Table Of ContentEnzyme Dynamics and Regulation
P. Boon Chock, Charles Y . Huang,
C. L. Tsou, and Jerry H. Wang
Editors
Enzytne Dynatnics
and Regulation
With 166 Illustrations
Springer-Verlag
New York Berlin Heidelberg
London Paris Tokyo
P. Boon Chock and Charles Y. Huang, Laboratory of Biochemistry, National
Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda,
Maryland 20892, USA
C. L. Tsou, Institute of Biophysics, Academia Sinica, Beijing, China
Jerry H. Wang, Department of Medical Biochemistry, The University of Calgary,
Calgary, Alberta T2N 4NI, Canada
Library of Congress Cataloging-in-Publication Data
Enzyme dynamics and regulation.
Papers contributed to the International Symposium
on the Dynamics of Soluble and I=obilized Enzyme
Systems, held May 26-30, 1986 in Beijing, China,
sponsored by the International Union of Biochemistry
Interest Group on Kinetics and Mechanisms of Enzymes
and Metabolic Networks and the Academia Sinica.
Includes bibliographies and index.
I. Enzyme kinetics-Congresses. 2. Immobilized
enzymes-Congresses. I. Chock, P. Boon.
II. International Symposium on the Dynamics of Soluble
and I=obilized Enzyme Systems (1986: Peking, China)
III. International Union of Biochemistry. Interest
Group on Kinetics and Mechanisms of Enzymes and Metabolic Networks.
IV. Chung-kuo k'o hsiieh yiian.
QP601.3.E59 1987 574.19'25 87-16522
© 1988 by Springer-Verlag New York Inc.
Softcover reprint of the hardcover 1st edition 1988
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ISBN-13: 978-1-4612-8330-0 e-ISBN-13: 978-1-4612-3744-0
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Preface
Knowledge of enzymes is basic to practically every branch of biochemical
investigation. The scope and direction of enzymology continue to expand
and shift while its foundation gains an ever-stronger foothold in physico-
chemical principles. Recent developments in concepts and techniques have
brought enzyme research into a changing yet exciting stage. For instance,
enzymes serve as indispensable tools in the phenomenal rise of molecular
biology. In turn, the resultant biotechnology thrusts enzymology to new
heights and territories. How does one utilize the long-established and newly
acquired information to proceed? To provide a current overview of this field,
the International Union of Biochemistry Interest Group on Kinetics and
Mechanisms of Enzymes and Metabolic Networks and the Academia Sinica
cosponsored the International Symposium on the Dynamics of Soluble and
Immobilized Enzyme Systems. As indicated by its name, the symposium also
sought to focus due attention on the kinetic, or time-dependent, element of
enzyme-catalyzed or regulated processes and on enzyme systems entrapped
within membranes or solid matrices. This volume collects papers contributed
to the symposium, which was held May 26-30, 1986, in Beijing, China, and
was attended by more than 100 leading scientists from 12 countries. The
diversity of these papers is reflected in the seven categories listed in the Table
of Contents. The success of the symposium was made possible by members of
the Organizing Committee, composed of P. Boon Chock, Carl Frieden,
Robert Y. Hsu, Charles Y. Huang, Jacques Ricard, C. L. Tsou, and Jerry H.
Wang; the American Society of Biological Chemists; and colleagues and
friends too numerous to single out. The success was especially aided by much-
appreciated financial support from the following organizations: Chandra
Djojonegoro, P.T. International Chemical Industrial Co., Ltd., Jakarta,
Indonesia; ClBA-GEIGY Corporation, Summit, New Jersey; Hoechst AG,
Frankfurt, West Germany; Merck Sharp & Dohme, Rahway, New Jersey;
Miles Laboratories, Inc., Elkhart, Indiana; Miwon USA, Inc., Hoboken, New
Jersey; Monsanto Company, St. Louis, Missouri; Smith Kline Beckman
vi Preface
Corporation, Philadelphia, Pennsylvania; and Springer-Verlag New York
Inc., New York, New York.
P. Boon Chock
Charles Y. Huang
C. L. Tsou
Jerry H. Wang
Contents
Preface.. . . .. . . .. .. . . .. . . . . . . .... .. . . ... . . . . . . .. . . .. . . . . . . . . v
Contributors and Participants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . X111
Enzyme Kinetics and Mechanisms
Mechanistic Studies on DNA Polymerase I
V. Mizrahi, P. A. Benkovic, R. D. Kuchta, M. C. Young,
K. A. Johnson, and S. J. Benkovic ........................... .
2 Assembly and Catalytic Functions of the Subunits of Succinyl
Coenzyme A Synthetase
William A. Bridger, William T. Wolodko, and Susan P. Williams 6
3 Fatty Acid Synthetase of Chicken Liver: A Novel Active-Site
Structure for Condensation Comprised of SH Groups from a
Cysteine Residue and an Oscillating Phosphopantetheine
Swinging Arm on Adjacent Subunits
Robert Y. Hsu . ............................................ 17
4 Regulatory Properties of Glucokinase
Kenneth E. Neet, Peter S. Tippett, and Robert P. Keenan . ........ 28
5 Mechanism of Activation of Calmodulin-Dependent
Phosphatase by Divalent Metal Ions
Charles Y. Huang, Marina Lanciotti, and Aile Zhang . ........... 40
6 Studies on the Mechanism and Molecular Mode of Regulation of
Fructose-1,6-bisphosphatase
Julie E. Scheffler and Herbert J. Fromm . ...................... 48
7 Phosphorylation and dAMP Inhibition of Snake Muscle
Fructose-1,6-bisphosphatase
Gen-jwl Xu, Guo-fu Hu, Fu-kun Zhao, and Qi-chang Xia ......... 55
viii Contents
8 Identification and Characterization of Intermediates in the
Mechanism of Enzyme Action
Bert L. Vallee and David S. Auld. . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
9 Conformational Dynamics in RNA-Protein Interactions:
Immobilization of the Functional Domains in tRNAfMet
and Methionyl-tRNA Synthetase
David C. H. Yang and Blair Q. Ferguson. . . . . . . . . . . . . . . . . . . . . 71
10 Structural and Kinetic Studies of E. coli Glutamine Synthetase
J. J. Villafranca, C. D. Eads, R. LoBrutto, F. C. Wedler,
and J. Colanduoni. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
11 Cu, Zn Superoxide Dismutase: A Case of Metalloenzyme
Catalysis in Which the Protein Moiety Plays a Major Role
Adelio Rigo, Lilia Calabrese, and Giuseppe Rotilio. . . . . . . . . . . . . . 84
Regulatory Enzymes
12 Dynamic Participation of Protein Domains in Catalysis by 2-0xo
Acid Dehydrogenase Multienzyme Complexes
Richard N. Perham ...... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
13 Membrane-Bound GTP-Transducin Efficiently Activates Retinal
cGMP Phosphodiesterase
Theodore G. Wensel and Lubert Stryer . . . . . . . . . . . . . . . . . . . . . .. 102
14 Signal Transduction in the p-Adrenoceptor-Dependent
Adenylate Cyclase
Alexander Levitzki . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 113
15 Acetyl-CoA Carboxylase: Correlation of Phosphorylation State
with Allosteric Properties and Physiological State
Haris Jami! and Neil B. Madsen. . . ... ... . ........ . . .. . .. . ... 121
16 Role of Cyclic Cascades in Metabolic Regulation
P. Boon Chock, Stewart R. Jurgensen, Sue Goo Rhee,
Earl R. Stadtman, and Jackie R. Vandenheede. . . . . . . . . . . . . . . .. 128
17 Regulation of Glutamine Synthetase Activity and Its
Biosynthesis in Escherichia coli: Mediation by Three Cycles
of Covalent Modification
Sue Goo Rhee, Wong Gi Bang, Ja Hyun Koo, Kyung Hee Min,
~and Sang Chul Park. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 136
Contents ix
18 Regulation of ATP, Mg-Dependent
Protein Phosphatases
Jackie R. Vandenheede, Carline Vanden Abeele,
and Wilfried M erlevede . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 146
19 Molecular Mechanisms of Allosteric Regulation in
Aspartate Transcarbamylase
Guy Herve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 155
20 Dynamic Interactions of the Second Messenger Systems
Chiayeng Wang, Rajendra K. Sharma, and Jerry H. Wang. . . . ... 162
21 Role of Multienzyme Complexes in the Integration of
Cellular Metabolism
B. I. Kurganov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 175
Enzyme-Mediated Processes
22 Dynamics of Deoxynucleotide Synthesis in Relation
to DNA Replication
Rolf Eliasson, Marc Fontecave, and Peter Reichard. .. ... .. . . . .. 181
23 Differential Stabilization of Left-Handed Z-DNA and Z-RNA
In Vitro and In Vivo
Thomas M. Jovin and Donna J. Arndt-Jovin. . . . . . . . . . . . . . . . . .. 190
24 Interaction of Restriction Endonucleases with
Phosphorothioate DNA
Fritz Eckstein. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 200
25 Role of Conformational Dynamics of Myosin in
Muscle Contraction
Tian Yow Tsong, A. Bertazzon, and W. F. Harrington. . . . . . . . . .. 206
26 Enzymatic Modulation of Cytoskeletal Self-Assembly:
ADP Ribosylation of Microtubule Protein Components
Daniel L. Purich and Robin M. Scaife. . . . . . . . . . . . . . . . . . . . . . .. 217
27 Human Angiogenin: An Organogenic Protein
Bert L. Vallee. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 224
Membrane-Bound and Immobilized Enzymes
28 Structure and Mechanism of Action of a Membrane-Bound
Enzyme: Chloroplast Coupling Factor
Gordon G. Hammes. .. . . . . ... . . . ... . . . . ... . . .. . .. . . . . . . . .. 226
x Contents
29 Electrostatic Effects and the Dynamics of Multienzyme
Reactions at the Surface of Plant Cells
Jacques Ricard and Georges Noat ........................... 235
30 Energy Transduction by Electroconformational Coupling
R. Dean Astumian, P. Boon Chock, Hans V. Westerhoff,
and Tian Yow Tsong ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 247
31 Topics in Petroleum Biotechnology
Ching T. Hou . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 261
Enzyme Methodology
32 Experimental Determination of Rate Constants in
Enzymatic Reactions
Carl Frieden and Michael H. Penner. . . . . . . . . . . . . . . . . . . . . . . .. 268
33 Applications of Alternative Substrate Kinetics: In Vivo and In
Vitro Data on Aminoglycoside Antibiotic Inactivating Enzymes
Dexter B. Northrop. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 275
34 Kinetics of Irreversible Modification of Enzyme Activity
Wei Liu and C. L. Tsou. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 289
35 Applications of Stable Isotopes in Biochemistry
Marion H. O'Leary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 301
36 Enzyme Dynamics in Nonaqueous Media at
Subzero Temperatures
PierreDouzou ............................................ 312
37 Kinetic-Structural Organization of Enzyme Systems
B. N. Goldstein. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 322
Enzyme Structure and Functions
38 Relation Between Structure and Function in
cAMP-Dependent Protein Kinases
Susan S. Taylor, Jose Bubis, Janusz Sowadski,
Jean A. Toner, and Lakshmi D. Saraswat . . . . . . . . . . . . . . . . . . . .. 327
39 Conformation and Dynamics of Oligomeric Enzymes
C. L. Tsou. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 342
Contents Xl
40 Coenzyme Binding Site ofNAD-Dependent
Isocitrate Dehydrogenase
Roberta F. Colman. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 351
41 Significance of Domain Structure of Calmodulin on the
Activa tion of Ca 2 + -Calmodulin Requiring Enzymes
K. Yagi, M. Yazawza, O. Minowa, M. Ikura, T. Hiraoki,
K. Hikichi, and H. Toda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 362
42 Modification of Leucyl-tRNA Synthetase by Affinity Labeling
and Limited Proteolysis
J. P. Shi, S. X. Lin, S. T. Huang, F. Miao, and Y. L. Wang. .. . .. 367
43 NAD Metabolism in Eukaryotic Cells: Purification and
Characterization ofNMN Adenylyltransferase from
Baker's Yeast
G. Magni, P. Natalini, I. Santarelli, A. Vita, N. Raffaelli,
and S. Ruggieri. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 377
44 Specific f3-o-Fucosidase from Aspergillus phoenicis
Zeng Yu-cheng, Gu Ya-jun, and Zhang Shu-zheng . . . . . . . . . . . . .. 385
Site-Directed Mutagenesis of Enzymes
45 Formation of Active Aspartate Transcarbamoylase from Defective
Polypeptide Chains Produced by Site-Directed Mutagenesis
Ying R. Yang, Susan R. Wente, and H. K. Schachman .......... 394
46 Catalytic Mechanisms Revealed by Protein Engineering of
Tyrosyl-tRNA Synthetase
Alan R. Fersht . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 405
47 Site-Directed Mutagenesis of Alkaline Phosphatase
Debra A. Kendall and E. T. Kaiser. . . . . . . . . . . . . . . . . . . . . . . . . .. 411
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 415
