Transporter Classification Database

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.

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.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

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.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

• Proton or sodium translocating F-type and V-type ATPases^[29]

5. Transport Electron Carriers

Ungrouped

• Disulfide bond formation protein B (DsbB)^[30]

6. Unused

Reserved for future expansion

7. Unused

Reserved for future expansion

Examples

• Cystic fibrosis transmembrane conductance regulator—3.A.1.202.1

See also

• List of proteins

References

External links

• Transporter Classification Database
• List at qmul.ac.uk

• Saier MH, Tran CV, Barabote RD (January 2006). "TCDB: the Transporter Classification Database for membrane transport protein analyses and information". Nucleic Acids Res. 34 (Database issue): D181–6. doi:10.1093/nar/gkj001. PMC 1334385. PMID 16381841. 

• Busch W, Saier MH (2002). "The transporter classification (TC) system, 2002". Crit. Rev. Biochem. Mol. Biol. 37 (5): 287–337. doi:10.1080/10409230290771528. PMID 12449427.