Transporter Classification Database
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Transporter Classification Database (or TCDB) is an International Union of Biochemistry and Molecular Biology (IUBMB) approved classification system for membrane transport proteins including ion channels.[1] This classification system was designed to be analogous to the EC number system for classifying enzymes, but it also uses phylogenetic information.
Contents
- 1 Classification
- 1.1 1. Channels/Pores
- 1.1.1 1.A α-Type channels
- 1.1.2 1.B β-Barrel porins
- 1.1.3 1.C Pore-forming toxins (proteins and peptides)
- 1.1.4 1.D Non-ribosomally synthesized channels
- 1.1.5 1.E Holins
- 1.1.6 1.F Vesicle fusion pores
- 1.1.7 1.G Viral fusion pores
- 1.1.8 1.H Paracellular channels
- 1.1.9 1.I Membrane-bound channels
- 1.1.10 Ungrouped
- 1.2 2. Electrochemical Potential-driven Transporters
- 1.3 3. Primary Active Transporters
- 1.4 4. Group Translocators
- 1.5 5. Transport Electron Carriers
- 1.6 6. Unused
- 1.7 7. Unused
- 1.8 8. Accessory Factors Involved in Transport
- 1.9 9. Incompletely Characterized Transport Systems
- 1.1 1. Channels/Pores
- 2 Examples
- 3 See also
- 4 References
- 5 External links
Classification
The upper level of classification and a few examples of proteins with known 3D structure:
1. Channels/Pores
1.A α-Type channels
- 1.A.1 Voltage-gated ion channel 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 channel of neurotransmitter receptors
- 1.A.10 Glutamate-gated ion channel of neurotransmitter receptors
- 1.A.11 Chloride channel
- 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 connexin
- 1.A.25 Gap-junction-forming innexin
- 1.A.26 Plant plasmodesmata
- 1.A.27 Phospholemman
- 1.A.28 Urea transporter (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 Annexin
- 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
1.B β-Barrel porins
1.C Pore-forming toxins (proteins and peptides)
1.D Non-ribosomally synthesized channels
1.E Holins
1.F Vesicle fusion pores
1.G Viral fusion pores
1.H Paracellular channels
1.I Membrane-bound channels
- 1.I.1 Nuclear pore complex family, including karyopherins
- 1.I.2 Plant plasmodesmata family
Ungrouped
- Voltage-gated ion channel like, including potassium channels KcsA and KvAP, and inward-rectifier potassium ion channel Kirbac[2]
- Large-conductance mechanosensitive channel, MscL[3]
- Small-conductance mechanosensitive ion channel (MscS)[4]
- CorA metal ion transporters[5]
- Ligand-gated ion channel of neurotransmitter receptors (acetylcholine receptor)[6]
- Aquaporins[7]
- Chloride channels[8]
- Outer membrane auxiliary proteins (polysaccharide transporter)[9]
- Porins and some other beta barrel proteins of outer membranes
2. Electrochemical Potential-driven Transporters
2.A Porters (uniporters, symporters, antiporters)
2.B Nonribosomally synthesized porters
2.C Ion-gradient-driven energizers
Ungrouped
- Mitochondrial carrier proteins[10]
- Major Facilitator Superfamily (Glycerol-3-phosphate transporter, Lactose permease, and Multidrug transporter EmrD)[11]
- Resistance-nodulation-cell division (multidrug efflux transporter AcrB, see multidrug resistance)[12]
- Dicarboxylate/amino acid:cation symporter (proton glutamate symporter)[13]
- Monovalent cation/proton antiporter (Sodium/proton antiporter 1 NhaA)[14]
- Neurotransmitter sodium symporter[15]
- Ammonia transporters[16]
- Drug/Metabolite Transporter (small multidrug resistance transporter EmrE - the structures are retracted as erroneous)[17]
3. Primary Active Transporters
3.A. P-P-bond hydrolysis-driven transporters
- P-type calcium ATPase (five different conformations)[18]
- Calcium ATPase regulators phospholamban and sarcolipin[19]
- ABC transporters: BtuCD,[20] multidrug transporter,[21] and molybdate uptake transporter[22]
- General secretory pathway (Sec) translocon (preprotein translocase SecY)[23]
3.B Decarboxylation-driven transporters
3.C Methyltransfer-driven transporters
3.D. Oxidoreduction-driven transporters
- Transmembrane cytochrome b-like proteins:[24] coenzyme Q - cytochrome c reductase (cytochrome bc1 ); cytochrome b6f complex; formate dehydrogenase, respiratory nitrate reductase; succinate - coenzyme Q reductase (fumarate reductase); and succinate dehydrogenase. See electron transport chain.
- Cytochrome c oxidases[25] from bacteria and mitochondria
3.E. Light absorption-driven transporters
- Bacteriorhodopsin-like proteins including rhodopsin (see also opsin)[26]
- Bacterial photosynthetic reaction centres and photosystems I and II[27]
- Light harvesting complexes from bacteria and chloroplasts[28]
Ungrouped Electrochemical potential-driven transporters
4. Group Translocators
4.A Phosphotransfer-driven group translocators
4.B Nicotinamide ribonucleoside uptake transporters
4.C Acyl CoA ligase-coupled transporters
5. Transport Electron Carriers
5.A Transmembrane 2-electron transfer carriers
5.B Transmembrane 1-electron transfer carriers
Ungrouped
- Disulfide bond formation protein B (DsbB)[30]
6. Unused
Reserved for future expansion
7. Unused
Reserved for future expansion
8. Accessory Factors Involved in Transport
8.A Auxiliary transport proteins
8.B Ribosomally synthesized protein/peptide toxins that target channels and carriers
8.C Non-ribosomally synthesized toxins that target channels and carriers
9. Incompletely Characterized Transport Systems
9.A Recognized transporters of unknown biochemical mechanism
9.B Putative transport proteins
9.C Functionally characterized transporters lacking identified sequences
Examples
See also
References
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ http://opm.phar.umich.edu/families.php?superfamily=8
- ↑ http://opm.phar.umich.edu/families.php?superfamily=12
- ↑ http://opm.phar.umich.edu/families.php?superfamily=11
- ↑ http://opm.phar.umich.edu/families.php?superfamily=72
- ↑ http://opm.phar.umich.edu/families.php?superfamily=14
- ↑ http://opm.phar.umich.edu/families.php?superfamily=7
- ↑ http://opm.phar.umich.edu/families.php?superfamily=10
- ↑ http://opm.phar.umich.edu/families.php?superfamily=188
- ↑ http://opm.phar.umich.edu/families.php?superfamily=21
- ↑ http://opm.phar.umich.edu/families.php?superfamily=15
- ↑ http://opm.phar.umich.edu/families.php?superfamily=16
- ↑ http://opm.phar.umich.edu/families.php?superfamily=20
- ↑ http://opm.phar.umich.edu/families.php?superfamily=66
- ↑ http://opm.phar.umich.edu/families.php?superfamily=67
- ↑ http://opm.phar.umich.edu/families.php?superfamily=13
- ↑ http://opm.phar.umich.edu/families.php?superfamily=77
- ↑ http://opm.phar.umich.edu/families.php?superfamily=22
- ↑ http://opm.phar.umich.edu/families.php?superfamily=70
- ↑ http://opm.phar.umich.edu/families.php?superfamily=17
- ↑ http://opm.phar.umich.edu/families.php?superfamily=18
- ↑ http://opm.phar.umich.edu/families.php?superfamily=198
- ↑ http://opm.phar.umich.edu/families.php?superfamily=19
- ↑ http://opm.phar.umich.edu/families.php?superfamily=3
- ↑ http://opm.phar.umich.edu/families.php?superfamily=4
- ↑ http://opm.phar.umich.edu/families.php?superfamily=6
- ↑ http://opm.phar.umich.edu/families.php?superfamily=2
- ↑ http://opm.phar.umich.edu/families.php?superfamily=1
- ↑ http://opm.phar.umich.edu/families.php?superfamily=5
- ↑ http://opm.phar.umich.edu/protein.php?search=2hi7
External links
- Transporter Classification Database
- List at qmul.ac.uk
- Lua error in package.lua at line 80: module 'strict' not found.
- Lua error in package.lua at line 80: module 'strict' not found.
