MoLECUlAR BIOLOGY INTELLIGENCE UNIT

PROTEIN TOXIN STRUCTURE

Michael W Parker, D.Phil. St. Vincent's Institute of Medical Research

Melbourne, Australia

Springer-Verlag Berlin Heidelberg GmbH RG. LANDES CoMPANY

AUSTIN

MOLECULAR BIOLOGY INTELLIGENCE UNIT PROTEIN TOXIN STRUCTURE

R.G. LANDES COMPANY Austin, Texas, U.S.A.

International Copyright © 1996 Springer-Verlag Berlin Heidelberg Originally published by Springer-Verlag, Heidelberg, Germany in 1996 Softcover reprint of the hardcover lst edition 1996

All rights reserved. No part of this book may be reproduced or transmitted in any form or by any means, elec­tronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher.

'Springer

International ISBN 978-3-662-22354-3

While the authors, editors and publisher believe that drug selection and dosage and the specifications and usage of equipment and devices, as set forth in this book, are in accord with current recommend­ations and practice at the time of publication, they make no warranty, expressed or implied, with respect to material described in this book. In view of the ongoing research, equipment development, changes in governmental regulations and the rapid accumulation of information relating to the biomedical sciences, the reader is urged to carefully review and evaluate the information provided herein.

Library of Congress Cataloging-in-Publication Data

Protein toxin structure I [edited by} Michael W. Parker. p. em. -(Molecular biology intelligence unit)

Includes bibliographical references and index. ISBN 978-3-662-22354-3 ISBN 978-3-662-22352-9 (eBook) DOI 10.1007/978-3-662-22352-9

1. Toxins-Structure-activity relationships. I. Parker, Michael W., 1959-. II. Series. QP631.P76 1996 615'.373-dc20

96-21770 CIP

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r,======CONTENTS====~

1. Introduction ............................................................................... 1 joseph E. Alouf

2. Insights into Membrane Insertion Ba~ed on Studies of Colicins ....................................................... 5 Ingrid R. Vetter, Michael W. Parker, Franc Pattus

and Demetrius Tsernoglou Domain Organization of the Colicins ................................................... 6 Receptor Binding .................................................................................. 8 Translocation ........................................................................................ 8 The Bacteriocidal Effect ........................................................................ 9 Structure of the Pore-Forming Domain .............................................. 10 Channel Formation ............................................................................. 14 Structure of the Receptor Binding and Translocation Domain ............ 16 Binding and Transport of Colicin N ................................................... 17 Immunity Proteins .............................................................................. 18 Conclusions ........................................................................................ 19

3. A Structure-Based Model of Diphtheria Toxin Action .............. 25 David Eisenberg, Charles E. Bell, Melanie J Bennett, R. john Collier,

Michael P. Schlunegger, Boyd A. Steere and Manfred S. Weiss Molecular Introduction ....................................................................... 27 Oligomeric Forms ofDT .................................................................... 33 Mechanism for Intoxication by DT .................................................... 37 The Mechanism of Action of the C Domain ....................................... 39

4. Insecticidal 8-Endoto:xins from Bacillus thuringiensis ................ 49 jade Li Cry 8-Endotoxin Structures ................................................................. 51 Structure of the Mosquitocidal and Cytolytic Toxin CytB .................. 64 Concluding Remarks .......................................................................... 69

5. Structure and Assembly of the Channel-Forming Aero monas Toxin Aero lysin ...................................................... 79 Michael W. Parker, J Thomas Buckley, F. Gisou van der Goot

and Demetrius Tsernoglou Primary Structures .............................................................................. 79 The 3-D Structure .............................................................................. 81 Aero lysin Is a Dimer ........................................................................... 82 Mobility .............................................................................................. 84 Inhibition by Zinc Ions ....................................................................... 84 Receptor Binding ................................................................................ 85 Activation ........................................................................................... 85 Oligomerization .................................................................................. 87 Channel Formation ............................................................................. 88 Mechanism of Toxic Action ................................................................ 89 Relationship to Other Toxins .............................................................. 89 Conclusions and Future Studies .......................................................... 90

6. The Anthrax Toxin ................................................................... 97 Carlo Petosa and Robert C. Liddington Intoxication by Anthrax ...................................................................... 98 Components of the Anthrax Toxin ................................................... 101 The PA63 Oligomer ........................................................................... 111 Homology With Iota-IB Toxin ......................................................... 111 A Hypothetical Model for Oligomerization

and Membrane Insertion ............................................................... 112 Concluding Remarks ........................................................................ 116

7. The Cholera Family ofEnterotoxins ....................................... 123 David L. Scott, Rong-Guang Zhang and Edwin M Westbrook B Subunit Architecture ..................................................................... 124 The A (Catalytic) Subunit-Overview .............................................. 133 Mechanism of Action ........................................................................ 138

8. E. coli Heat Labile Enterotoxin and Cholera Toxin B-Pentamer-Crystallographic Studies of Biological Activity ............................................................... 14 7 Ethan A. Merritt, Focco van den Akker and Wim G.] Hoi Architecture of the AB5 Assembly ..................................................... 150 Receptor Binding Site ....................................................................... 155 TheActiveSiteofLT ........................................................................ 158 Therapeutic Applications .................................................................. 163

9. Shiga Toxin ............................................................................ 173 Marie E. Fraser, Maia M. Chernaia, Yuri V. Kozlov

and Michael N. G. james Description of the Holotoxin ............................................................ 174 B Pentamer ....................................................................................... 177 The Pore and A2 ............................................................................... 180 Other A-B Interactions ..................................................................... 183 The A Subunit .................................................................................. 184 Future Research ................................................................................ 186

10. Structural Insights into Pertussis Toxin Action ...................... 191 Penelope E. Stein, Bart Hazes and Randy J Read Structure ofPertussis Toxin .............................................................. 194 Receptor Binding .............................................................................. 199 Intracellular Trafficking .................................................................... 202 ATP-Binding to Pertussis Toxin ....................................................... 203 Future Directions .............................................................................. 209

11. Structure ofT oxic Shock Syndrome T oxin-1 ... ....................... 217 Douglas H Ohlendorf, David T. Mitchell, G. Sridhar Prasad,

R. Radhakrishnan, Cathleen A. Earhart and Patrick M Schlievert Biological Relevance .......................................................................... 217 Structure ofTSST-1 ......................................................................... 219 Functionally Important Features ....................................................... 223

12. Structure of Staphylococcal Enterotoxins ...................... .......... 231 S. Swaminathan, William Furey and Martin Sax Structure of SEB ............................................................................... 233 Structure of SEC2 ............................................................................. 233 Modeling of SEA and SEE ................................................................ 235 Mutational Analysis on SEB and Structural Features ......................... 236 TCR Binding Site ............................................................................. 239 MHCII Binding Site inS. Enterotoxins ............................................ 241 Possible Biological Role of the a4 Face of SEB .................................. 243 Emetic Site ........................................................................................ 243 V~ Specificity .................................................................................... 243 Oligomer Binding Fold and the Binding

of Glycosphingolipids to SEB ........................................................ 247 Conclusion ........................................................................................ 247

13. The Structure of Ribosome Inactivating Proteins from Plants ............................................................... 253 jon D. Robertus and Arthur F Monzingo Biochemistry Background of RIPs ..................................................... 254 X-Ray Structure of RIPs .................................................................... 255 Ricin A Chain ................................................................................... 256 The Ricin B Chain ............................................................................ 265

14. The Structures and Evolution of Snake Toxins of the Three-Finger Folding Type .......................................... 271 Dominique Housset and juan C Fontecilla-Camps Structural Comparison ofThree-Finger Snake Toxins ...................... 272 The Evolution ofThree-Finger Snake Toxins ................................... 281

15. The Structure of a Virally Encoded Fungal Toxin from Ustilago Maydis that Inhibits Fungal and Mammalian Calcium Channels ........................................ 291 Fei Gu, Anis Khimani, Stan Rane, William H. Flurkey,

Robert F Bozarth and Thomas J Smith KP4 Structure ................................................................................... 293 Mechanisms ofKP4 Action Suggested by Its Structure ..................... 296 Biochemical Studies on KP4 Mechanism of Action ........................... 297 Conclusions ...................................................................................... 298

rr============== EDITOR ================il

Michael W. Parker, D.Phil. The Ian Potter Foundation Protein Crystallography Laboratory

St. Vincent's Institute of Medical Research Melbourne, Australia Chapter 2, Chapter 5

t======== CONTRIBUTORS ==========I

Joseph E. Alouf Institut Pasteur Unite des Toxines Microbiennes Paris, France Chapter I

Charles E. Bell Molecular Biology Institute

and UCLA DOE Laboratory of Structural Biology and Molecular Medicine

University of California at Los Angeles

Los Angeles, California, USA Chapter 3

Melanie J. Bennett Department of Biochemistry

and Biophysics School of Medicine, University

of Pennsylvania Philadelphia, Pennsylvania, USA Chapter3

Robert F. Bozarth Department ofLife Sciences Indiana State University Terre Haute, Indiana, USA Chapter I5

J. Thomas Buckley Department of Biochemistry

and Microbiology University of Victoria British Columbia, Canada Chapter 5

Maia M. Chernaia Medical Research Council of Canada

Group in Protein Structure and Function

Department of Biochemistry University of Alberta Edmonton, Alberta, Canada Chapter 9

R. John Collier Department of Microbiology

and Molecular Genetics Harvard Medical School, Shipley

Institute of Medicine Boston, Massachusetts, USA Chapter3

Cathleen A. Earhart Department of Biochemistry University of Minnesota Medical

School Minneapolis, Minnesota, USA Chapter II

David Eisenberg Molecular Biology Institute

and UCLA DOE Laboratory of Structural Biology and Molecular Medicine

University of California at Los Angeles

Los Angeles, California, USA Chapter3

William H. Flurkey Department of Chemistry Indiana State University Terre Haute, Indiana, USA Chapter 15

Juan C. Fontecilla-Camps Institut de Biologie Structurale Jean­

Pierre Ebel, CEA-CNRS Grenoble, France Chapter14

Marie E. Fraser Medical Research Council of Canada

Group in Protein Structure and Function

Department of Biochemistry University of Alberta Edmonton, Alberta, Canada Chapter 9

William Furey Biocrystallography Laboratory VA Medical Center Pittsburgh, Pennsylvania, USA Chapter 12

FeiGu Department ofBiological Sciences Purdue University West Lafayette, Indiana, USA Chapter 15

Bart Hazes Department of Medical Microbiology

and Immunology University of Alberta Edmonton, Alberta, Canada Chapter 10

WimG.J. Hol Biomolecular Structure Center Howard Hughes Medical Institute University ofWashington School of

Medicine Seattle, Washington, USA Chapter 8

Dominique Housset lnstitut de Biologie Structurale Jean­

Pierre Ebel, CEA-CNRS Grenoble, France Chapter 14

Michael N.G. James Medical Research Council of Canada

Group in Protein Structure and Function

Department of Biochemistry University of Alberta Edmonton, Alberta, Canada Chapter 9

Anis Khimani Department of Life Sciences Indiana State University Terre Haute, Indiana, USA Chapter 15

Yuri V. Kozlov Englehardt Institute of Molecular

Biology, Academy of Sciences of Russia

University of Oslo Center for Medical Studies

Moscow, Russia Chapter 9

Jade Li Molecular Research Council

Laboratory of Molecular Biology Cambridge, England Chapter4

Robert C. Liddington Dana-Farber Cancer Institute Boston, Massachusetts, USA Chapter 6

Ethan A. Merritt Department of Biological Structure Biomolecular Structure Center University ofWashington School

of Medicine Seattle, Washington, USA ChapterS

David T. Mitchell Department of Biochemistry University of Minnesota Medical

School Minneapolis, Minnesota, USA Chapter 11

Arthur F. Monzingo Department of Chemistry

and Biochemistry University ofTexas Austin, Texas, USA Chapter 13

Douglas H. Ohlendorf Department of Biochemistry University of Minnesota Medical

School Minneapolis, Minnesota, USA Chapter 11

Franc Pattus Departement Recepteurs et Proteines

Membranaires CNRS, Ecole Superieure

de Biotechnologie de Strasbourg Illkirch, F ranee Chapter 2

Carlo Petosa Dana-Farber Cancer Institute Boston, Massachusetts, USA Chapter6

G. Sridhar Prasad Molecular Biology Department Scripps Research Institute LaJolla, California, USA Chapter 11

R. Radhakrishnan Center of Macromolecular

Crystallography Department of Pharmacology University of Alabama

at Birmingham Birmingham, Alabama, USA Chapter 11

Stan Rane Department of Biological Sciences Purdue University West Lafayette, Indiana, USA Chapter 15

Randy J. Read Department of Medical

Microbiology and Immunology University of Alberta Edmonton, Alberta, Canada Chapter IO

Jon D. Robertus Department of Chemistry

and Biochemistry University ofTexas Austin, Texas, USA Chapter 13

Martin Sax Biocrystallography Laboratory VA Medical Center Pittsburgh, Pennsylvania, USA Chapter I2

Patrick M. Schlievert Department of Microbiology University of Minnesota Medical

School Minneapolis, Minnesota, USA Chapter II

Michael P. Schlunegger Molecular Biology Institute

and UCLA DOE Laboratory of Structural Biology and Molecular Medicine

University of California at Los Angeles

Los Angeles, California, USA Chapter3

David L. Scott Medical Services Massachusetts General Hospital Boston, Massachusetts, USA Chapter 7

Thomas J. Smith Department ofBiological Sciences Purdue University West Lafayette, Indiana, USA Chapter I5

Boyd A. Steere Molecular Biology Institute

and UCLA DOE Laboratory of Structural Biology and Molecular Medicine

University of California at Los Angeles

Los Angeles, California, USA Chapter 3

Penelope E. Stein Department of Medical

Microbiology and Immunology University of Alberta Edmonton, Alberta, Canada Chapter IO

S. Swaminathan Biocrystallography Laboratory VA Medical Center Pittsburgh, Pennsylvania, USA Chapter I2

Demetrius T sernoglou Department of Biochemical Sciences Universidt di Roma "La Sapienza" Rome, Italy Chapter 2, Chapter 5

Focco van den Akker Department of Biological Structure Biomolecular Structure Center University ofWashington School

of Medicine Seattle, Washington, USA Chapter8

F. Gisou van der Goot Departement de Biochimie U niversite de Geneve Geneva, Switzerland Chapter 5

Ingrid R. Vetter Max-Planck-Institute for Molecular

Physiology Dortmund, Germany Chapter 2

Manfred S. Weiss Molecular Biology Institute

and UCLA DOE Laboratory of Structural Biology and Molecular Medicine

University of California at Los Angeles

Los Angeles, California, USA Chapter 3

Edwin M. Westbrook Center for Mechanistic Biology

and Biotechnology Argonne National Laboratory Argonne, Illinois, USA Department of Biochemistry,

Molecular Biology and Cell Biology Northwestern University Evanston, Illinois, USA Chapter 7

Rong-Guang Zhang Center for Mechanistic Biology

and Biotechnology Argonne National Laboratory Argonne, Illinois, USA Chapter 7

AcKNOWLEDGMENTS I wish to thank Dr. Colin Blake for introducing me to the world

of protein crystallography and Pro£ Demetrius Tsernoglou in whose lab my interest in toxin structures developed. I thank the Wellcome Trust for their support of my work through the award of a Wellcome Australian Senior Research Fellowship in Medical Science. Finally, I wish to thank Marisa Bertocchi for her assistance in preparing the manuscript of this book.

Michael W. Parker May 1996