Enzymatic Reaction Mechanisms
by Frey, Perry A.; Hegeman, Adrian D.Edition: 1st
Format: Hardcover
Pub. Date: 2007-01-27
Publisher(s): Oxford University Press
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Summary
The past fifteen years have seen a tremendous surge in knowledge about enzymatic catalysis. This is largely due to the empowerment of this vibrant and mature field by the fruits of methodological advances. Enzymatic Reaction Mechanisms presents the current state of understanding about mechanisms of enzymatic catalysis, focusing on the chemical mechanisms facilitated by enzymes.
Author Biography
Perry A. Frey is Robert H. Ables Professor of Biochemistry at the University of Wisconsin at Madison Adrian D. Hegenen is NIH Postdoctoral Fellow at the University of Wisconsin at Madison
Table of Contents
| Enzymes and Catalytic Mechanisms | p. 1 |
| Catalysis and the Active Site | p. 1 |
| Rate Enhancement in Enzymatic Catalysis | p. 3 |
| Conformational Mobility in Catalysis | p. 5 |
| Substrate-Induced Conformational Changes | p. 5 |
| Catalysis of Multistep Reactions | p. 6 |
| Structural Mobility in Enzymes | p. 6 |
| Acid-Base Catalysis | p. 9 |
| Acids and Bases | p. 9 |
| Acid- and Base-Catalyzed Reactions | p. 11 |
| Nucleophilic Catalysis | p. 16 |
| Electrophilic Catalysis | p. 21 |
| Catalysis of Enolization | p. 21 |
| Imine Formation by Lysine | p. 23 |
| Catalysis by Metal Ions | p. 26 |
| Hydrogen Bonding | p. 30 |
| Strong and Weak Hydrogen Bonds | p. 30 |
| Hydrogen Bonding in Catalysis | p. 32 |
| Binding Energy in Catalysis | p. 34 |
| Binding and Activation Energy | p. 34 |
| The Active Site as an Entropy Trap | p. 36 |
| Dissecting the Binding Effect in Enzymatic Action | p. 40 |
| Stabilization of the Transition State | p. 41 |
| Binding the Near Attack Conformation | p. 46 |
| Destabilization of Ground States | p. 48 |
| Rate Enhancement through Binding of Remote Groups | p. 48 |
| Characterization of Active Sites | p. 53 |
| Competitive Inhibitors: Analogs of Substrates | p. 53 |
| Group-Selective Chemical Modification | p. 53 |
| Site-Directed Mutagenesis | p. 57 |
| Affinity Labeling | p. 59 |
| Why Are Enzymes Large Molecules? | p. 62 |
| Sizes of Enzymatic Binding Domains | p. 62 |
| Catalytic Antibodies | p. 63 |
| Kinetics of Enzymatic Reactions | p. 69 |
| Steady-State Kinetics | p. 69 |
| One-Substrate Reactions | p. 70 |
| Two-Substrate Reactions | p. 74 |
| Three-Substrate Reactions | p. 89 |
| Isotope Effects | p. 91 |
| Classes of Isotope Effects | p. 91 |
| Measurement of Isotope Effects | p. 95 |
| Transient-Phase Kinetics | p. 101 |
| Reaction Characteristics | p. 101 |
| Transient Methods | p. 102 |
| pH-Rate Profiles | p. 111 |
| Profile Interpretation | p. 111 |
| Measurements of pH-Rate Profiles | p. 111 |
| Allosteric Regulation | p. 117 |
| Theory | p. 118 |
| Binding Equations for Cooperative Systems | p. 120 |
| Aspartate Transcarbamoylase | p. 123 |
| Coenzymes I: Organic Coenzymes | p. 129 |
| Nicotinamide Coenzymes | p. 129 |
| Structures and Functions of Nicotinamide Coenzymes | p. 129 |
| Stereospecificity of Hydride Transfer | p. 132 |
| NAD[superscript +] as a Coenzyme | p. 134 |
| Thiamine Pyrophosphate | p. 141 |
| Structure | p. 141 |
| Reaction Mechanism | p. 141 |
| [alpha]-Lipoamide | p. 147 |
| Pyridoxal-5[prime]-Phosphate | p. 148 |
| Enzymatic Reactions Facilitated by Pyridoxal-5[prime]-Phosphate | p. 149 |
| Pyridoxal-5[prime]-Phosphate-Stabilized Amino Acid Carbanions | p. 149 |
| Mechanisms of Pyridoxal-5[prime]-Phosphate-Dependent Reactions | p. 151 |
| Flavin Coenzymes | p. 158 |
| Structures of Flavin Coenzymes | p. 158 |
| Mechanisms of Flavin Catalysis | p. 159 |
| Biotin | p. 163 |
| Structure and Role as a Carboxyl Carrier | p. 163 |
| Chemistry of Biotin and N[superscript 1]-Carboxybiotin | p. 164 |
| Mechanism of Biotin-Dependent Carboxylation | p. 164 |
| Phosphopantetheine Coenzymes | p. 165 |
| Structures of Phosphopantetheine Coenzymes | p. 165 |
| Mechanism of Phosphopantetheine Action | p. 165 |
| Folate Compounds | p. 167 |
| Folate Compounds of One-Carbon Metabolism | p. 168 |
| Enzymes in Tetrahydrofolate Metabolism | p. 170 |
| Biological Importance of Folate | p. 171 |
| Amino Acid-Based Coenzymes | p. 172 |
| Pyruvoyl Decarboxylases | p. 172 |
| Methylidene Imidazolinone-Dependent Deaminases | p. 173 |
| Quinoproteins | p. 174 |
| Coenzymes II: Metallic Coenzymes | p. 189 |
| Vitamin B[subscript 12] Coenzymes | p. 190 |
| Chemistry of B[subscript 12] Coenzymes | p. 190 |
| Adenosylcobalamin-Dependent Enzymes | p. 193 |
| Methylcobalamin-Dependent Enzymes | p. 199 |
| Heme Coenzymes | p. 201 |
| Chemistry of Oxygen and Heme | p. 201 |
| Heme Enzymes | p. 204 |
| Oxygen Binding and Electron Transfer | p. 209 |
| Mononuclear Nonheme Iron | p. 210 |
| Monooxygenases | p. 210 |
| Dioxygenases | p. 217 |
| Oxo-Fe[subscript 2] Complexes | p. 217 |
| Structures | p. 218 |
| Reactions of Di-iron Enzymes | p. 219 |
| Metallopterin Enzymes | p. 222 |
| Molybdopterin and Tungstopterin | p. 222 |
| Iron-Sulfur Centers | p. 227 |
| Structures | p. 227 |
| Catalytic Functions | p. 230 |
| S-Adenosylmethionine and Iron-Sulfur Centers | p. 234 |
| Catalytic Action of S-Adenosylmethionine and [4Fe-4S] Centers | p. 234 |
| Stoichiometric Reactions of S-Adenosylmethionine and [4Fe-4S] Centers | p. 236 |
| Divalent Metal Ions | p. 237 |
| Electrostatic Activation of Coordinated Water | p. 237 |
| Electrostatic Activation of Enolization | p. 238 |
| Copper as a Cofactor | p. 240 |
| Copper Proteins | p. 240 |
| Other Copper Enzymes | p. 241 |
| Nickel Coenzymes | p. 243 |
| Nickel in Methanogenesis | p. 243 |
| Other Nickel Coenzymes | p. 245 |
| Long-Range Electron Transfer | p. 247 |
| Biological Electron Transfer | p. 247 |
| Marcus Theory | p. 248 |
| Enzyme Inhibition | p. 253 |
| Two-Substrate Analogs | p. 254 |
| Inhibition and Binding | p. 254 |
| PALA and Aspartate Transcarbamylase | p. 254 |
| Suicide Inactivation | p. 255 |
| Thymidylate Synthase | p. 255 |
| [beta]-Hydroxydecanoyl Thioester Dehydratase | p. 260 |
| [gamma]-Aminobutyrate Aminotransferase | p. 262 |
| Kinetics of Slow-Binding and Tight-Binding Inhibition | p. 268 |
| Slow Binding | p. 268 |
| Tight Binding | p. 269 |
| Slow-Binding Inhibition | p. 270 |
| Dihydrofolate Reductase | p. 271 |
| Prostaglandin H Synthase | p. 274 |
| Tight-Binding Inhibition | p. 280 |
| HMG-CoA Reductase | p. 280 |
| Alanine Racemase | p. 285 |
| 5-Enolpyruvoylshikimate-3-Phosphate Synthase | p. 289 |
| Acetylcholinesterase | p. 291 |
| Acyl Group Transfer: Proteases and Esterases | p. 297 |
| Chemistry of Acyl Transfer | p. 297 |
| Serine Proteases | p. 300 |
| Chymotrypsin | p. 301 |
| Subtilisin | p. 311 |
| Cysteine Proteases | p. 314 |
| Papain | p. 315 |
| Caspases | p. 317 |
| Aspartic Proteases | p. 317 |
| Molecular Properties | p. 318 |
| Mechanism of Action | p. 320 |
| Metalloproteases | p. 323 |
| Carboxypeptidase A | p. 324 |
| Thermolysin | p. 327 |
| Esterases | p. 328 |
| Structure and Function | p. 328 |
| Phospholipase A[subscript 2] | p. 329 |
| Isomerization | p. 333 |
| Aldose and Ketose Isomerases | p. 333 |
| Chemistry | p. 333 |
| Phosphoglucose Isomerase | p. 334 |
| Triosephosphate Isomerase | p. 335 |
| Xylose Isomerase | p. 341 |
| Phosphomutases | p. 341 |
| [alpha]-Phosphoglucomutase | p. 341 |
| [beta]-Phosphoglucomutase | p. 343 |
| Phosphoglycerate Mutases | p. 343 |
| Racemases and Epimerases | p. 346 |
| Proline Racemase | p. 346 |
| Glutamate Racemase | p. 350 |
| Mandelate Racemase | p. 352 |
| UDP-Galactose 4-Epimerase | p. 355 |
| Ribulose-5-P 4-Epimerase | p. 360 |
| UDP-N-Acetylglucosamine-2-Epimerase | p. 361 |
| Chorismate Mutase | p. 364 |
| [delta superscript 5]-3-Ketosteroid Isomerase | p. 366 |
| Radical Isomerizations | p. 368 |
| Glutamate Mutase | p. 369 |
| Methylmalonyl CoA Mutase | p. 371 |
| Lysine 2,3-Aminomutase | p. 376 |
| Newer Isomerases | p. 379 |
| UDP-Galactopyranose Mutase | p. 379 |
| Pseudouridine Synthase | p. 379 |
| Decarboxylation and Carboxylation | p. 387 |
| Chemistry of Decarboxylation and Carboxylation | p. 387 |
| Decarboxylases | p. 388 |
| Pyruvate Decarboxylase | p. 389 |
| Amino Acid Decarboxylases | p. 394 |
| Acetoacetate Decarboxylase | p. 403 |
| Mevalonate Pyrophosphate Decarboxylase | p. 405 |
| Radical-Based Decarboxylases | p. 407 |
| Orotidine Monophosphate Decarboxylase | p. 414 |
| Carboxylases | p. 418 |
| Ribulose-1,5-Bisphosphate Carboxylase | p. 419 |
| Phosphoenolpyruvate Carboxylase | p. 425 |
| Vitamin K-Dependent Carboxylase | p. 426 |
| Addition and Elimination | p. 433 |
| [alpha],[beta]-Elimination/Addition Reactions | p. 433 |
| Cofactor-Independent [alpha],[beta]-Elimination/Addition Reactions | p. 434 |
| Cofactor-Dependent [alpha],[beta]-Elimination/Addition Reactions | p. 440 |
| [beta],[alpha]-Elimination/Addition Reactions | p. 456 |
| Methylidene Imidazolone-Dependent Elimination and Addition | p. 456 |
| Carbonic Anhydrase | p. 462 |
| Isomerization and Elimination | p. 465 |
| Catalytic Process | p. 465 |
| Coenzyme B[subscript 12]-Dependent Elimination | p. 466 |
| Phosphotransfer and Nucleotidyltransfer | p. 476 |
| Chemistry of Phosphoryl Group Transfer | p. 476 |
| Phosphomonoesters | p. 476 |
| Phosphodiesters | p. 483 |
| Phosphotriesters | p. 483 |
| Five-Member Ring Phosphoesters | p. 484 |
| Enzymatic Phosphoryl Group Transfer | p. 487 |
| Single and Double Displacements | p. 487 |
| Phosphotransferases | p. 489 |
| Protein Phosphorylation: Protein Kinase A | p. 502 |
| Phosphomonoesterases | p. 509 |
| Enzymatic Nucleotidyl Group Transfer | p. 521 |
| Nucleotidyltransferases | p. 521 |
| Phosphodiesterases | p. 539 |
| ATP-Dependent Synthetases and Ligases | p. 547 |
| Ligation and the Energy of ATP | p. 547 |
| Activation by Phosphorylation | p. 548 |
| Glutamine Synthetase | p. 548 |
| Carbamoyl Phosphate Synthetase | p. 554 |
| Activation by Adenylylation | p. 559 |
| DNA Ligase | p. 559 |
| Aminoacyl-tRNA Synthetases | p. 561 |
| Ubiquitin | p. 566 |
| Glycosyl Group Transferases | p. 569 |
| Chemical Mechanisms | p. 570 |
| Chemistry of Glycoside Hydrolysis | p. 570 |
| Enzymatic Glycosyl Transfer | p. 573 |
| Glycosyltransferases | p. 575 |
| Sucrose Phosphorylase | p. 575 |
| Glycogen Phosphorylase | p. 577 |
| Purine Nucleoside Phosphorylase | p. 584 |
| Glycosidases | p. 587 |
| Families and Structures | p. 587 |
| Lysozyme | p. 589 |
| T4 Lysozyme | p. 595 |
| Nitrogen and Sulfur Transferases | p. 597 |
| Nitrogen Transfer | p. 597 |
| Aspartate Aminotransferase | p. 597 |
| Tyrosine 2,3-Aminomutase | p. 602 |
| Amidotransfer | p. 604 |
| Glutamine:PRPP Amidotransferase | p. 607 |
| Sulfur Transfer | p. 609 |
| Biotin Synthase | p. 611 |
| Lipoyl Synthase | p. 612 |
| Carbon-Carbon Condensation and Cleavage | p. 617 |
| Chemistry | p. 617 |
| Enolization of Acetyl CoA | p. 619 |
| Acetyl CoA in Ester Condensations | p. 619 |
| Citrate Synthase | p. 620 |
| Thiolases | p. 627 |
| Carbanionic Mechanisms | p. 630 |
| Transaldolase | p. 631 |
| Transketolase | p. 634 |
| Serine Hydroxymethyltransferase | p. 639 |
| Carbocationic Mechanisms | p. 645 |
| Farnesyl Pyrophosphate Synthase | p. 645 |
| Squalene Synthase | p. 648 |
| Alkyltransferases | p. 655 |
| Chemistry of Alkylation | p. 655 |
| Biological Alkylations | p. 655 |
| Alkylation Mechanisms | p. 656 |
| Enzymatic Alkylation | p. 657 |
| Protein Farnesyltransferase | p. 657 |
| Catechol O-Methyltransferase | p. 661 |
| S-Adenosylmethionine Synthetase | p. 665 |
| Methionine Synthases | p. 670 |
| Oxidoreductases | p. 679 |
| Pyridine Nucleotide-Dependent Dehydrogenases | p. 680 |
| Alcohol Dehydrogenase | p. 680 |
| Lactate Dehydrogenase | p. 686 |
| Short-Chain Alcohol Dehydrogenases | p. 687 |
| Glyceraldehyde-3-P Dehydrogenase | p. 690 |
| Glutamate Dehydrogenase | p. 693 |
| Disulfide Oxidoreductases | p. 694 |
| Dihydrolipoyl Dehydrogenase | p. 694 |
| Ribonucleotide Reductases | p. 698 |
| Classes of Ribonucleotide Reductases | p. 700 |
| Structural Relationships of Ribonucleotide Reductases | p. 705 |
| Oxidases and Oxygenases | p. 710 |
| Oxidases | p. 710 |
| D-Amino Acid Oxidase | p. 710 |
| Monoamine Oxidases | p. 716 |
| Isopenicillin-N Synthase | p. 718 |
| Urate Oxidase | p. 721 |
| Monooxygenases | p. 722 |
| Lactate Monooxygenase | p. 722 |
| Cytochrome P450 Monooxygenases | p. 722 |
| Iron-Methane Monooxygenase | p. 727 |
| [alpha]-Ketoglutarate-Dependent Oxygenases | p. 732 |
| Dopamine [beta]-Monooxygenase | p. 735 |
| Copper-Methane Monooxygenase | p. 737 |
| Nitric Oxide Synthase | p. 738 |
| Dioxygenases | p. 741 |
| Intradiol Dioxygenases | p. 741 |
| Extradiol Dioxygenases | p. 744 |
| Complex Enzymes | p. 749 |
| Multienzyme Complexes | p. 750 |
| [alpha]-Ketoacid Dehydrogenase Complexes | p. 750 |
| Pyruvate Dehydrogenase Complex | p. 750 |
| Fatty Acid Synthesis | p. 757 |
| Acetyl CoA Carboxylase | p. 757 |
| Fatty Acid Synthases | p. 761 |
| Modular Enzymes | p. 763 |
| Polyketide Synthases | p. 763 |
| Nonribosomal Polypeptide Synthetases | p. 767 |
| Ribosomal Protein Synthesis | p. 768 |
| RNA Polymerase | p. 768 |
| The Ribosome | p. 770 |
| Energy-Coupling Enzymes | p. 777 |
| Nitrogenase | p. 777 |
| Cytochrome c Oxidase | p. 782 |
| ATP Synthase | p. 786 |
| Myosin and Muscle Contraction | p. 792 |
| Appendices | p. 803 |
| Haldane Relationships for Some Kinetic Mechanisms | p. 803 |
| Inhibition Patterns for Three-Substrate Kinetic Mechanisms | p. 804 |
| Equations for Number of Occupied Sites in the Binding of a Ligand to a Multisite Macromolecule | p. 804 |
| Derivation of Steady-State Kinetic Equations by the King-Altman Method | p. 805 |
| Index | p. 809 |
| Table of Contents provided by Ingram. All Rights Reserved. |
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