Glycoside Hydrolases provides a detailed overview of the biochemical, biophysical, and protein engineering properties of glycoside hydrolases, a class of enzymes in growing use across various applications. Here, more than a dozen global experts discuss the structural and catalytic mechanisms of specific glycoside hydrolases, followed by their implications in biotechnological applications of different industrial sectors such as the food and feed industry, paper and pulp industry, the bioenergy sector and the pharmaceutical industry. Authors consider how the application of glycoside hydrolases may boost industrial production of valued products, and the broader environmental and sustainability goals of converting agrowaste into valued products. This book helps researchers and students across industry and academia gain deep knowledge of glycoside hydrolases, to advance new experimental research and applications from biofuel to drug discovery.
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Table of Contents
Contributors
About the Editors
Preface
CHAPTER 1 Carbohydrates and Carbohydrate-Active enZymes (CAZyme): An overview
Parmeshwar Vitthal Gavande, Arun Goyal, and Carlos M.G.A. Fontes
1.1 Introduction
1.1.1 Various carbohydrate polymers present in nature
1.1.2 Natural source of polysaccharides
1.1.3 Requirement for deconstruction of carbohydrates
1.1.4 Carbohydrate-active enzymes
1.1.5 Carbohydrate-active enzyme database (CAZy)
1.1.6 Multienzyme complexes of CAZyme: The cellulosome
1.1.7 Commercially available CAZyme libraries
1.2 Conclusion
References
CHAPTER 2 Glycoside hydrolases: Mechanisms, specificities, and engineering
Antoni Planas
2.1 Structures, functions, and classifications
2.2 Glycosidase mechanisms for hydrolysis of glycans and glycoconjugates
2.2.1 General mechanisms: Inverting vs. retaining
2.2.2 Retaining glycosidases with enzyme nucleophile: Ring distortion and covalent intermediate
2.2.3 Retaining glycosidases by substrate-assisted catalysis: Oxazoline/oxazolonium intermediate
2.2.4 Retaining glycosidases by neighboring-group participation through a 1,2-epoxide intermediate
2.2.5 Retaining glycosidases by an unusual NAD+-dependent mechanism
2.2.6 Inverting glycosidases
2.3 Protein engineering of glycosidases for improved and novel properties
2.3.1 Thermostability
2.3.2 Substrate specificity
2.4 Glycosidases acting in reverse for glycosynthesis: Transglycosidases and glycosynthases
2.4.1 Transglycosidases
2.4.2 Glycosynthases
2.5 Concluding remarks
References
CHAPTER 3 Endo-?-1,4-glucanase
Parmeshwar Vitthal Gavande and Arun Goyal
3.1 Introduction
3.1.1 Cellulase
3.1.2 Cellulase evolution and conservation in nature
3.1.3 Endo-?-1,4-glucanase
3.1.4 Exoglucanase
3.1.5 ?-glucosidase
3.1.6 Cellulosome
3.2 Endoglucanases belong to various GH families
3.2.1 GH5 family
3.2.2 GH6 family
3.2.3 GH7 family
3.2.4 GH8 family
3.2.5 GH9 family
3.2.6 GH12 family
3.2.7 GH44 family
3.2.8 GH45 family
3.2.9 GH48 family
3.3 Synergism of endo-?-1,4-glucanase with exoglucanase and ?-glucosidase
3.4 Endo-?-1,4-glucanase-producing microorganisms
3.4.1 Biochemical properties, kinetics, and catalytic efficiency of endoglucanases
3.5 Structure of endo-?-1,4-glucanases
3.5.1 Mechanism of cellulose hydrolysis in endoglucanases
3.6 Multifunctionality of endoglucanases
3.6.1 Broad substrate specificity of various endoglucanases
3.6.2 Significance of multifunctional endoglucanases
3.7 Processivity of endoglucanases
3.8 Applications of endoglucanases
3.9 Conclusion
Authors' contribution
References
CHAPTER 4 Cellobiohydrolases
Tulika Sinha, Kanika Sharma, and Syed Shams Yazdani
4.1 Introduction
4.2 Structure and mode of action of cellobiohydrolases
4.2.1 The catalytic domain (CD)
4.2.2 The carbohydrate-binding module (CBM)
4.2.3 The linker
4.2.4 The dissociation mechanism of processive CBH1
4.3 Biochemical and biophysical properties of cellobiohydrolases
4.3.1 pH and temperature
4.3.2 Metal ions
4.3.3 Surfactants
4.4 Protein engineering and strain improvement for higher enzyme activity and productivity
4.4.1 Enhanced activity
4.4.2 Enhanced thermostability
4.4.3 Enhanced performance in nonconventional media
4.4.4 Engineering cellulase for pH stability
4.5 Industrial applications of CBH
4.5.1 Bioconversion
4.5.2 Pulp and paper industry
4.5.3 Food processing industry
4.5.4 Textile industry
4.5.5 Agriculture
4.5.6 Animal feed
4.5.7 Detergent industry
4.6 Conclusion and future perspective
References
CHAPTER 5 ?-Glucosidase: Structure, function and industrial applications
Sauratej Sengupta, Maithili Datta, and Supratim Datta
5.1 Introduction
5.2 Classification
5.3 Structure
5.4 Reaction mechanism
5.4.1 Substrate recognition and specificity
5.4.2 Glycone and aglycone specificity
5.5 Function and distribution
5.6 Characteristics
5.6.1 Biophysical characteristics
5.6.2 Biochemical characteristics
5.6.3 Product inhibition and enhancement of activity in the presence of glucose
5.6.4 Substrate inhibition
5.7 Industrial applications
5.7.1 Biofuels
5.7.2 Food industry
5.7.3 Pharmaceutical industries
Acknowledgments
References
CHAPTER 6 Endo-?-1,3-glucanase
Parmeshwar Vitthal Gavande and Arun Goyal
6.1 Introduction
6.2 The role of endo-?-1,3-glucanase in nature
6.2.1 ?-1,3-Glucan
6.2.2 Exo-?-1,3-glucanase
6.2.3 Endo-?-1,3-glucanase
6.2.4 Classification of endo-?-1,3-glucanases
6.3 Sources of endo-?-1,3-glucanase
6.4 Endo-?-1,3-glucanases of different families, their structure, and mechanism
6.4.1 The family GH5
6.4.2 The family GH16
6.4.3 The family GH17
6.4.4 The family GH55
6.4.5 The family GH64
6.4.6 The family GH81
6.4.7 The family GH128, GH152, GH157, GH158
6.5 Applications of endo-?-1,3-glucanases
6.6 Conclusion
References
Further reading
CHAPTER 7 Diversity of microbial endo-?-1,4-xylanases
Peter Biely, Katari�na S?uchova�, and Vladimi�r Puchart
7.1 Introduction
7.2 Chemical structure of plant xylans
7.3 Enzymes of xylan hydrolysis
7.4 Endoxylanases-Xylan depolymerizing enzymes
7.4.1 Molecular architecture of xylanases
7.4.2 Classification into glycoside hydrolase families
7.4.3 Mode of action and structure-function relationship
7.5 Synergism of endoxylanases with debranching xylanolytic enzymes
7.6 Application of xylanases
7.7 Conclusions and future prospects
References
CHAPTER 8 ?-D-Xylosidases: Structure-based substrate specificities and their applications
Satoshi Kaneko and Zui Fujimoto
8.1 Introduction
8.2 Structures of ?-xylosidases
8.2.1 GH3
8.2.2 GH39
8.2.3 GH43
8.2.4 GH52
8.2.5 GH120
8.2.6 Other families
8.3 Substrate specificities of the ?-xylosidases
8.3.1 GH1
8.3.2 GH2
8.3.3 GH3
8.3.4 GH5
8.3.5 GH10
8.3.6 GH11
8.3.7 GH30
8.3.8 GH39
8.3.9 GH43
8.3.10 GH51
8.3.11 GH52
8.3.12 GH54
8.3.13 GH116
8.3.14 GH120
8.4 Applications of ?-xylosidases
References
CHAPTER 9 Arabinofuranosidases
Priyanka Pisalwar, Austin Fernandes, Devashish Tribhuvan, Saurav Gite, and Shadab Ahmed
9.1 Introduction
9.2 Classification
9.2.1 Classification on the basis of substrate specificity and mechanism of action
9.2.2 Classification on the basis of amino acid sequencing and structural similarity
9.3 Structural and functional characteristics of arabinofuranosidases
9.3.1 Effect of metal ions
9.3.2 Carbohydrate-binding modules (CBM) associated with arabinofuranosidases
9.4 Substrate specificity and biochemical properties of arabinofuranosidases
9.4.1 Substrate specificity
9.4.2 Physical and chemical properties
9.5 Industrial applications of arabinofuranosidase
9.5.1 Biofuel and biochemical industry
9.5.2 Food and animal feed industry
9.5.3 Beverage industry
9.5.4 Paper and pulp industry
9.5.5 Probiotic and pharmaceutical industry
9.6 Future trends and scope of arabinofuranosidases
9.6.1 Protein engineering
9.6.2 Development of new modular enzymes with enhanced substrate degradation potential
9.7 Conclusions
References
CHAPTER 10 Glycoside hydrolase family 16-Xyloglucan:xyloglucosyl transferases and their roles in plant cell wall structure and mechanics
Barbora Stratilova�, Stanislav Kozmon, Eva Stratilova�, and Maria Hrmova
10.1 Plant cell walls are protective multicomposite hydrogels
10.1.1 Plant cell wall composition and function
10.1.2 Plant cell wall structure and organization
10.2 Plant xyloglucan:xyloglucosyl transferases
10.2.1 Nomenclature and classification
10.2.2 Catalytic mechanism
10.2.3 Structural properties
10.2.4 Enzyme activity methods
10.2.5 Reactions with xyloglucan-derived and other substrates
10.2.6 Genetics approaches to the XTH gene function
10.3 The function of XTH enzymes in plant cell walls
10.3.1 Plant cell wall dynamics
10.3.2 Roles of XTH enzymes in cell wall restructuring
10.4 Conclusions and future directions
Author contributions
Funding
Conflict of interest
References
CHAPTER 11 Endo-arabinase: Source and application
Dixita Chettri and Anil Kumar Verma
11.1 Introduction
11.2 Hemicellulose structure and hydrolysis of arabinans
11.3 Source and biochemical characteristics
11.4 Structure and mechanism of action
11.5 Application of arabinase
11.6 Safety assessment
11.7 Conclusion and future prospects
Acknowledgment
Conflict of interest
References
CHAPTER 12 Overview of structure-function relationships of glucuronidases
Samar Ballabha Mohapatra and Narayanan Manoj
12.1 Introduction
12.2 Xylanolytic ?-glucuronidases
12.2.1 GH67 ?-glucuronidases
12.2.2 GH115 ?-glucuronidases
12.3 Non-xylanolytic GH4 ?-glucuronidase
12.3.1 Active site architecture and the substrate specificity of GH4 TmAgu4B
12.3.2 Mechanism of hydrolysis by GH4 AguA
12.4 ?-Glucuronidases
12.4.1 GH1 ?-glucuronidase
12.4.2 GH2 ?-glucuronidases
12.4.3 GH30 ?-glucuronidase
12.4.4 GH79 ?-glucuronidases
12.4.5 GH154 ?-glucuronidase
12.4.6 GH169 ?-glucuronidase
12.5 Perspectives on the development of applications of glucuronidases
12.5.1 Xylanolytic ?-glucuronidases
12.5.2 Inhibitors of ?-glucuronidases
Credit
References
CHAPTER 13 Mannanases and other mannan-degrading enzymes
Caio Cesar de Mello Capetti, Andrei Nicoli Gebieluca Dabul, Vanessa de Oliveira Arnoldi Pellegrini, and Igor Polikarpov
13.1 Mannan structure
13.2 Enzymes involved in the mannan degradation
13.2.1 ?-mannanases
13.2.2 Other enzymes important for mannan degradation
13.3 Production of ?-mannanases
13.4 Industrial applications of ?-mannanases
13.4.1 Oil drilling
13.4.2 Biofuel production
13.4.3 Production of manno-oligosaccharides
13.4.4 Paper and pulp production
13.4.5 Textile industry
13.4.6 Detergents
13.4.7 Pharmaceutical and food industry
13.5 Concluding remarks
References
CHAPTER 14 Structure, function, and protein engineering of GH53 ?-1,4-galactanases
Sebastian J. Muderspach, Kenneth Jensen, Kristian B.R.M. Krogh, and Leila Lo Leggio
14.1 Introduction, classification, and structure overview of ?-1,4-galactanases
14.2 Biological functions and diversity
14.2.1 Galactans in the plant cell walls
14.2.2 Degradation of plant cell wall galactans in plant pathogens via GH53 enzymes
14.2.3 Characterized GH53 galactanases from human gut microbiome
14.2.4 Plant cell wall remodeling for mobilization of energy resources or fruit ripening
14.2.5 GH53 galactanases from extremophiles
14.3 Related enzyme activities
14.3.1 Other microbial endo-galactanases
14.3.2 ?-galactosidases and exo-?-1,4-galactanases
14.3.3 ?-L-arabinofuranosidase and endo-1,5-?-L-arabinanase
14.4 GH53-associated modules and domains
14.4.1 Association of GH53 with carbohydrate-binding modules
14.4.2 Association of GH53 with other domains
14.5 Biotechnological applications
14.5.1 GH53 galactanases in enzymatic degradation of biomass
14.5.2 Prebiotic galactooligosaccharide production
14.5.3 Other industrial uses
14.6 Structure-function studies
14.6.1 Conformation of substrate in a computationally derived BlGal-galactononaose complex
14.6.2 Substrate-binding sites in GH53 galactanase crystal structures and their implication on product profile
14.6.3 Structural features inducing thermostability in GH53 galactanases
14.6.4 Prediction of structural features from sequence alignments and AlphaFold models
14.7 Protein engineering
14.7.1 Modulating thermostability and pH optimum
14.7.2 Changing the product profile
14.8 Conclusions and future directions
References
CHAPTER 15 Structural and functional insights and applications of ? galactosidase
Azra Shafi and Qayyum Husain
15.1 ? Galactosidase
15.2 Glycoside hydrolase families
15.3 Sources of ?-galactosidases
15.3.1 Bacterial ?-Gals
15.3.2 ?-Gals from filamentous fungi
15.3.3 ?-Gals from yeasts
15.3.4 ?-Gals from plants
15.3.5 ?-Gals from animals
15.3.6 Recombinant ?-Gals
15.4 Lactose intolerance
15.5 Structural characterization of ?-Gal
15.5.1 The active site
15.5.2 Metal binding sites
15.6 Functional characterization of ?-Gal
15.6.1 Mode of action and reaction mechanism
15.6.2 Hydrolysis and transgalactosylation activities of ?-Gal
15.7 Applications of ?-Gal
15.7.1 Lactose-hydrolyzed milks
15.7.2 ?-Gal supplements
15.7.3 Treatment of industry effluents
15.7.4 Synthesis of GOS
15.7.5 Reactors and biosensors
15.8 Conclusion
References
CHAPTER 16 ?-L-Rhamnosidases: Structures, substrate specificities, and their applications
Satoshi Kaneko and Zui Fujimoto
16.1 Introduction
16.2 Structure of ?-L-rhamnosidases
16.2.1 GH78
16.2.2 GH106
16.3 Substrate specificities of ?-L-rhamnosidases
16.3.1 GH78
16.3.2 GH106
16.3.3 Unknown family
16.4 Applications of ?-L-rhamnosidases
References
CHAPTER 17 Diversity and biotechnological applications of microbial glucoamylases
Sanjeev Kumar, Priyakshi Nath, Arindam Bhattacharyya, Suman Mazumdar, Rudrarup Bhattacharjee, and T. Satyanarayana
17.1 Introduction
17.2 Production of glucoamylase: Microbes, substrate, nutrients, and fermentation system
17.3 Thermophilic and mesophilic fungal glucoamylases
17.4 Production of native glucoamylases
17.5 Recombinant glucoamylases
17.6 Multiple molecular forms of glucoamylases
17.7 Structural characteristics of glucoamylases
17.8 Biotechnological applications of glucoamylase
17.9 Role of glucoamylase in starch conversion to sugar syrup
17.10 Role of glucoamylase in HFCS
17.11 Role of glucoamylase in the brewing and baking industry
17.12 Conclusion
References
Index
Authors
Arun Goyal Professor and Former Head, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India.. Prof. Arun Goyal, M.Sc., M.Tech., Ph.D., is currently a Professor in the Department of Biosciences and Bioengineering, at the Indian Institute of Technology Guwahati, in Assam, India. Prof. Goyal has over 18 years of teaching and 30 years of research experience. His research mainly focuses on structure and functional analysis of plant cell wall degrading enzymes and their applications. Prof. Goyal obtained his M.Sc. and M.Tech. degrees from the Indian Institute of Technology Delhi and Ph.D. from the Indian Institute of Technology Kanpur, India. Prof. Goyal has handled many national and international collaborative research projects, sponsored by various funding agencies of the Government of India such as DBT, DST and CSIR. So far 30 students have obtained Ph.D. under his supervision and 12 students are continuing their Ph.D. Prof. Goyal has published more than 265 research papers in various National and International reputed journals and over 30 book chapters. Kedar Sharma Postdoctoral Research Associate, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gujrat, India.Visiting Fellow, National Institute of Environmental Health Sciences, North Carolina, USA. Dr. Kedar Sharma, M.Sc., Ph.D. currently working as Visiting Fellow at National Institute of Environmental Health Sciences, North Carolina, USA. He worked as Postdoctoral Research Associate, at Department of Biological Engineering, at Indian Institute of Technology Gandhinagar, Gujarat, India. Dr. Sharma has over 7 years of research experience. He completed his Bachelors of Science in Biotechnology from University of Rajasthan, Jaipur and his Masters in Biotechnology from Guru Ghasidas Vishwavidyalaya (Central University) Bilaspur, Chhattisgarh, India. He completed Ph.D. from Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati. His Ph.D. work as focused on structural and functional characterization of xylanolytic enzymes and other glycoside hydrolases and their application in production of xylooligosaccharides. Currently, he is working on elucidating the structure and fusion mechanism of viral entry into the host cell. He received a IUCr Young Scientist award from International Union for Crystallography, and several best poster and oral presentation awards from different organizations. Dr. Sharma has published 33 research papers in various international reputed journals and 5 book chapters.
