The Enzymes, Vol II: Kinetics and Mechanism, 3rd Edition

The Enzymes /

KINETICS AND MECHAjYlSM VOLUME I1

Third Edition

CONTRIBUTORS THOMAS C.BRUICE G. POPJAK W. W. CLELAND J. H. RICHARDS SAMUEL J. DI MAR1 IRWIN A. ROSE GORDON G. HAMMES PAUL R. SCHIMMEL ALBERT S. MILDVAN ESMOND E. SNELL SERGE N. TIMASHEFF

ADVISORY BOARD WILLIAM P. JENCKS JOHN M. BUCHANAN DANIEL E. KOSHLAND, JR. W. W. CLELAND EMIL L. SMITH

THE ENZYMES Kinetics and Mechanism

Edited by P A U L D. BOYER Molecular Biology Institute University of Calijornia Los Angeles, California

Volume I1 THIRD EDITION

A C A D E M I C P R E S S New York and London

1970

COPYRIGHT 6 1970, BY ACADEMIC PRESS, INC. ALL RIGHTS RESERVED NO PART OF THIS BOOK MAY BE REPRODUCED IN ANY FORM, BY PHOTOSTAT, MICROFILM, RETRIEVAL SYSTEM, OR ANY OTHER MEANS, WITHOUT WRITTEN PERMISSION FROM THE PUBLISHERS.

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United Kingdom Edition published by ACADEMIC PRESS, INC. (LONDON) LTD.

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PRINTED IN THE UNITED STATES OF AMERICA

Contents ix xi xiii

List of Contributors Preface Contents of Other Volumes

1.

Steady State Kinetics

W. W. CLELAND 1 2 6 6 61

I. Introduction 11. Nomenclature and Notation 111. Basic Theory IV. The Tools of the Kineticist V. Derivation of Rate Equations 2.

Rapid Reactions and Transient States

GORDON G. HAMMW AND PAUL R. SCHIMMEL I. Introduction 11. Kinetic Systems Far from Equilibrium 111. Kinetic Systems Near Equilibrium IV. Application of Fast Reaction Techniques 3.

67 71 83

108

Stereospecificity of Enzymic Reactions

G. POPJAR I. Introduction 11. Enzyme Specificity and Historical Background to Recent Investigations V

116 119

vi

CONTENTS

111. Notations of Molecular Asymmetry IV. Stereospecificity of Nicotinamide-Adenine DinucleotideDependent Oxidoreductases V. Asymmetrical Methyl Groups. Stereospecificity of Synthesis of Malate VI. Reactions of the Citric Acid Cycle VII. Reactions at Isolated Double Bonds VIII. Stereospecificity of Reactions of Polyprenyl Biosynthesis IX. Coenzyme Bxz-Dependent Reactions X. Epilogue

129 134 157 164 179 186 204 214

Proximity Effects and Enzyme Catalysis

4.

THOMAS C. BRUICE I. Introduction 11. Evaluation of Concepts Concerning the Propinquity Effect 111. Physical Organic Models Establishing the Role of Solvehion and Strain IV. Miscellaneous Intramolecular Reactions V. Activation Parameters and Kinetic Order VI. Approximation through Noncovalent Forces

5.

217 220 226 238 250 255

Enzymology of Proton Abstraction and Transfer Reactions

IRWIN A. ROSE I. Introduction 11. General Topics 111. Migrations [HS + SHI IV. a, p Eliminations V. Proton Dissociation-Replacement Reactions VI. C-H Fission in Other Catalyses 6.

28 1 283 290 302 312 318

Kinetic Isotope Effects in Enzymic Reactions

J. H. RICHARDS I. Introduction 11. Primary Isotope Effects 111. Secondary Isotope Effects

32 1 322 329

7. Schiff Base Intermediates in Enzyme Catalysis

ESMOND E. SNELLAND SAMUEL J. DI MARI I. Introduction 11. Schiff Base Formation: Nature and Catalytic Effects

335 336

vii

CONTENTS

111. Enzymes That Contain a Carbonyl Group (Category I) IV. Schiff Base Enzymes Lacking a Carbonyl Group (Category 11) V. Concluding Remarks

8.

346 358 362

Some Physical Probes of Enzyme Stnrcfure in SoIution

SERGEN. TIMASHEFF I. Introduction 11. Secondary and Tertiary Structures 111. Infrared Spectroscopy IV. Ultraviolet Absorption of Peptide Groups V. Circular Dichroism and Optical Rotatory Dispersion VI. Ultraviolet Difference Spectroscopy VII. Fluorescence Spectroscopy VIII. Ionizable Groups IX. Geometry and Quaternary Structure X. Conclusions

9.

371 373 374 379 381 408 4 18 430 440 442

Metals in Enzyme Catalysis

ALBERTS. MILDVAN I. Introduction 11. Properties of Metal Ions Relevant to Catalysis 111. Coordination Schemes of Enzymes, Metals, and Substrates IV. Enzyme Bridge Complexes (M--E--S) V. Substrate Bridge Complexes ( E S - M I

440 448 463 477 478

VI. Metal Bridge Complexes (E-M-S

485

and