Biochemistry and Molecular Biology of Vitamin Ba and PQQ-dependent Proteins

Edited by Ana Iriarte Herbert M. Kagan Marino Martinez-Carrion

Springer Basel AG

Editors

Prof. Dr. Ana Iriarte Prof. Dr. Marino Martinez-Carrion Division of Molecular Biology and Biochemistry School of Biological Sciences University of Missouri Kansas City, MO 64110 USA

Prof. Dr. Herbert M. Kagan Department of Biochemistry Boston University School of Medicine 80E Concord Street Boston, MA 02118-2394 USA

Library of Congress Cataloging-in-Publication Data Biochemistry and molecu1ar biology of vitamin Be and PQQ-dependent proteins / edited by Ana Iriarte, Herbert M. Kagan, Marino Martinez-Carrion.

p. cm. Includes bibliographical references and index. ISBN 978-3-0348-9549-1 ISBN 978-3-0348-8397-9 (eBook) DOI 10.1007/978-3-0348-8397-9

1. Vitamin Be--Congresses. 2. PQQ (Biochemistry)--Congresses. 3. Enzymes--Regulation--Congresses. I. Iriarte, Ana. H. Kagan, Herbert M. IH. Martinez-Carrion, Marino. QP772.P9 B535 2000 612.3'99--dc21

Deutsche Bibliothek Cataloging-in-Publication Data Biochemistry and molecular biology of vitamin Be and PQQ-dependent proteins / ed. by Ana Iriarte ... - Basel; Boston; Berlin : Birkhäuser, 2000

ISBN 978-3-0348-9549-1

The publisher and editor can give no guarantee for the information on drug dosage and administration contained in this publication. The respective user must check its accuracy by consulting other sources of reference in each individual case.

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© 2000 Springer Basel AG Origlnally published by Birkhäuser Verlag in 2000 Softcover reprint of the hardcover 1st edition 2000 Printed on acid-free paper produced from chlorine-free pulp. TFC =

ISBN 978-3-0348-9549-1

987654321

Since the meeting in Capri in 1994, we have lost the vitality and input of the following members of the International Advisory Council. This volume is dedicated to their memory:

Jorge Churchich Paolo Fasella Alton Meister

CONTENTS

Preface ................................................................................................................................................. XIII

Acknowledgements ............................................................................................................ ................... XIV

Molecular Regulation of Enzymes Controlling Levels of Vitamin B6 Genetic and Genomic Approaches for Delineating the Pathway ofPyridoxal5'-Phosphate Coenzyme Biosynthesis in Escherichia coli ME. Winkler ............................................................................................................................................. 3

Enzymes Catalysing Formation of Pyridoxal Phosphate from Vitamin B6 D.B. McCormick ..................................................................................................................................... 11

A Divergence in the Biosynthetic Pathway and a New Role for Vitamin B6 M Ehrenschaft, ME. Daub, P. Bilski, MY. Li, c.F. Chignell, A.E. Jenns and K.R. Chung ................. 17

Molecular Cloning and Catalytic Properties of Human Brain Pyridoxal Kinase H.S Lee, B.J Moon, S Y. Choi and O.S Kwon ...................................................................................... 23

Regulation of Gene Expression of PLP-dependent Proteins Regulation of the Aspartate and Alanine Aminotransferases in Human and Rodents M Aggerbeck, F. Beurton, C. Tomkiewicz, M Garlatti, M Plee-Gautier, B. Antoine, C. Forest, F. Muzeau and R. Barouki .......................................................................................................................... 29

Mimosine's Mechanism is Pyridoxal-Phosphate Independent E. Oppenheim and P.J Stover ................................................................................................................ 35

Environmental Stimuli and Regulatory Factors Affecting the Expression ofthe Glutamic Acid Decarboxylase System in Escherichia coli A. Tramonti, P. Visca, F. Bossa and D. De Biase ................................................................................. .41

PQQ and Quinoproteins: Biology and Regulation The Membrane Glucose Dehydrogenase of Escherichia coli C. Anthony, R.A. Salleh, P.L. James and G.E. Cozier ........................................................................... .49

Structural Properties of Homodimeric Quinoprotein Ethanol Dehydrogenase from Pseudomonas aeruginosa H. Garisch, T Keitel, A. Diehl, T Knaute, Z Dauter and W Hahne .................................................... 55

Physiological Importance of Pyrroloquinoline Quinone R. Rucker, T Stites, F Steinberg and A. Mitchell .................................................................................. 61

VIII

Mechanism of Topa Quinone Biogenesis in Copper Amine Oxidase Studied by Site-Directed Mutagenesis and X-ray Crystallography K Tanizawa, H Matsunami and H Yamaguchi .................................................................................... 67

Lysyl Oxidase Activates the Transcription Activity of Collagen III Promoter: Possible Involvement of KU Antigen M Giampuzzi, R. Gusmano and A. Di Donato .. ..................................................................................... 71

TGF-~ 1 Regulation of Gingival Lysyl Oxidase and Connective Tissue Growth Factor MI. Uzel, H-H Hong, MC SheffandP.C Trackman ......................................................................... 77

Pyridoxine, Dopa Decarboxylase, and Tetrahydroisoquinoline Derivatives in Parkinson's Disease M Ebadi, P. Govitrapong and JR. Haselton ......................................................................................... 83

Lysyl Oxidase Lysyl Oxidase: A Family of Multifunctional Proteins K Cziszar, C Jourdan-Le Saux, SF.T. Fong, KSK Fong and CD. Boyd .......................................... 91

Structural Aspects of Lysyl Oxidase F. T. Greenaway, C Qui, and F. Ryvkin ................................................................................................. 97

Chemotaxis of Vascular Smooth Muscle Cells by Lysyl Oxidase W Li and H Kagan .... .......................................................................................................................... 101

Evolution and Biological Implications Biological Implications of the Different Hsp70 Binding Properties of Mitochondrial and Cytosolic Aspartate Aminotransferase A. Artigues, M T. Bengoechea-Alonso, D.L. Crawford, A. Iriarte, and M Martinez-Carrion ............ 111

Molecular Evolution of Alanine: Glyoxylate Aminotransferase Intracellular Targeting JD. Holbrook and CJ Danpure .......................................................................................................... 117

Common Structural Elements in the Architecture of the Cofactor-Binding Domains in Unrelated Families of Pyridoxal-dependent Enzymes A.I. Denesyuk, KA. Denessiouk, J V Lehtonen, T. Korpela and MS Johnson .................................. 123

Mitochondrial Localization of Eukaryotic NifS-Like Proteins Y Nakai, Y Yoshihara, M Nakai, H Hayashi and H Kagamiyama ................................................... 129

Mechanistic Studies of 8-Amino-7-0xononanoate Synthase SP. Webster, D. Alexeev, D.J Campopiano, L.J Mullan, L. Sawyer and R.L. Baxter ....................... 135

Tryptophan Synthase, Tryptophanase and Serine Transhydroxymethylase Structure and Function of Tryptophan Synthase

IX

E. W. Miles, YX Fan, KH. Jhee, H.s. Ro, P. McPhie, S. Rhee and D.R. Davies ................................ 145

Salt Bridging and Mova1ent Cation Binding Regulate Catalysis and Channeling in Tryptophan Synthase MF Dunn, E. U Woehl, D. Ferrari, 0. Hur, U Banik, L.-H. Yang and E. W. Miles .......................... 151

Equilibrium Isotope Effects: Evidence for Low-Barrier H-Bonding in Tryptophanase D. Niks, TH. Morton and MF Dunn ................................................................................................... 157

3-Dimensiona1 Structures of Rabbit Cytoso1ic and E. coli Serine Hydroxymethyltransferase V Schirch, J.N Scarsdale, M di Salvo, S. Della Fratte and H. T Wright ........................................... 161

Role of Y65 and E57 in Escherichia coli Serine Hydroxymethy1transferase S. Angelaccio, R. Contestabile, P. Di Giovine, F Bossa and V Schirch .. ........................................... 167

Reaction and Structure of 1-aminocyc1opropane-l-carboxy1ate Deaminase M Honma, T Murakami, T Ose, H. Matsui and I Tanaka ................................................................. 171

Transaminases Refined Reaction Mechanism of Aspartate Aminotransferase H. Hayashi, H. Mizguchi, Y Nakajima, I Miyahara, K Hirotsu and H. Kagamiyama ...................... 177

lH and 15N NMR Spectroscopy of Aspartate Aminotransferase and Related Schiff Bases and Tautomerism in Enzyme Active Sites D.E. Metzler, CM Metzler, E. T Mollova and T Higaki .................................................................... 183

Structure, Induced Fit and Substrate Recognition of E. coli Branched-Chain Amino Acid Aminotransferase K Hirotsu, M Goto, I Miyahara, H. Hayashi, H. Kagamiyama and K Okada .. ............................... 189

Structure and Mechanisms of Quinoenzymes Tryptophan TryptophY1quinone Enzymes: Structure and Function V Davidson .............................................. ............................................................................................. 197

Continuous-Flow Column Electrolytic Spectroe1ectrochemica1 Method for Determination of Protein Redox Potentials - Application to Quinoproteins T Ikeda, A. Sato, K Takagi, M Torimura and K Kano ...................................................................... 203

Enantiose1ectivity of PQQ-containing Alcohol Dehydrogenases: Kinetic, Thermodynamic, and Molecular Modeling A. Jongejan and J.A. Jongejan ............................................................................................................. 209

x

Structural Studies of a Soluble Monomeric Quinohemoprotein Alcohol Dehydrogenase from Pseudomonas putida HKS F.s. Mathews and Z Chen .................................................................................................................... 213

Electron Transport Systems for Quinohemoprotein Type II Alcohol Dehydrogenase of Pseudomonas putidaHKS K. Matsushita, T Yamashita, N Aoki, H Toyama and 0. Adachi ....................................................... 219

Cellular and Molecular Biology: Models with PLP-Dependent Proteins Activation and Transformation of Cells Induce Translocation of Ornithine Decarboxylase (ODC) to the Surface Membrane M Heiskala, J. Zhang, S. Hayashi, E. Holtta and L.C Andersson ...................................................... 227

A Partially Folded Conformation Is Not the Only Requirement for Import of Mitochondrial Aspartate Aminotransferase J.R. Mattingly, C Torella and A.J. Yanez ............................................................................................ 233

Engineering of B6 Enzymes E. Sandmeier, B. Mouratou, P. Kasper, R. Graber, D. de Vries, P. Mehta, H Gehring and P. Christen ..................................................................................................................................... 239

Association of Newly Synthesized Mitochondrial Aspartate Aminotransferase with Cytosolic Factors B. Lain, CA. Tanase, A. lriarte, A.E. Johnson and M Martinez-Carrion ........................................... 245

Heterologous Expression and Purification of Serine Palmitoyltranferase H lkushiro, H Hayashi and H Kagamiyama ...................................................................................... 251

Dehydratases, Lyases and Other PLP-dependent Proteins 5-Aminolevulinate Synthase: Pre-Steady State Reaction and Functional Role of Specific Active Site Residues G.C Ferreira .............................................. .......................................................................................... 257

Functional Role ofPLP in Bacterial Phosphorylases R. Schinzel, D. Palm, B. Bock and B. Nidetsky ..................................................................................... 265

Inhibition and Structural Changes of O-Acetylserine Sulthydrylase-A from Salmonella typhimurium upon Binding Sulfate and Chloride Anions CH Tai, P. Burkhard, J.N Jansonius and P.F. Cook ......................................................................... 271

Structure-Function Relationships of Porcine Pyridoxal Kinase Y.C Leung, HY. Wong, J.E. Churchich, S.CL. LoandF. Kwok ........................................................ 277

The Contribution of a Conformationally-Mobile, Active-Site Loop to the Reaction Catalysed by Glutamate Semialdehyde Aminomutase R. Contestabile, S. Angelaccio, R. May tum, F. Bossa and R.A. John .................................................. 281

XI

The Reactions of Glutamate I-Semialdehyde Aminomutase with (R) and (8) Enantiomers of a Novel, Mechanism-Based Inhibitor, 2, 3-Diaminopropyl Sulfate R.A. John, K Khayer, T Jenn, M Akhtar, D. Gani and R. Contestabile ............................................. 285

Structure and Function of E. Coli Pyridoxine Phosphate Oxidase M di Salvo, E. Yang, M Safo, F. Musayevand V Schirch ................................................................. 289

Molecular Pathology and Medicine Role of Branched Chain Aminotransferase Isoenzymes in the Central Nervous System S.M Hutson, E. Lieth and KF. LaNoue ............................................................................................... 295

Modulation of Gene Expression by Vitamin B6 Y. Natori, T OkaandM Kuwahata ................................................ ..................................................... 301

Pyridoxal 5'-phosphate and Calcium Channels K Dakshinamurti, KJ. Lal, NS. Dhalla, S. Musat and X Wang ........................................................ 307

GAB A-aminotransferase, a Target for Antiepileptic Drug Therapy P. Storici, G. Capitani, D. De Biase, R.A. John, J.N Jansonius and T Schirmer ............................... 316

Decarboxylases and D-Amino Acid Transaminase Mouse Ornithine Decarboxylase: Structural Comparisons to Other PLP-Dependent Enzymes ML. Hackert, A. Kern, M Oliveira, J. Almrud, D. Carroll and S. Ernst ........................................... 321

Structural and Mechanistic Studies of Trypanosoma brucei Ornithine Decarboxylase MA. Phillips ................................................... ...................................................................................... 327

Mechanistic Analysis of Dialkylglycine Decarboxylase MD. Toney, X Zhou and S Sun ........................................................................................................... 333

Studies on an Active Site Residue, EI77, That Affects Binding of the Coenzyme in D-Amino Acid Transaminase, and Mechanistic Studies on a Suicide Substrate P. W. van Ophem, B. W. Lepore, K Kishimoto, D. Ringe and J.M Manning ....................................... 339

Biotechnology and Applications of Emerging Technologies Functional Properties ofImmobilized Pyridoxal 5'-phosphate-dependent Enzymes Probed by Absorption Microspectrophotometry A. Mozzarelli, B. Campanini, S Bettati and A. Peracchi ..................................................................... 349

Characterization of Recombinant Porcine Pyridoxal Kinase Using Surface Plasmon Resonance Biosensor Technique C C F ong, W. P. Lai, M Yang, Y. C Leung and M S. Wong ................................................................ 355

Three-Dimensional Model of the ATP-Binding Domain of Pyridoxal Kinase CK. Lau, A.K.M Leung, F.T Chau, F. Kwokand SCL. Lo .............................................................. 359

XII

Structural Fluctuations of Pyridoxal Kinase: Effect ofViscogen Cosolvents Y.c. Leung and J.E. Churchich ............................................................................................................ 363

The Aspartate Aminotransferase Folding Intermediates Recognized by GroEL are Partially Folded Monomers that Bind Pyridoxal Phosphate MJ. McNeill, S. Scherrer, F. Donate, C. Torella, A. Iriarte and M Martinez-Carrion ...................... 369

Author Index ......................................................................................................................................... 375

PREFACE

Since the first international meeting on Vitamin B6 involvement in catalysis took place in 1962, there have been periodic meetings every three or four years. In 1990, scientists studying another cofactor, PQQ, which had already attracted the scientific community's interest for its possible involvement in amino acid decarboxylation and reactions involving amino groups, joined forces with those investigating pyridoxal phosphate-dependent enzymes. Since then, the international PQQ/quinoproteins meetings have been held jointly. In the years following the original meeting 37 years ago in Rome, Italy, the scientific gatherings have taken place in Moscow, Russia (1966); Nagoya, Japan (1967); Leningrad (St. Petersburg), Russia (1974); Toronto, Canada (1979); Athens, Greece (1983); Turku, Finland (1987); Osaka, Japan (1990); and Capri, Italy (1996). For the first time in the history of these symposia, the international meeting was held in the United States, from October 31 through November 5, 1999, in Santa Fe, New Mexico.

The scientific program focus shifted significantly beyond the original emphasis on catalysis to aspects such as cellular and genetic regulation of events involving proteins that require pyridoxal phosphate or quinoproteins. The growing awareness of the involvement of these proteins in biotechnology processes and fundamental physiological events, as well as their implication in diseases, was also represented, with emphasis on the molecular basis of these events.

The meeting was symposium S278, sponsored by the International Union of Biochemistry and Molecular Biology (IUBMB).

This volume incorporates highlights of the presentations made during the meeting, which have been speedily processed in order to share the information with the scientific community in a timely fashion.

The Editors

Ana Iriarte Herbert M. Kagan Marino Martinez-Carrion

ACKNOWLEDGEMENTS

Honorary President ESMOND E. SNELL (USA)

International Advisory Board Osao Adachi (Japan) Robert Barouki (France) Temir Berezov (Russia) Francesco Bossa (Italy) Philipp Christen (Switzerland) Jorge Churchich (Hong Kong) Krishnamurti Dakshinamurti (Canada) Shawn Doonan (United Kingdom) Johannis Duine (The Netherlands) Athanasios Evangelopoulos (Greece) Toshio Fukui (Japan) Robert John (United Kingdom) Hiroyuki Kagamiyama (Japan) Herbert M. Kagan (USA)

U.S. Organizing Committee Marino Martinez-Carrion, President Laura Batenic, Secretary/Treasurer

Jorge Churchich James Manning Paul Cook Scott Matthews Leodis Davis Donald McConnick David Dooley

Sponsors

Jack F. Kirsch (USA) Timo Korpela (Finland) Johan Jansonius (Switzerland) Gennaro Marino (Italy) Marino Martinez-Carrion (USA) Donald McConnick (USA) David Metzler (USA) Yoshimasa Morino (Japan) Verne Schirch (USA) Klaus Schnackerz (Gennany) Kenji Soda (Japan) Yuri Torchinsky (Israel) Edith Wilson-Miles (USA)

Edith Wilson-Miles Michael Dunn David Metzler Herbert Kagan Verne Schirch Jack Kirsch

International Union of Biochemistry and Molecular Biology (IUBMB); Bayer Corporation, Pharmaceutical Division; BioMo1ecular Instruments, Division of Thenno Instrument Systems; Chiron Corporation; Merck, Sharp & Donne Research Laboratories; MitoKor; Parke-Davis Pharmaceutical Division of Warner-Lambert Corp.; School of Biological Sciences, University of Missouri-Kansas City