Transporter Classification Database

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.

Contents

  • Classification 1
    • 1. Channel/Pores 1.1
      • 1.A α-Type channels 1.1.1
      • 1.B β-Barrel porins 1.1.2
      • 1.C Pore-forming toxins (proteins and peptides) 1.1.3
      • 1.D Non-ribosomally synthesized channels 1.1.4
      • 1.E Holin 1.1.5
      • 1.F Vesicle fusion pores 1.1.6
      • 1.G Viral fusion pores 1.1.7
      • 1.H Paracellular channel 1.1.8
      • 1.I Membrane-bound channel 1.1.9
      • Ungrouped 1.1.10
    • 2. Electrochemical Potential-driven Transporters 1.2
      • 2.A Porters (uniporter, symporter, antiporter) 1.2.1
      • 2.B Nonribosomally synthesized porters 1.2.2
      • 2.C Ion-gradient-driven energizers 1.2.3
      • Ungrouped 1.2.4
    • 3. Primary Active Transporters 1.3
      • 3.A. P-P-bond hydrolysis-driven transporters 1.3.1
      • 3.B Decarboxylation-driven transporters 1.3.2
      • 3.C Methyltransfer-driven transporters 1.3.3
      • 3.D. Oxidoreduction-driven transporters 1.3.4
      • 3.E. Light absorption-driven transporters 1.3.5
      • Ungrouped Electrochemical potential-driven transporters 1.3.6
    • 4. Group Translocators 1.4
      • 4.A Phosphotransfer-driven group translocators 1.4.1
      • 4.B Nicotinamide ribonucleoside uptake transporters 1.4.2
      • 4.C Acyl CoA ligase-coupled transporters 1.4.3
    • 5. Transport Electron Carriers 1.5
      • 5.A Transmembrane 2-electron transfer carriers 1.5.1
      • 5.B Transmembrane 1-electron transfer carriers 1.5.2
      • Ungrouped 1.5.3
    • 6. Unused 1.6
    • 7. Unused 1.7
    • 8. Accessory Factors Involved in Transport 1.8
      • 8.A Auxiliary transport proteins 1.8.1
      • 8.B Ribosomally synthesized protein/peptide toxins that target channels and carriers 1.8.2
      • 8.C Non-ribosomally synthesized toxins that target channels and carriers 1.8.3
    • 9. Incompletely Characterized Transport Systems 1.9
      • 9.A Recognized transporters of unknown biochemical mechanism 1.9.1
      • 9.B Putative transport proteins 1.9.2
      • 9.C Functionally characterized transporters lacking identified sequences 1.9.3
  • Examples 2
  • See also 3
  • References 4
  • External links 5

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.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

Ungrouped

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

3.B Decarboxylation-driven transporters

3.C Methyltransfer-driven transporters

3.D. Oxidoreduction-driven transporters

3.E. Light absorption-driven transporters

Ungrouped Electrochemical potential-driven transporters

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

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

  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.  
  2. ^ http://opm.phar.umich.edu/families.php?superfamily=8
  3. ^ http://opm.phar.umich.edu/families.php?superfamily=12
  4. ^ http://opm.phar.umich.edu/families.php?superfamily=11
  5. ^ http://opm.phar.umich.edu/families.php?superfamily=72
  6. ^ http://opm.phar.umich.edu/families.php?superfamily=14
  7. ^ http://opm.phar.umich.edu/families.php?superfamily=7
  8. ^ http://opm.phar.umich.edu/families.php?superfamily=10
  9. ^ http://opm.phar.umich.edu/families.php?superfamily=188
  10. ^ http://opm.phar.umich.edu/families.php?superfamily=21
  11. ^ http://opm.phar.umich.edu/families.php?superfamily=15
  12. ^ http://opm.phar.umich.edu/families.php?superfamily=16
  13. ^ http://opm.phar.umich.edu/families.php?superfamily=20
  14. ^ http://opm.phar.umich.edu/families.php?superfamily=66
  15. ^ http://opm.phar.umich.edu/families.php?superfamily=67
  16. ^ http://opm.phar.umich.edu/families.php?superfamily=13
  17. ^ http://opm.phar.umich.edu/families.php?superfamily=77
  18. ^ http://opm.phar.umich.edu/families.php?superfamily=22
  19. ^ http://opm.phar.umich.edu/families.php?superfamily=70
  20. ^ http://opm.phar.umich.edu/families.php?superfamily=17
  21. ^ http://opm.phar.umich.edu/families.php?superfamily=18
  22. ^ http://opm.phar.umich.edu/families.php?superfamily=198
  23. ^ http://opm.phar.umich.edu/families.php?superfamily=19
  24. ^ http://opm.phar.umich.edu/families.php?superfamily=3
  25. ^ http://opm.phar.umich.edu/families.php?superfamily=4
  26. ^ http://opm.phar.umich.edu/families.php?superfamily=6
  27. ^ http://opm.phar.umich.edu/families.php?superfamily=2
  28. ^ http://opm.phar.umich.edu/families.php?superfamily=1
  29. ^ http://opm.phar.umich.edu/families.php?superfamily=5
  30. ^ http://opm.phar.umich.edu/protein.php?search=2hi7

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