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.A α-Type channels
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
Ungrouped
- Voltage-gated ion channel like, including potassium channels KcsA and KvAP, and inward-rectifier potassium ion channel Kirbac [1]
- Large-conductance mechanosensitive channel, MscL [2]
- Small-conductance mechanosensitive ion channel (MscS) [3]
- CorA metal ion transporters [4]
- Ligand-gated ion channel of neurotransmitter receptors (acetylcholine receptor) [5]
- Aquaporins [6]
- Chloride channels [7]
- Outer membrane auxiliary proteins (polysaccharide transporter) [8]
- 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 [9]
- Major Facilitator Superfamily (Glycerol-3-phosphate transporter, Lactose permease, and Multidrug transporter EmrD) [10]
- Resistance-nodulation-cell division (multidrug efflux transporter AcrB, see multidrug resistance)[11]
- Dicarboxylate/amino acid:cation symporter (proton glutamate symporter) [12]
- Monovalent cation/proton antiporter (Sodium/proton antiporter 1 NhaA) [13]
- Neurotransmitter sodium symporter [14]
- Ammonia transporters [15]
- Drug/Metabolite Transporter (small multidrug resistance transporter EmrE - the structures are retracted as erroneous) [16]
3.A. P-P-bond hydrolysis-driven transporters
- P-type calcium ATPase (five different conformations) [17]
- Calcium ATPase regulators phospholamban and sarcolipin[18]
- ABC transporters: BtuCD, multidrug transporter, and molybdate uptake transporter
- General secretory pathway (Sec) translocon (preprotein translocase SecY) [19]
3.B Decarboxylation-driven transporters
3.C Methyltransfer-driven transporters
3.D. Oxidoreduction-driven transporters
- Transmembrane cytochrome b-like proteins [20]: 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 [21] from bacteria and mitochondria
3.E. Light absorption-driven transporters
- Bacteriorhodopsin-like proteins including rhodopsin (see also opsin)[22]
- Bacterial photosynthetic reaction centres and photosystems I and II [23]
- Light harvesting complexes from bacteria and chloroplasts [24]
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
- Disulfide bond formation protein B (DsbB) [26]
6. Unused
Reserved for future expansion
7. Unused
Reserved for future expansion
8. Accessory Factors Involved in Transport
9. Incompletely Characterized Transport Systems
Examples
- Cystic fibrosis transmembrane conductance regulator -- 3.A.1.202.1
See also
References
- ^ Saier MH, Yen MR, Noto K, Tamang DG, Elkan C (2009). "The Transporter Classification Database: recent advances". Nucleic Acids Res. 37 (Database issue): D274–8. doi:10.1093/nar/gkn862. PMC 2686586. PMID 19022853.
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External links
- Transport Classification Database
- List at qmul.ac.uk
- Saier MH, Tran CV, Barabote RD (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.
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- 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.