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
5.A Transmembrane 2-electron transfer carriers
5.B Transmembrane 1-electron transfer carriers
Ungrouped
- 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
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
- 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.