Carbohydrate-Modifying Biocatalysts

832 Pages·2011·35.278 MB·\832

by  Peter Grunwald (Editor)

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Contents
Preface
1. Basics in Carbohydrate Chemistry 1
xxi
Heinrich Hühnerfuss
1.1 Introduction 1
1.2 Classification of Carbohydrates  2
1.2.1 Monosaccharides 2
1.2.1.1 Configuration and nomenclature  4
1.2.1.2 Ring structures of carbohydrates 5
1.2.2 Disaccharides 10
1.2.3 Oligosaccharides 12
1.2.4 Polysaccharides 13
1.3 Reactions of Carbohydrates 16
1.3.1 Oxidation of Carbohydrates 16
1.3.2 Reduction of Carbohydrates 18
1.3.3 Nucleophilic Reactions 19
O N
1.3.4 Acylation and Alkylation of Monosaccharides 20
1.3.5 Formation of -Glycosides and -Glycosides 21
2. Glycoconjugates: A Brief Overview 29
1.4 Glycoproteins 26
Peter Grunwald
2.1 Introduction 29
2.2 Glycoconjugates: General Features and Glycosylation 30
N
2.3 Glycoproteins 35
2.4 -Glycosylation of Proteins 43
2.4.1 Quality Control and ER-Associated Degradation 45
2.4.2 Cytosolic Degradation 51
2.5 Mucins 55
2.6 Glycosaminoglycans and Proteoglycans 61
2.6.1 Heparin 62
vi Contents
2.6.2 Heparan Sulfate 64
2.6.3 Chondroitin and Dermatan Sulfate 66
2.6.4 Keratan Sulfate 68
2.7 Peptidoglycans 69
2.8 Glycolipids, Lipopolysaccharides and Toxins 72
2.8.1 Lipopolysaccharides 75
2.8.2 Toxins 80
2.9 Carbohydrates and Antibiotics 83
2.10 Antibiotics and Resistance 89
3. Oligosaccharides and Glycoconjugates
2.11 Concluding Remarks 96
in Recognition Processes 119
Thisbe K. Lindhorst
3.1 Introduction 119
3.2 The Lectins and Their Ligands 120
3.2.1 Classification of Lectins  121
3.2.2 Characteristics of Important Lectin Classes 124
3.2.2.1 The R- and L-type lectins 124
3.2.2.2 The P-type lectins 126
3.2.2.3 The C-type lectins 126
3.2.2.4 The collectins: A subgroup
of C-type lectins 128
3.2.2.5 The selectins: A subgroup
of C-type lectins 129
3.2.2.6 The I-type lectins 131
3.2.2.7 The S-type lectins 133
3.3 Recognition of Carbohydrates 136
3.3.1 Formation of a Carbohydrate–
Lectin Complex 136
3.3.2 Networks of Stabilizing Interactions 138
2+
3.3.3 Complexation via Ca 142
3.3.4 Weak Interactions and the Water Problem 145
3.3.5 Hydrophobic Interactions with Carbohydrates 146
3.3.6 Binding to the Bacterial Lectin FimH 147
3.4 The Biological Role of Carbohydrate–Lectin
Interactions 148
3.4.1 Clearance of Glycoproteins by Interaction
with ASGPR 149
Contents vii
3.4.2 Leukocyte Trafficking  150
3.4.3 Galectins in Signaling 152
3.4.4 Type 1 Fimbriae-Mediated Bacterial Adhesion 156
3.5 Multivalency of Carbohydrate–Protein Interactions 157
3.6 Model Systems for the Investigation
of Carbohydrate–Protein Interactions 164
3.6.1 Multivalent Glycomimetics: Glycodendrimers
and Successors 165
3.6.2 Testing Bacterial Adhesion 171
3.6.3 Tailoring Carbohydrate Surfaces to Mimic
Cellular Adhesion to the Glycocalyx 173
4. 3G.l7y cCoosnidcelu Hsiyodnrso alnadse Osu tlook 118735
Motomitsu Kitaoka
4.1 Introduction 183
4.2 Classification  186
4.2.1 Anomeric Configuration of the Substrate  186
4.2.2 Location of the Hydrolyzed Linkage 186
4.2.3 Anomeric Retention and Inversion 187
4.3 Mechanisms of Action 188
4.3.1 Retaining GHs 188
4.3.1.1 Typical retaining GHs 188
4.3.1.2 Substrate-assisted catalysis
of retaining GHs 189
+
4.3.1.3 NAD -dependent catalysis
of retaining GHs 190
4.3.2 Inverting GHs 191
4.3.3 Hydrolysis and Transglycosylation 192
4.4 Chemoenzymatic Syntheses Using GHs
with Engineered Substrates 195
4.5 Chemoenzymatic Syntheses Using Mutant GHs 196
5. 4 D.i6s aCcocnhcalruiddien gP Rhoemspahrkosr ylases: Mechanistic Diversity 200
and Application in the Glycosciences 205
Christiane Luley-Goedl and Bernd Nidetzky
5.1 Introduction 205
viii Contents
5.2 Disaccharide Phosphorylases: Classification, 
Structure, and Function 207
5.3 Phosphorylase Mechanisms 211
5.3.1 Cellobiose and Chitobiose Phosphorylase 211
5.3.2 Sucrose Phosphorylase 215
5.3.3 Retaining α,α-Trehalose Phosphorylase  219
5.4 Novel Application of Disaccharide Phosphorylases
in Synthesis 223
5.4.1 Multi-Step Enzymatic Synthesis
of Disaccharides and Other Glycosides 226
N
5.4.1.1 Coupling to sucrose conversion 226
5.4.1.2 Lacto- -biose 227
5.4.1.3 Glucosylglycerol 229
5.4.2 Engineering of Cellobiose Phosphorylase
for Altered Substrate Specificity   230
6. Enzymatic and Chemoenzymatic Synthesis of
5.6 Conclusions 231
Nucleotide Sugars: Novel Enzymes, Novel Substrates,
Novel Products, and Novel Routes 237
Leonie Engels and Lothar Elling
6.1 Introduction 237
6.2 Novel Enzymes 240
6.2.1 UDP-Nucleotidylyltransferases 240
6.2.2 dTDP-Nucleotidylyltransferases 241
6.2.3 Salvage Pathway Enzymes 242
6.3 Novel Substrates and Novel Products 244
6.3.1 Screening of Novel Substrates 244
6.3.2 Novel Substrates for Nucleotidylyltransferases 246
6.3.3 Novel Substrates for Salvage Pathway Enzymes 246
6.3.4 Nucleotide Furanose Sugars 248
6.3.5 Nucleotide Phosphono Sugars 249
6.3.6 Nucleotide Carba Sugars 250
In situ
6.4 Novel Routes 250
6.4.1 Combinatorial Biocatalysis for
(Re)Generation of Nucleotide Sugars 250
6.5 Conclusions 251
Contents ix
7. Iteratively Acting Glycosyltransferases 255
Marta Luzhetska and Andreas Bechthold
7.1 Introduction 255
7.2 Iteratively Acting GTs Involved in Polysaccharide
Biosynthesis in Plants 256
7.2.1 GTs Involved in Biosynthesis of Starch 257
7.2.2 GTs Involved in Biosynthesis of Structural
Polysaccharides 258
7.2.2.1 GTs involved in hemicellulose
biosynthesis 258
7.2.2.2 GTs involved in cellulose biosynthesis 261
7.3 Iteratively Acting GTs Involved in Natural
Product Biosynthesis 261
7.3.1 GTs Involved in Natural Product Biosynthesis 262
7.3.2 GTs Involved in Biosynthesis of Aureolic
Acid-Type Compounds 264
7.3.3 GTs Involved in Biosynthesis of Anthracyclines 266
7.3.4 GTs Involved in Biosynthesis of Angucyclines 266
7.3.5 GTs Involved in Biosynthesis of Macrocyclic
Lactones 268
7.3.6 GTs Involved in Biosynthesis of
Oligosaccharides 269
8. Bacterial Glycosyltransferases Involved in Molecular
7.4 Concluding Remarks 269
Mimicry of Mammalian Glycans 279
Warren Wakarchuk
8.1 Introduction 279
8.2 Sialyltransferases 291
8.2.1 GT-52 and GT-80 (GT-B Folds) 291
8.2.2 GT-42 (Modified GT-A Folds)  297
8.2.3 GT-38 and Other Polymerizing
Glycosyltransferases 300
N
8.2.4 Microbial GAG Polymerases 303
8.3 Galactosyltransferases and -acetylhexosamine
Transferases 305