Glycoside Hydrolases

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-β-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-β-1,4-glucanase

3.1.4 Exoglucanase

3.1.5 β-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-β-1,4-glucanase with exoglucanase and β-glucosidase

3.4 Endo-β-1,4-glucanase-producing microorganisms

3.4.1 Biochemical properties, kinetics, and catalytic efficiency of endoglucanases

3.5 Structure of endo-β-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 β-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-β-1,3-glucanase
Parmeshwar Vitthal Gavande and Arun Goyal

6.1 Introduction

6.2 The role of endo-β-1,3-glucanase in nature

6.2.1 β-1,3-Glucan

6.2.2 Exo-β-1,3-glucanase

6.2.3 Endo-β-1,3-glucanase

6.2.4 Classification of endo-β-1,3-glucanases

6.3 Sources of endo-β-1,3-glucanase

6.4 Endo-β-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-β-1,3-glucanases

6.6 Conclusion
References
Further reading

CHAPTER 7 Diversity of microbial endo-β-1,4-xylanases
Peter Biely, Katarı´na Sˇuchova´, and Vladimı´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 β-D-Xylosidases: Structure-based substrate specificities and their applications
Satoshi Kaneko and Zui Fujimoto

8.1 Introduction

8.2 Structures of β-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 β-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 β-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 α-glucuronidases

12.2.1 GH67 α-glucuronidases

12.2.2 GH115 α-glucuronidases

12.3 Non-xylanolytic GH4 α-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 β-Glucuronidases

12.4.1 GH1 β-glucuronidase

12.4.2 GH2 β-glucuronidases

12.4.3 GH30 β-glucuronidase

12.4.4 GH79 β-glucuronidases

12.4.5 GH154 β-glucuronidase

12.4.6 GH169 β-glucuronidase

12.5 Perspectives on the development of applications of glucuronidases

12.5.1 Xylanolytic α-glucuronidases

12.5.2 Inhibitors of β-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 β-mannanases

13.2.2 Other enzymes important for mannan degradation

13.3 Production of β-mannanases

13.4 Industrial applications of β-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 β-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 β-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 β-galactosidases and exo-β-1,4-galactanases

14.3.3 α-L-arabinofuranosidase and endo-1,5-α-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 β galactosidase
Azra Shafi and Qayyum Husain

15.1 β Galactosidase

15.2 Glycoside hydrolase families

15.3 Sources of β-galactosidases

15.3.1 Bacterial β-Gals

15.3.2 β-Gals from filamentous fungi

15.3.3 β-Gals from yeasts

15.3.4 β-Gals from plants

15.3.5 β-Gals from animals

15.3.6 Recombinant β-Gals

15.4 Lactose intolerance

15.5 Structural characterization of β-Gal

15.5.1 The active site

15.5.2 Metal binding sites

15.6 Functional characterization of β-Gal

15.6.1 Mode of action and reaction mechanism

15.6.2 Hydrolysis and transgalactosylation activities of β-Gal

15.7 Applications of β-Gal

15.7.1 Lactose-hydrolyzed milks

15.7.2 β-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 α-L-Rhamnosidases: Structures, substrate specificities, and their applications
Satoshi Kaneko and Zui Fujimoto

16.1 Introduction

16.2 Structure of α-L-rhamnosidases

16.2.1 GH78

16.2.2 GH106

16.3 Substrate specificities of α-L-rhamnosidases

16.3.1 GH78

16.3.2 GH106

16.3.3 Unknown family

16.4 Applications of α-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