TC number
Encyclopedia
Transporter Classification database (or TCDB) is an International Union of Biochemistry and Molecular Biology
(IUBMB) approved classification system for membrane transport proteins including ion channel
s. This classification system was designed to be analogous to the EC number
system for classifying enzymes, but it also uses phylogenetic information.
International Union of Biochemistry and Molecular Biology
The International Union of Biochemistry and Molecular Biology is an international non-governmental organisation concerned with biochemistry and molecular biology...
(IUBMB) approved classification system for membrane transport proteins including ion channel
Ion channel
Ion channels are pore-forming proteins that help establish and control the small voltage gradient across the plasma membrane of cells by allowing the flow of ions down their electrochemical gradient. They are present in the membranes that surround all biological cells...
s. This classification system was designed to be analogous to the EC number
EC number
The Enzyme Commission number is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze....
system for classifying enzymes, but it also uses phylogenetic information.
Classification
The upper level of classification and a few examples of proteins with known 3D structure:1.A α-Type channels
- 1.A.1 Voltage-gated ion channelVoltage-gated ion channelVoltage-gated ion channels are a class of transmembrane ion channels that are activated by changes in electrical potential difference near the channel; these types of ion channels are especially critical in neurons, but are common in many types of cells....
superfamily - 1.A.2 Animal inward-rectifier K+ channel
- 1.A.3 Ryanodine-inositol-1,4,5-trisphosphate receptor Ca2+ channel
- 1.A.4 Transient receptor potential Ca2+ channel
- 1.A.5 Polycystin cation channel
- 1.A.6 Epithelial Na+ channel
- 1.A.7 ATP-gated cation channel
- 1.A.8 Major intrinsic protein
- 1.A.9 Ligand-gated ion channelLigand-gated ion channelLigand-gated ion channels are one type of ionotropic receptor or channel-linked receptor. They are a group of transmembrane ion channels that are opened or closed in response to the binding of a chemical messenger , such as a neurotransmitter.The binding site of endogenous ligands on LGICs...
of neurotransmitter receptors - 1.A.10 Glutamate-gated ion channel of neurotransmitter receptors
- 1.A.11 Chloride channelChloride channelChloride channels are a superfamily of poorly understood ion channels consisting of approximately 13 members.Chloride channels display a variety of important physiological and cellular roles that include regulation of pH, volume homeostasis, organic solute transport, cell migration, cell...
- 1.A.12 Organellar chloride channel
- 1.A.13 Epithelial chloride channel
- 1.A.14 Nonselective cation channel-1
- 1.A.15 Nonselective cation channel-2
- 1.A.16 Yeast stretch-activated, cation-selective, Ca2+ channel
- 1.A.17 Chloroplast outer-membrane solute channel
- 1.A.18 Chloroplast membrane anion-channel-former
- 1.A.19 Influenza virus matrix-2 channel
- 1.A.20 gp91phox phagocyte NADPH-oxidase-associated cyt b558 H+-channel
- 1.A.21 Apoptosis regulator
- 1.A.22 Large-conductance mechanosensitive ion channel
- 1.A.23 Small-conductance mechanosensitive ion channel
- 1.A.24 Gap-junction-forming connexinConnexinConnexins, or gap junction proteins, are a family of structurally-related transmembrane proteins that assemble to form vertebrate gap junctions . Each gap junction is composed of two hemichannels, or connexons, which are themselves each constructed out of six connexin molecules...
- 1.A.25 Gap-junction-forming innexinInnexinAn innexin is a member of a class of proteins which is used to create gap junctions in invertebrates. The innexin protein and its vertebrate homologue pannexin1 have 4 transmembrane spanning units and, like the vertebrate connexin gap junction protein, 6 innexin subunits together form a channel,...
- 1.A.26 Plant plasmodesmataPlasmodesmataPlasmodesmata are microscopic channels which traverse the cell walls of plant cells and some algal cells, enabling transport and communication between them. Species that have plasmodesmata include members of the Charophyceae, Charales and Coleochaetales , as well as all embryophytes, better known...
- 1.A.27 Phospholemman
- 1.A.28 Urea transporterUrea transporterAn urea transporter is a membrane transport protein, transporting urea. Humans and other mammals have two types of urea transport proteins, UT-A and UT-B. The UT-A proteins are important for renal urea handling and are produced by alternative splicing of the SLC14A2 gene...
(channel) - 1.A.29 Urea/amide channel
- 1.A.30 H+- or Na+-translocating bacterial MotAB flagellar motor/ExbBD outer-membrane transport energizer superfamily
- 1.A.31 AnnexinAnnexinAnnexin is a common name for a group of cellular proteins. They are found in all kingdoms with the exception of the bacteria....
- 1.A.32 Type B influenza virus NB channel
- 1.A.33 Cation-channel-forming heat-shock protein 70
- 1.A.34 Envelope virus E1 channel
- 1.A.35 Metal-ion transporter (channel)
- 1.A.36 Intracellular chloride channel
Ungrouped
- Voltage-gated ion channelVoltage-gated ion channelVoltage-gated ion channels are a class of transmembrane ion channels that are activated by changes in electrical potential difference near the channel; these types of ion channels are especially critical in neurons, but are common in many types of cells....
like, including potassium channelPotassium channelIn the field of cell biology, potassium channels are the most widely distributed type of ion channel and are found in virtually all living organisms. They form potassium-selective pores that span cell membranes...
s KcsA and KvAP, and inward-rectifier potassium ion channelInward-rectifier potassium ion channelInwardly rectifying potassium channels are a specific subset of potassium selective ion channels. To date, seven subfamilies have been identified in various mammalian cell types...
Kirbac http://opm.phar.umich.edu/families.php?superfamily=8 - Large-conductance mechanosensitive channel, MscL http://opm.phar.umich.edu/families.php?superfamily=12
- Small-conductance mechanosensitive ion channel (MscS)Mechanosensitive ion channelMechanosensitive channels are found in a number of tissues and organisms and are thought to be the sensors for a number of systems including the senses of touch, hearing and balance, as well as participating in cardiovascular regulation and osmotic homeostasis...
http://opm.phar.umich.edu/families.php?superfamily=11 - CorA metal ion transporters http://opm.phar.umich.edu/families.php?superfamily=72
- Ligand-gated ion channelLigand-gated ion channelLigand-gated ion channels are one type of ionotropic receptor or channel-linked receptor. They are a group of transmembrane ion channels that are opened or closed in response to the binding of a chemical messenger , such as a neurotransmitter.The binding site of endogenous ligands on LGICs...
of neurotransmitterNeurotransmitterNeurotransmitters are endogenous chemicals that transmit signals from a neuron to a target cell across a synapse. Neurotransmitters are packaged into synaptic vesicles clustered beneath the membrane on the presynaptic side of a synapse, and are released into the synaptic cleft, where they bind to...
receptors (acetylcholine receptorAcetylcholine receptorAn acetylcholine receptor is an integral membrane protein that responds to the binding of acetylcholine, a neurotransmitter.-Classification:...
) http://opm.phar.umich.edu/families.php?superfamily=14 - AquaporinAquaporinAquaporins are proteins embedded in the cell membrane that regulate the flow of water.Aquaporins are integral membrane proteins from a larger family of major intrinsic proteins that form pores in the membrane of biological cells....
s http://opm.phar.umich.edu/families.php?superfamily=7 - Chloride channelChloride channelChloride channels are a superfamily of poorly understood ion channels consisting of approximately 13 members.Chloride channels display a variety of important physiological and cellular roles that include regulation of pH, volume homeostasis, organic solute transport, cell migration, cell...
s http://opm.phar.umich.edu/families.php?superfamily=10 - Outer membrane auxiliary proteins (polysaccharide transporter) http://opm.phar.umich.edu/families.php?superfamily=188
- PorinsPorin (protein)Porins are beta barrel proteins that cross a cellular membrane and act as a pore through which molecules can diffuse. Unlike other membrane transport proteins, porins are large enough to allow passive diffusion, i.e., they act as channels that are specific to different types of molecules...
and some other beta barrelBeta barrelA beta barrel is a large beta-sheet that twists and coils to form a closed structure in which the first strand is hydrogen bonded to the last.Beta-strands in beta-barrels are typically arranged in an antiparallel fashion...
proteins of outer membraneOuter membraneThe bacterial outer membrane is found in Gram-negative bacteria. Its composition is distinct from that of the cytoplasmic membrane - among other things, the outer leaflet of the membrane includes a complex lipopolysaccharide whose lipid portion acts as an endotoxin - and it is linked to the cell's...
s
Ungrouped
- Mitochondrial carrier proteinCarrier proteinCarrier proteins are proteins involved in the movement of ions, small molecules, or macromolecules, such as another protein, across a biological membrane. Carrier proteins are integral membrane proteins; that is they exist within and span the membrane across which they transport substances. The...
s http://opm.phar.umich.edu/families.php?superfamily=21 - Major Facilitator Superfamily (Glycerol-3-phosphate transporter, Lactose permeasePermeaseThe permeases are membrane transport proteins, a class of multipass transmembrane proteins that facilitate the diffusion of a specific molecule in or out of the cell by passive transport...
, and Multidrug transporter EmrD) http://opm.phar.umich.edu/families.php?superfamily=15 - Resistance-nodulation-cell division (multidrug efflux transporter AcrB, see multidrug resistanceMultidrug resistanceMultiple drug resistance or Multidrug resistance is a condition enabling a disease-causing organism to resist distinct drugs or chemicals of a wide variety of structure and function targeted at eradicating the organism...
)http://opm.phar.umich.edu/families.php?superfamily=16 - Dicarboxylate/amino acid:cation symporter (proton glutamate symporter) http://opm.phar.umich.edu/families.php?superfamily=20
- Monovalent cation/proton antiporter (Sodium/proton antiporter 1 NhaA) http://opm.phar.umich.edu/families.php?superfamily=66
- NeurotransmitterNeurotransmitterNeurotransmitters are endogenous chemicals that transmit signals from a neuron to a target cell across a synapse. Neurotransmitters are packaged into synaptic vesicles clustered beneath the membrane on the presynaptic side of a synapse, and are released into the synaptic cleft, where they bind to...
sodium symporter http://opm.phar.umich.edu/families.php?superfamily=67 - Ammonia transporters http://opm.phar.umich.edu/families.php?superfamily=13
- Drug/Metabolite Transporter (small multidrug resistance transporter EmrE - the structures are retracted as erroneous) http://opm.phar.umich.edu/families.php?superfamily=77
3.A. P-P-bond hydrolysis-driven transporters
- P-type calcium ATPaseCalcium ATPaseCalcium ATPase is a form of P-ATPase that transfers calcium after a muscle has contracted. The calcium ATPase are:*Plasma membrane Ca2+ ATPase *Sarcoplasmic reticulum Ca2+ ATPase - Plasma membrane Ca2+ ATPase :...
(five different conformations) http://opm.phar.umich.edu/families.php?superfamily=22 - Calcium ATPase regulators phospholambanPhospholambanPhospholamban, also known as PLN, is a protein that in humans is encoded by the PLN gene. Phospholamban is a 52-amino acid integral membrane protein that regulates the Ca2+ pump in cardiac muscle and skeletal muscle cells.- Function :...
and sarcolipinhttp://opm.phar.umich.edu/families.php?superfamily=70 - ABC transporters: BtuCD, multidrug transporter, and molybdate uptake transporter
- General secretory pathwaySecretory pathwayThe secretory pathway is a series of steps a cell uses to move proteins out of the cell; a process known as secretion. The path of a protein destined for secretion has its origins in the rough endoplasmic reticulum, a membrane-bound compartment in the cell...
(Sec) transloconTransloconThe translocon is the complex of proteins associated with the translocation of nascent polypeptides across membranes. In eukaryotes the polypeptides are transported into the interior space of the endoplasmic reticulum from the cytosol...
(preprotein translocase SecY) http://opm.phar.umich.edu/families.php?superfamily=19
3.D. Oxidoreduction-driven transporters
- Transmembrane cytochrome b-like proteins http://opm.phar.umich.edu/families.php?superfamily=3: coenzyme Q - cytochrome c reductaseCoenzyme Q - cytochrome c reductaseIn enzymology, a ubiquinol—cytochrome-c reductase is an enzyme that catalyzes the chemical reactionThus, the two substrates of this enzyme are dihydroquinone and ferri- cytochrome c, whereas its 3 products are quinone , ferro- cytochrome c, and H+.This enzyme belongs to the family of...
(cytochrome bc1 ); cytochrome b6f complex; formate dehydrogenase, respiratory nitrate reductaseNitrate reductaseNitrate reductases are molybdoenzymes that reduce nitrate to nitrite .* Eukaryotic nitrate reductases are part of the sulfite oxidase family of molybdoenzymes....
; succinate - coenzyme Q reductaseSuccinate - coenzyme Q reductaseSuccinate dehydrogenase or succinate-coenzyme Q reductase or Complex II is an enzyme complex, bound to the inner mitochondrial membrane of mammalian mitochondria and many bacterial cells...
(fumarate reductase); and succinate dehydrogenase. See electron transport chainElectron transport chainAn electron transport chain couples electron transfer between an electron donor and an electron acceptor with the transfer of H+ ions across a membrane. The resulting electrochemical proton gradient is used to generate chemical energy in the form of adenosine triphosphate...
. - Cytochrome c oxidaseCytochrome c oxidaseThe enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein complex found in bacteria and the mitochondrion.It is the last enzyme in the respiratory electron transport chain of mitochondria located in the mitochondrial membrane...
s http://opm.phar.umich.edu/families.php?superfamily=4 from bacteriaBacteriaBacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and mitochondria
3.E. Light absorption-driven transporters
- BacteriorhodopsinBacteriorhodopsinBacteriorhodopsin is a protein used by Archaea, the most notable one being Halobacteria. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell...
-like proteins including rhodopsinRhodopsinRhodopsin, also known as visual purple, is a biological pigment of the retina that is responsible for both the formation of the photoreceptor cells and the first events in the perception of light. Rhodopsins belong to the G-protein coupled receptor family and are extremely sensitive to light,...
(see also opsinOpsinOpsins are a group of light-sensitive 35–55 kDa membrane-bound G protein-coupled receptors of the retinylidene protein family found in photoreceptor cells of the retina. Five classical groups of opsins are involved in vision, mediating the conversion of a photon of light into an electrochemical...
)http://opm.phar.umich.edu/families.php?superfamily=6 - Bacterial photosynthetic reaction centrePhotosynthetic reaction centreA photosynthetic reaction center is a complex of several proteins, pigments and other co-factors assembled together to execute the primary energy conversion reactions of photosynthesis...
s and photosystemPhotosystemPhotosystems are functional and structural units of protein complexes involved in photosynthesis that together carry out the primary photochemistry of photosynthesis: the absorption of light and the transfer of energy and electrons...
s I and II http://opm.phar.umich.edu/families.php?superfamily=2 - Light harvesting complexes from bacteriaBacteriaBacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and chloroplasts http://opm.phar.umich.edu/families.php?superfamily=1
Ungrouped Electrochemical potential-driven transporters
- Proton or sodium translocating F-type and V-type ATPaseATPaseATPases are a class of enzymes that catalyze the decomposition of adenosine triphosphate into adenosine diphosphate and a free phosphate ion. This dephosphorylation reaction releases energy, which the enzyme harnesses to drive other chemical reactions that would not otherwise occur...
s http://opm.phar.umich.edu/families.php?superfamily=5
Ungrouped
- Disulfide bond formation protein B (DsbB) http://opm.phar.umich.edu/protein.php?search=2hi7
External links
- Transporter Classification Database
- List at qmul.ac.uk