Transporter Classification Database

The 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][2][3]

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.A.1 Voltage-gated ion channel superfamily
• 1.A.2 Animal inward-rectifier K+ channel
• 1.A.3 Ryanodine-inositol-1,4,5-trisphosphate receptor Ca2+ channel
• 1.A.4 Transient receptor potential Ca2+ channel
• 1.A.5 Polycystin cation channel
• 1.A.6 Epithelial Na+ channel
• 1.A.7 ATP-gated cation channel
• 1.A.8 Major intrinsic protein
• 1.A.9 Ligand-gated ion channel of neurotransmitter receptors
• 1.A.10 Glutamate-gated ion channel family of neurotransmitter receptors
• 1.A.11 Chloride channel
• 1.A.12 Organellar chloride channel
• 1.A.13 Epithelial chloride channel
• 1.A.14 Nonselective cation channel-1
• 1.A.15 Nonselective cation channel-2
• 1.A.16 Yeast stretch-activated, cation-selective, Ca2+ channel
• 1.A.17 Chloroplast outer-membrane solute channel
• 1.A.18 Chloroplast membrane anion-channel-former
• 1.A.19 Influenza virus matrix-2 channel
• 1.A.20 gp91phox phagocyte NADPH-oxidase-associated cyt b558 H+-channel
• 1.A.21 Apoptosis regulator
• 1.A.22 Large-conductance mechanosensitive ion channel
• 1.A.23 Small-conductance mechanosensitive ion channel
• 1.A.24 Gap-junction-forming connexin
• 1.A.25 Gap-junction-forming innexin
• 1.A.26 Plant plasmodesmata
• 1.A.27 Phospholemman
• 1.A.28 Urea transporter (channel)
• 1.A.29 Urea/amide channel
• 1.A.30 H+- or Na+-translocating bacterial MotAB flagellar motor/ExbBD outer-membrane transport energizer superfamily
• 1.A.31 Annexin
• 1.A.32 Type B influenza virus NB channel
• 1.A.33 Cation-channel-forming heat-shock protein 70
• 1.A.34 Envelope virus E1 channel
• 1.A.35 CorA metal ion transporter
• 1.A.36 Intracellular chloride channel
• 1.A.50 Calcium ATPase regulators phospholamban and sarcolipin

1.B β-Barrel porins

• 1.B.1 General bacterial porin family
• 1.B.2 Chlamydial porin (CP) family
• 1.B.3 Sugar porin (SP) family
• 1.B.4 Brucella-Rhizobium porin (BRP) family
• 1.B.5 Pseudomonas OprP porin (POP) family
• 1.B.6 OmpA-OmpF porin (OOP) family
• 1.B.7 Rhodobacter PorCa porin (RPP) family
• 1.B.8 Mitochondrial and plastid porin (MPP) family
• 1.B.9 FadL outer membrane protein (FadL) family
• 1.B.10 Nucleoside-specific channel-forming outer membrane porin (Tsx) family
• 1.B.11 Outer membrane fimbrial usher porin (FUP) family
• 1.B.12 Autotransporter-1 (AT-1) family
• 1.B.13 Alginate export porin (AEP) family
• 1.B.14 Outer membrane receptor (OMR) family
• 1.B.15 Raffinose porin (RafY) family
• 1.B.16 Short chain amide and urea porin (SAP) family
• 1.B.17 Outer membrane factor (OMF) family
• 1.B.18 Outer membrane auxiliary (OMA) protein family
• 1.B.19 Glucose-selective OprB porin (OprB) family
• 1.B.20 Two-partner secretion (TPS) family
• 1.B.21 OmpG porin (OmpG) family
• 1.B.22 Outer bacterial membrane secretin (secretin) family
• 1.B.23 Cyanobacterial porin (CBP) family
• 1.B.24 Mycobacterial porin
• 1.B.25 Outer membrane porin (Opr) family
• 1.B.26 Cyclodextrin porin (CDP) family
• 1.B.31 Campylobacter jejuni major outer membrane oorin (MomP) family
• 1.B.32 Fusobacterial outer membrane porin (FomP) family
• 1.B.33 Outer membrane protein insertion porin (Bam complex) (OmpIP) family
• 1.B.35 Oligogalacturonate-specific porin (KdgM) family
• 1.B.39 Bacterial porin, OmpW (OmpW) family
• 1.B.42 Outer membrane lipopolysaccharide export porin (LPS-EP) family
• 1.B.43 Coxiella porin P1 (CPP1) family
• 1.B.44 Probable protein translocating porphyromonas gingivalis porin (PorT) family
• 1.B.49 Anaplasma P44 (A-P44) porin family
• 1.B.54 Intimin/Invasin (Int/Inv) or Autotransporter-3 (AT-3) family
• 1.B.55 Poly-acetyl-D-glucosamine porin (PgaA) family
• 1.B.57 Legionella major-outer membrane protein (LM-OMP) family
• 1.B.60 Omp50 porin (Omp50 Porin) family
• 1.B.61 Delta-proteobacterial porin (Delta-porin) family
• 1.B.62 Putative bacterial porin (PBP) family
• 1.B.66 Putative beta-barrel porin-2 (BBP2) family
• 1.B.67 Putative beta barrel porin-4 (BBP4) family
• 1.B.68 Putative beta barrel porin-5 (BBP5) superfamily
• 1.B.70 Outer membrane channel (OMC) family
• 1.B.71 Proteobacterial/verrucomicrobial porin (PVP) family
• 1.B.72 Protochlamydial outer membrane porin (PomS/T) family
• 1.B.73 Capsule biogenesis/assembly (CBA) family
• 1.B.78 DUF3374 electron transport-associated porin (ETPorin) family

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

• 1.C.3 α-Hemolysin (αHL) family
• 1.C.4 Aerolysin family
• 1.C.5 ε-toxin family
• 1.C.13 Leukocidin family
• 1.C.14 Cytohemolysin (CHL) family
• 1.C.43 Lysenin family
• 1.C.74 Snake cytotoxin (SCT) family

1.I Membrane-bound channels

• 1.I.1 Nuclear pore complex family, including karyopherins
• 1.I.2 Plant plasmodesmata family

Ungrouped

• Voltage-gated ion channel like, including potassium channels KcsA and KvAP, and inward-rectifier potassium ion channel Kirbac
• Large-conductance mechanosensitive channel, MscL
• Small-conductance mechanosensitive ion channel (MscS)
• CorA metal ion transporters
• Ligand-gated ion channel of neurotransmitter receptors (acetylcholine receptor)
• Aquaporins
• Chloride channels
• Outer membrane auxiliary proteins (polysaccharide transporter)
• Porins and some other beta barrel proteins of outer membranes

2. Electrochemical Potential-driven Transporters

2.A Porters (uniporters, symporters, antiporters)

• Amino acid transporters

Ungrouped

• Mitochondrial carrier proteins
• Major facilitator superfamily (Glycerol-3-phosphate transporter, Lactose permease, and Multidrug transporter EmrD)
• Resistance-nodulation-cell division superfamily (multidrug efflux transporter AcrB, see multidrug resistance)
• Dicarboxylate/amino acid:cation symporter (proton glutamate symporter)
• Monovalent cation/proton antiporter (Sodium/proton antiporter 1 NhaA)
• Neurotransmitter sodium symporter
• Ammonia transporter
• Drug/Metabolite Transporter

3. Primary Active Transporters

3.A. P-P-bond hydrolysis-driven transporters

• P-type calcium ATPase
• ABC transporters including BtuCD, molybdate uptake transporter, Cystic fibrosis transmembrane conductance regulator and others
• General secretory pathway (Sec) translocon (preprotein translocase SecY)

3.D. Oxidoreduction-driven transporters

• Transmembrane cytochrome b-like proteins: 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 from bacteria and mitochondria

3.E. Light absorption-driven transporters

• Bacteriorhodopsin-like proteins including rhodopsin (see also opsin)
• Bacterial photosynthetic reaction centres and photosystems I and II
• Light harvesting complexes from bacteria and chloroplasts

Ungrouped Electrochemical potential-driven transporters

• Proton or sodium translocating F-type and V-type ATPases

5. Transport Electron Carriers

Ungrouped

• Disulfide bond formation protein B (DsbB)

6. Unused

Reserved for future expansion

7. Unused

Reserved for future expansion

References

1. Saier, Milton H.; Reddy, Vamsee S.; Tamang, Dorjee G.; Västermark, Åke (January 2014). "The Transporter Classification Database". Nucleic Acids Research 42 (D1): D251–D258. doi:10.1093/nar/gkt1097. Retrieved 1 March 2016.
2. Saier, M. H.; Yen, M. R.; Noto, K.; Tamang, D. G.; Elkan, C. (1 January 2009). "The Transporter Classification Database: recent advances". Nucleic Acids Research 37 (Database): D274–D278. doi:10.1093/nar/gkn862. Retrieved 1 March 2016.
3. Saier, M. H.; Tran, C. V.; Barabote, R. D. (1 January 2006). "TCDB: the Transporter Classification Database for membrane transport protein analyses and information". Nucleic Acids Research 34 (90001): D181–D186. doi:10.1093/nar/gkj001. Retrieved 1 March 2016.

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. doi:10.1093/nar/gkj001. PMC 1334385. PMID 16381841.
• 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.
• Classification of human transporters in pharmacology