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. This classification system was designed to be analogous to the EC number system for classifying enzymes, but it also uses phylogenetic information.

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

1. Channels/Pores

• • 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

• • Mitochondrial carrier proteins [9]
  • Major Facilitator Superfamily (Glycerol-3-hosphate 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

• Light absorption-driven transporters:
  • Bacteriorhodopsin-like proteins including rhodopsin (see also opsin)[17]
  • Bacterial photosynthetic reaction centres and photosystems I and II [18]
  • Light harvesting complexes from bacteria and chloroplasts [19]
• 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
• Electrochemical potential-driven transporters
  • Proton or sodium translocating F-type and V-type ATPases [22]
• P-P-bond hydrolysis-driven transporters
  • P-type calcium ATPase (five different conformations) [23]
  • Calcium ATPase regulators phospholamban and sarcolipin[24]
  • ABC transporters: BtuCD, multidrug transporter, and molybdate uptake transporter
  • General secretory pathway (Sec) translocon (preprotein translocase SecY) [25]

4. Group Translocators

5. Transport Electron Carriers

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

8. Accessory Factors Involved in Transport

9. Incompletely Characterized Transport Systems

Examples

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

See also

• List of proteins

External links

• Transport 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. PMID 16381841. PMC: 1334385. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=16381841. 

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