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Advances in MICROBIAL PHYSIOLOGY VOLUME 40 This Page Intentionally Left Blank Advances in MICROBIAL PHYSIOLOGY Edited by R. K. POOLE Department of Molecular Biology and Biotechnology The Krebs Institute for Biomolecular Research The University of Sheffield Firth Court, Western Bank ShefJield SIO 2TN, UK Volume 40 ACADEMIC PRESS San Diego London Boston New York Sydney Tokyo Toronto This book is printed on acid-free paper. Copyright 0 1998 by ACADEMIC PRESS All Rights Reserved. No part of this publication 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. Academic Press 525 B Street, Suite 1900, San Diego, California 92101-4495, USA http://www.apnet.com Academic Press 24-28 Oval Road, London N W l 7DX, UK ISBN 0-12-027740-9 A catalogue record for this book is available from the British Library Typeset by Keyword Typesetting Services Ltd, Wallington, UK Printed in Great Britain by MPG Books Ltd, Bodmin, Cornwall 98 99 00 01 02 03 M P 9 8 7 6 5 4 3 2 1 Contents CONTRIBUTORS TO VOLUME 4 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix The Biochemistry, Physiology and Genetics of PQQ and PQQ-containing Enzymes Pat M. Goodwin and Chris Anthony 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2. PQQ in bacteria. . . . , . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 3. The quinoprotein dehydrogenases containing PQQ , . . . . . . . . . . . . 7 4. The importance of divalent metal ions in the structure and function of PQQ-containing quinoproteins . . . . . . . . . . . , . . . . . . 20 5. The structure and mechanism of PQQ-containing quinoproteins . . 26 6. Quinoproteins in energy transduction . . . . . . . . . . . . . . . . . . . . , 35 7. The physiological functions of the quinoprotein dehydrogenases . . 42 8. Synthesis of PQQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . , . . . . . . 5 1 9. Regulation of synthesis of PQQ and quinoprotein dehydrogenases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 9 10. Concluding remarks. . . . . . . . . . . . . . . . . . , . . . . . . . . , . . . . . . 6 6 Acknowledgements . . . . . . . . . . . . . . . . . , . . . . . . . . . . . . . . . . 6 7 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . , . . . . . . 6 7 Molecular Phylogeny as a Basis for the Classification of Transport Proteins from Bacteria, Archaea and Eukarya Milton H. Saier, Jr 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 3 2. Considerations for the systematic classification of transmembrane solute permeases. . . . . , . . . . . . . . . . . . . . . . . . . 84 vi CONTENTS 3. Proposed transport protein classification system . . . . . . . . . . . . . . 86 4 . Diverse evolutionary origins of integral membrane transport protein families . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95 5 . The major facilitator superfamily (MFS) . . . . . . . . . . . . . . . . . .107 6. The ATP-binding cassette (ABC) superfamily. . . . . . . . . . . . . . . 109 7. Prokaryotic genome sequence analyses. . . . . . . . . . . . . . . . . . . . 121 8. Independent evolution of distinct transport modes and energy-coupling mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 9 . Proposed independent evolution of different channel and carrier 127 families . . . . . . . . . . . . . . . . . . .