Covalent Catalysis by Enzymes Leonard B. Spector Covalent Catalysis by Enzymes With 61 Figures Springer-Verlag New York Heidelberg Berlin Dr. Leonard B. Spector The Rockefeller University York Avenue New York, New York 10021, USA Library of Congress Cataloging in Publication Data Spector, Leonard B. Covalent catalysis by enzymes. Bibliography: p. Includes index. 1. Enzymes. I. Title. QP601.S5623 574.19'25 81-23251 AACR2 © 1982 by Springer-Verlag New York, Inc. Softcover reprint of the hardcover 1st edition 1982 All rights reserved. No part of this book may be translated or reproduced in any form without written permission from Springer-Verlag, 175 Fifth Avenue, New York, New York 10010, U.S.A. The use of general descriptive names, trade names, trademarks, etc. in this publication, even if the former are not especially identified, is not to be taken as a sign that such names, as understood by the Trade Marks and Merchandise Marks Act, may accord­ ingly be used freely by anyone. 9 8 765 432 1 ISBN-13:978-1-4612-5665-6 e-ISBN-13:978-1-4612-5663-2 DOl: 10.1007/978-1-4612-5663-2 To F. Lipmann and H. Bunche Preface Some years ago one of my students and I reported that the acetate kinase reaction is mediated by a phosphorylated form of the enzyme [R. S. Anthony and L. B. Spector, lBe 245, 6739 (1970)]. The reversible reaction between ATP and acetate to give acetyl phosphate and ADP had hitherto been thought to proceed by direct transfer of a phosphoryl group from A TP to acetate in a single-displacement reaction. But now it became clear that acetate kinase was one of that substantial number of enzymes whose mech­ anism is that of the double displacement. For some reason, I began to wonder about the possibility that all enzymes, like acetate kinase, are double­ displacement enzymes, and do their work by covalent catalysis. For one thing, I could not think of a single instance of an enzyme for which single­ displacement catalysis had been proved, and inquiries on this point among knowledgeable friends elicited the same negative response. Moreover, it was long known that the two other kinds of chemical catalysis~homo­ geneous and heterogeneous~occur through the intermediary formation of a covalent bond between catalyst and reactant. I began to feel confident that chemical catalysis by enzymes must happen the same way. But how could ')ne be sure? There seemed to me to be only one way: to search the literature for authentic cases of covalent catalysis by enzymes and to see if their number and chemical diversity are sufficiently large to warrant my confidence. The results of that literature search form the substance of this book. In Chapter 1, I set out the main reasons for believing in covalent catalysis by all enzymes. The next six chapters give the evidence for this belief, with examples of individual enzymes which seem to me to be pertinent or inter­ esting or both, and which illustrate the diverse forms which covalent catalysis takes among enzymes. The treatment given each enzyme is short and terse. viii Preface Inevitably, there is speculation on controversial subjects; but speculation and controversy are, after all, inseparable from an advancing science, and are often an impulse to new advances. Chapter 8 sums it all up. The reader who is in a hurry can acquaint himself with the main arguments by simply reading Chapters 1 and 8. To Drs. O. W. Griffith and E. B. Keller I am grateful for their many helpful comments. New York City L. B. S. February 1982 Contents Chapter 1 The Thesis 1 Nonenzymic Chemical Catalysis: Its Resemblance to Enzymic Catalysis 2 Enzymic Catalysis 8 Steric Inversion and Covalent Catalysis 10 Why Covalent Catalysis Is Favored Over Single- Displacement Catalysis 11 Is Covalent Catalysis a Means of Stabilizing Very Reactive (Hypothetical) Intermediates? 15 Enzymes as Phase Transfer Catalysts and Energy Transducers 20 A Definition of Catalysis 21 Enzymes as Transferases 22 Chapter 2 Oxidoreductases 23 Flavoenzymes 23 NAD Enzymes 33 Copper Enzymes 39 Copper-Heme Enzymes 42 Heme Enzymes 43 Disulfide Enzymes 46 Summary 48 x Contents Chapter 3 Transferases 60 Methionine Synthase [EC 2.1.1.13] 61 N-Methylglutamate Synthase [EC 2.1.1.21] 62 Serine Hydroxymethyltransferase [EC 2.1.2.1] 63 Transcarboxylase [EC 2.1.3.1] 65 Glycine Amidinotransferase [EC 2.1.4.1 ] 68 Transketolase [EC 2.2.1.1] 69 Transaldolase [EC 2.2.1.2] 72 Arylamine Acetyltransferase [EC 2.3.1.5] 74 Acetyl-CoA Acetyltransferase [EC 2.3.1.9] 75 [Acyl-Carrier-Protein] Malonyltransferase fEC 2.3.1.39] 76 Transglutaminase [EC 2.3.2.13] 77 Sucrose Phosphorylase [EC 2.4.1.7] 78 Adenine Phosphoribosyltransferase [EC 2.4.2.7] 80 Thiaminase [EC 2.5.1.2] 83 Aspartate Aminotransferase [EC 2.6.1.1] 84 Hexokinase [EC 2.7.1.1 ] 87 Pyruvate Kinase [EC 2.7.1.40] 91 Acetate Kinase [EC 2.7.2.1] 92 Phosphoglycerate Kinase [EC 2.7.2.3] 96 Nucleosidediphosphate Kinase [EC 2.7.4.6] 98 Phosphoglucomutase [EC 2.7.5.1] 99 Galactose-I-Phosphate Uridylyltransferase [EC 2.7.7.10] 100 Pyruvate, Orthophosphate Dikinase [EC 2.7.9.1] 102 Rhodanese [EC 2.8.1.1] 103 3-Ketoacid CoA-Transferase [EC 2.8.3.5] 104 Chapter 4 Hydrolases 114 Carboxylesterase [EC 3.1.1.1] 115 Alkaline Phosphatase [EC 3.1.3.1] 117 Acid Phosphatase [EC 3.1.3.2] 120 Glucose-6-Phosphatase [EC 3.1.3.9] 121 5'-Nucleotide Phosphodiesterase [EC 3.1.4.1] 122 Arylsulfatase [EC 3.1.6.1] 123 /J-Galactosidase [EC 3.2.1.23] 124 NADase [EC 3.2.2.5] 127 Carboxypeptidase A [EC 3.4.17.1] 128 Chymotrypsin [EC 3.4.21.1J 131 Papain [EC 3.4.22.2] 135 Pepsin [EC 3.4.23.1 J 137 Contents Xl Glutaminase [EC 3.5.l.2J 142 Inorganic Pyrophosphatase [EC 3.6.1.1 J 143 Adenosine Triphosphatase [EC 3.6.1.3J 144 Chapter 5 Lyases 155 Pyruvate Decarboxylase [EC 4.1.1.1 J 155 Acetoacetate Decarboxylase [EC 4.1.1.4J 157 Glutamate Decarboxylase [EC 4.1.1.15J 158 Histidine Decarboxylase [EC 4.1.1.22J 160 Phosphoenolpyruvate Carboxykinase [EC 4.1.1.32J 162 Fructose Diphosphate Aldolase [EC 4.1.2.13] 163 3-Hydroxy-3-Methylglutaryl-Coenzyme A Synthase [EC 4.l.3.5J 166 Citrate Lyase [EC 4.l.3.6J 167 ATP Citrate Lyase [EC 4.1.3.8J 168 Tryptophanase [EC 4.l.99.1J 170 Carbonic Anhydrase [EC 4.2.1.1 J 172 Dehydroquinase [EC 4.2.1.10J 174 Enolase [EC 4.2.1.11 J 175 Propanediol Dehydrase [EC 4.2.1.28] 177 Phenylalanine Ammonia-Lyase [EC 4.3.l.5J 179 Chapter 6 Isomerases 186 Alanine Racemase [EC 5.1.1.1 J 186 Proline Racemase [EC 5.1.1.4] 188 Phenylalanine Racemase [EC 5.1.1.11 J 190 Mandelate Racemase [EC 5.l.2.2] 192 Uridine Diphosphoglucose Epimerase [EC 5.1.3.2] 194 Triosephosphate Isomerase [EC 5.3.1.1] 195 Steroid Ll-Isomerase [Ee 5.3.3.1] 196 Phosphoglycerate Mutase [EC 5.4.2.1] 197 DNA Topoisomerase [EC 5.4.2.-] 198 D-a-Lysine Mutase [EC 5.4.3.4] 199 Chapter 7 Ligases 202 Tryptophanyl-tRNA Synthetase [EC 6.1.1.2] 203 Phenylalanyl-tRNA Synthetase [EC 6.1.1.20] 205 Carnosine Synthetase [EC 6.3.2.11] 207 Acetyl-CoA Synthetase [EC 6.2.1.1] 208 Xll Contents Succinyl-CoA Synthetase [EC 6.2.1.5] 209 Long-Chain Fatty Acyl-CoA Synthetase [EC 6.2.1.3] 212 Pyruvate Carboxylate [EC 6.4.1.1] 215 DNA Ligase (NAD) [EC 6.5.1.2] 217 Chapter 8 Summary 223 Key to Numbering and Classification of Enzymes 227 Index 237 .