A Functional-Phylogenetic Classification System For
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MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, June 2000, p. 354–411 Vol. 64, No. 2 1092-2172/00/$04.00ϩ0 Copyright © 2000, American Society for Microbiology. All Rights Reserved. A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters MILTON H. SAIER, JR.* Department of Biology, University of California at San Diego, La Jolla, California 92093-0116 Downloaded from INTRODUCTION .......................................................................................................................................................355 TRANSPORT NOMENCLATURE ...........................................................................................................................356 CONSIDERATIONS FOR THE SYSTEMATIC CLASSIFICATION OF TRANSMEMBRANE SOLUTE TRANSPORTERS...............................................................................................................................................357 THE TC SYSTEM ......................................................................................................................................................358 Category 1: Channels and Pores ..........................................................................................................................359 1.A. ␣-Type channels..........................................................................................................................................359 1.B. -Barrel porins ...........................................................................................................................................359 1.C. Pore-forming toxins....................................................................................................................................359 1.D. Non-ribosomally synthesized channels....................................................................................................359 http://mmbr.asm.org/ Category 2: Electrochemical Potential-Driven Porters......................................................................................359 2.A. Porters (uniporters, symporters, and antiporters) ................................................................................359 2.B. Non-ribosomally synthesized porters .......................................................................................................359 2.C. Ion gradient-driven energizers..................................................................................................................359 Category 3: Primary Active Transporters............................................................................................................359 3.A. Diphosphate bond hydrolysis-driven transporters.................................................................................359 3.B. Decarboxylation-driven transporters........................................................................................................359 3.C. Methyl transfer-driven transporters ........................................................................................................359 3.D. Oxidoreduction-driven transporters ........................................................................................................359 3.E. Light absorption-driven transporters ......................................................................................................360 Category 4: Group Translocators .........................................................................................................................360 on September 8, 2019 at CONCORDIA UNIV 4.A. Phosphotransfer-driven group translocators ..........................................................................................360 Category 8: Accessory Factors Involved in Transport.......................................................................................360 8.A. Auxiliary transport proteins......................................................................................................................360 Category 9: Incompletely Characterized Transport Proteins ...........................................................................360 9.A. Transporters of unknown biochemical mechanism................................................................................360 9.B. Putative but uncharacterized transport proteins ...................................................................................360 9.C. Functionally characterized transport proteins with unidentified sequences......................................360 FAMILIES OF TRANSPORTERS ...........................................................................................................................360 CHARACTERISTICS OF THE FAMILIES............................................................................................................367 CROSS-REFERENCING PERMEASES BY ACCESSION NUMBER ...............................................................367 GROUPING TRANSPORT SUBSTRATES BASED ON BIOLOGICAL SIGNIFICANCE .............................376 DISTRIBUTION OF TRANSPORTER TYPES BASED ON SUBSTRATE SPECIFICITY.............................377 SUBSTRATE SELECTIVITIES ................................................................................................................................379 Cytoplasmic Membrane Channel Proteins (Excluding Porins) .......................................................................379 Bacterial Outer Membrane Porins.......................................................................................................................380 Secondary Carriers.................................................................................................................................................380 Primary Carriers for Inorganic Ions ...................................................................................................................394 CELLULAR MACROMOLECULAR EXPORT SYSTEMS..................................................................................395 CLASSIFICATION OF TRANSPORTERS OF UNKNOWN MECHANISM.....................................................395 PREDICTIONS OF TRANSPORT MODE BASED ON PROTEIN TOPOLOGY............................................399 RECOGNIZED DISTRIBUTION OF TRANSPORTER FAMILIES IN THE THREE DOMAINS OF LIFE...............................................................................................................................................................401 TRANSPORT PROTEINS FOR WHICH THREE-DIMENSIONAL STRUCTURAL DATA ARE AVAILABLE.........................................................................................................................................................404 TRANSPORTER FAMILIES INCLUDING NONTRANSPORTING HOMOLOGS.........................................404 AUXILIARY TRANSPORT PROTEINS..................................................................................................................405 CONCLUSIONS AND PERSPECTIVES.................................................................................................................407 ACKNOWLEDGMENTS ...........................................................................................................................................407 ADDENDUM IN PROOF..........................................................................................................................................407 REFERENCES ............................................................................................................................................................408 * Mailing address: Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116. Phone: (858) 534-4084. Fax: (858) 534-7108. E-mail: [email protected]. 354 VOL. 64, 2000 CLASSIFICATION OF TRANSMEMBRANE SOLUTE TRANSPORTERS 355 “To know truly is to know by causes.” ogy with chemical reactions catalyzed by enzymes, the protein- Francis Bacon aceous nature of all types of permeases became firmly established (reviewed by Kaback [58]). “To me life consists simply in this, in the fluctuation between With the advent of gene-sequencing technologies, the pri- two poles, in the hither and thither between the two foundation mary structures of permeases first became available. Hydro- pillars of the world.” phobicity analyses of these sequences revealed the strikingly Herman Hesse hydrophobic nature of various types of integral membrane transporters (19, 68, 70, 95). Current multidisciplinary ap- INTRODUCTION proaches are slowly yielding three-dimensional structural in- formation about transport systems. However, since only a few Downloaded from Transport systems serve the cell in numerous capacities such systems have yielded to X-ray crystallographic analyses (118–123). First, they allow entry of all essential nutrients into (see, for example, references 26, 140, and 142 as well as Table the cytoplasmic compartment and subsequently into or- 21 below), we still base our views of solute transport on mo- ganelles, allowing metabolism of exogenous sources of carbon, lecular models that provide reasonable pictures of transport nitrogen, sulfur, and phosphorus. Second, they provide a systems and the processes they catalyze without providing ab- means for the regulation of metabolite concentrations by cat- solute assurance of accuracy (45, 59, 143). alyzing the excretion of end products of metabolic pathways It is well recognized that any two proteins that can be shown from organelles and cells. Third, they mediate the active ex- to be homologous (i.e., that exhibit