
- Journal of Applied Crystallography, Vol. 30, Issue 6, p. 1022-1025
Recombinant production and characterization of full-length and truncated β-1,3-glucanase PglA from Paenibacillussp. S09
journal, November 2013
- Cheng, Rui; Chen, Jinping; Yu, Xiaohong
- BMC Biotechnology, Vol. 13, Issue 1
Yeasts collectively extend the limits of habitable temperatures by secreting glutathione
journal, April 2020
- Laman Trip, Diederik S.; Youk, Hyun
- Nature Microbiology, Vol. 5, Issue 7
Crystal Structure and Site-directed Mutagenesis of Bacillus macerans Endo-1,31,4--glucanase
journal, February 1995
- Hahn, Michael; Olsen, Ole; Politz, Oliver
- Journal of Biological Chemistry, Vol. 270, Issue 7
Rational design of thermostability in bacterial 1,3-1,4-β-glucanases through spatial compartmentalization of mutational hotspots
journal, September 2016
- Niu, Chengtuo; Zhu, Linjiang; Xu, Xin
- Applied Microbiology and Biotechnology, Vol. 101, Issue 3
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
The 1.5 Å structure of endo-1,3-β-glucanase from Streptomyces sioyaensis : evolution of the active-site structure for 1,3-β-glucan-binding specificity and hydrolysis
journal, August 2008
- Hong, Tang-Yao; Hsiao, Yu-Yuan; Meng, Menghsiao
- Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 9