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

Classification[edit]

The upper level of classification and a few examples of proteins with known 3D structure:

1. Channels/Pores[edit]

1.A α-Type channels[edit]

1.B β-Barrel porins[edit]

1.C Pore-forming toxins (proteins and peptides)[edit]

1.D Non-ribosomally synthesized channels[edit]

1.E Holins[edit]

1.F Vesicle fusion pores[edit]

1.G Viral fusion pores[edit]

1.H Paracellular channels[edit]

1.I Membrane-bound channels[edit]

Ungrouped[edit]

2. Electrochemical Potential-driven Transporters[edit]

2.A Porters (uniporters, symporters, antiporters)[edit]

2.B Nonribosomally synthesized porters[edit]

2.C Ion-gradient-driven energizers[edit]

Ungrouped[edit]

  • 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. Primary Active Transporters[edit]

3.A. P-P-bond hydrolysis-driven transporters[edit]

3.B Decarboxylation-driven transporters[edit]

3.C Methyltransfer-driven transporters[edit]

3.D. Oxidoreduction-driven transporters[edit]

3.E. Light absorption-driven transporters[edit]

Ungrouped Electrochemical potential-driven transporters[edit]

  • Proton or sodium translocating F-type and V-type ATPases [25]

4. Group Translocators[edit]

4.A Phosphotransfer-driven group translocators[edit]

4.B Nicotinamide ribonucleoside uptake transporters[edit]

4.C Acyl CoA ligase-coupled transporters[edit]

5. Transport Electron Carriers[edit]

5.A Transmembrane 2-electron transfer carriers[edit]

5.B Transmembrane 1-electron transfer carriers[edit]

Ungrouped[edit]

  • Disulfide bond formation protein B (DsbB) [26]

6. Unused[edit]

Reserved for future expansion

7. Unused[edit]

Reserved for future expansion

8. Accessory Factors Involved in Transport[edit]

8.A Auxiliary transport proteins[edit]

8.B Ribosomally synthesized protein/peptide toxins that target channels and carriers[edit]

8.C Non-ribosomally synthesized toxins that target channels and carriers[edit]

9. Incompletely Characterized Transport Systems[edit]

9.A Recognized transporters of unknown biochemical mechanism[edit]

9.B Putative transport proteins[edit]

9.C Functionally characterized transporters lacking identified sequences[edit]

Examples[edit]

See also[edit]

References[edit]

  1. ^ Saier MH, Yen MR, Noto K, Tamang DG, Elkan C (January 2009). "The Transporter Classification Database: recent advances". Nucleic Acids Res. 37 (Database issue): D274–8. doi:10.1093/nar/gkn862. PMC 2686586. PMID 19022853. 

External links[edit]