Continued from properties of families 2
This subclass includes transport systems that use the free energy of P-P bond hydrolysis to drive the movement of substances against their chemical or electrochemical potential gradient. The transport protein may be transiently phosphorylated during the transport cycle (the 3.A.3 and 3.A.4 groups) but the substrate itself is not phosphorylated. These transporters occur universally in all domains of life.
| TC no. a | Family | Substrates b | Size range c | Number of transmembrane segmentsd | Distributione | nf | Examples |
| 3.A.1 | ABC | all kinds of inorganic and organic molecules of small, intermediate and large sizes, from simple ions to macromolecules | 1000-2000 (multidomain; usually multisubunit) | (5)2; (6)2; 12 variable | A, B, E | 3 | maltose transporter MalEFGK of Escherichia coli; multidrug resistance protein MDR of Homo sapiens |
| 3.A.2 | F-ATPase | H+; Na+ | >4000 (multiple subunits) | (2)10 + (1)2 +(5)1 | A, B, E (chloro; mito) | 2 | FoF1-ATPase of human Mito |
| 3.A.3 | P-ATPase | cations (uptake and/or efflux):Na+: K+; H+: K+; Ca2+/ K+; Na+; H+; K+; Ca2+; Ca2+/Mn2+; Mg2+; Mn2+; Cu2+; Cu+/Ag+; Ag+; Zn2+/ Cd2+/ Co2+/Ni2+/Pb2+; Cl (some systems may be specific for one or only a few of these heavy metal cations); phospholipids (flipping) | 600-1200 (sometimes multisubunit) | (6-12), 8, 10 | A, B, E | 3 | KdpABC (K+ uptake) of Escherichia coli |
| 3.A.4 | ArsAB | arsenite, antimonite, (tellurite?) | c. 1100 (multidomain; two subunits) | 12 | A, B, E | 2 | arsenite efflux pump ArsAB of Escherichia coli |
| 3.A.5 | IISP | proteins | >2000 (multiple subunits) | SecY (10) SecE 1SecG 1 or 2 | A, B, E | type II secretory pathway system SecAYEG of Escherichia coli | |
| 3.A.6 | IIISP | proteins | >2000 (multiple subunits) | >10 integral membrane constituents | B | 2 | type III secretory pathway system YscNDRSTUC; LcrD of Yersinia species |
| 3.A.7 | IVSP | proteins, protein-DNA complexes | >2000 (multiple subunits) | >10 integral membrane constituents | B | 2 | type IV secretory pathway system VirB2-11 of Agrobacterium tumefaciens |
| 3.A.8 | MPT | Mitol proteins | >2000 (multiple subunits) | >9 integral membrane constituents | E (Mito) | 1 | Mitol transport protein complex Tom and Tim of Saccharomyces cerevisiae |
| 3.A.9 | CEPT | chloroplast proteins | >2000 (multiple subunits) | several integral membrane constituents | E (Chloro) | 1 | chloroplast transport protein complex IAP of Pisum sativum |
| 3.A.10 | H+-PPase | H+ | 650-800 | 15 | B, E (Pl vacuoles) | 2 | vacuolar H+-diphosphatase of Arabidopsis thaliana |
| 3.A.11 | DNA-T | single-stranded DNA | >1000 (multiple subunits) | 3 subunits | B | 1 | competence-related DNA transformation transporter ComEA-EC-FA of Bacillus subtilis |
| 3.A.12 | S-DNA-T | DNA, DNA-protein complexes | 600-1350 | 2, 4, 6 | B | 2 | cell division protein FtsK of Escherichia coli |
| 3.A.13 | FPhE | viruses | 109 + 348 + 476 | 1 | Bp | 1 | filamentous phage assembly/export channel |
| 3.A.14 | FPE | proteins | 320-420 + 350-570 | 3 | B | 1 | competence-related pilin exporter of Bacillus subtilis |
3.B Decarboxylation-driven transporters
Systems that drive ion transport at the expense of free energy of decarboxylation of a cytoplasmic substrate are included here. Only prokaryotic cells are known to harbor such systems.
| TC no. a | Family | Substrates b | Size range c | Number of transmembrane segmentsd | Distributione | nf | Examples |
| 3.B.1 | NaT-DC | Na+ | c. 1000 (4 subunits) | 10 | A, B | 2 | oxaloacetate decarboxylase of Salmonella typhimurium |
3.C Methyl-transfer-driven transporters
This subclass currently contains a single family; probably only in Archaea.
| TC no. a | Family | Substrates b | Size range c | Number of transmembrane segmentsd | Distributione | nf | Examples |
| 3.C.1 | NaT-MMM | Na+ | c. 8 subunits; most integral membrane constituents | 6-7(A), 1(B), 8(C), 2-7(D), 0-2(E), 1(F), 1(G), 1(H) | A | 1 | Na+-transporting methyltetrahydro-methanopterin: coenzyme M methyl-transferase of Methanobacterium thermoautotrophicum |
3.D Oxidoreduction-driven transporters
This subclass contains systems where the transport of a solute is driven by the free energy of oxidation of a reduced substrate transmitted by the flow of electrons. Transporters of this type are universal although some families are restricted to one or another domain of life.
| TC no. a | Family | Substrates b | Size range c | Number of transmembrane segmentsd | Distributione | nf | Examples |
| 3.D.1 | NDH | Na+; H+ (efflux) | 14-40 subunits | multiple integral membrane subunits | B, E (Mito, Chloro) | 2 | NDH of Escherichia coli |
| 3.D.2 | PTH | H+ (efflux) | c. 2000 (13 proteins; 3 domains; dimeric) | (12-14)2 | B, E (Mito) | 2 | PTH of Escherichia coli |
| 3.D.3 | QCR | H+ (efflux) | 2000-6000 multiple (3-11) subunits; dimeric | 8 (C), 1 (D), 1(G), 1(J), 1(K) | B, E (Mito; chloro) | cytochrome bc1 complex of Bos taurus | |
| 3.D.4 | COX | H+ (efflux) | 2000-6000 multiple (3-11) subunits; dimeric | E: 12 (I), 2 (II), 7 (III), 1 (IV), 1 (VIa), 1 (VIc), 1(VIIa), 1(VIIb), 1 (VIIc), 1 (VIII) B: 12 (I), 2(II) | A, B, E, (Mito) | 3 | cytochrome c oxidase of Bos taurus |
| 3.D.5 | Na-NDH | Na+ (efflux) | multiple subunits | 9(B); 1(C): 5(D); 6(E); 3(F) | B | 1 | Na+-translocating NADH-quinol reductase of Vibrio alginolyticus |
| 3.D.6 | NFO | H+ or Na+ (efflux) | multiple subunits | 5 + 1 + 6 + 1 + 24 + 9 | B | 1 | H+- or Na+- translocating NADH:ferredoxin oxidoreductase,rnfA-H of Rhodobacter capsulatus |
| 3.D.7 | HHO | H+ (efflux) | multiple subunits | 2(D); 6(E);4(G); 1(A); 5(C) | A, B | 1 | H2:heterodisulfide oxidoreductase of Methanosarcina mazei |
| 3.D.8 | FMF-DH | H+ or Na+ (efflux) | multiple subunits | 2(F); 1(G) | A | 1 | formyl methanofuran dehydrogenase Fwd A-G of Methanobacterium thermoautotrophicum |
| 3.D.9 | F420H2DH | reduced donor, H+ | Mr of complex about 120| 1(F); 14(N); 14(M); 19(L); 2(K); 5(J); 1(I); 7(H); 3(A) | A | 1 | F420H2DH of Methanosarcina mazei | |
A single family of archebacterial proteins is involved in light-driven transport. However, homologous retinal-binding proteins have been found in fungi where they behave as heat-shock proteins and possibly as molecular chaperones. The light-driven reduction of the photosynthetic reaction center is only auxiliary to subsequent oxidation in the cytochrome b6f complex where the efflux of hydrons actually takes place.
| TC no. a | Family | Substrates b | Size range c | Number of transmembrane segmentsd | Distributione | nf | Examples |
| 3.E.1 | MR | H+ (efflux); Cl (uptake) | c. 250 | 7 | A, E(Fu) | 2 | bacteriorhodopsin of Halobacterium salinarum |
| 3.E.2 | PRC | H+ (efflux) | multiple subunits | 5+5+1 | B, E (Chloro) | 2 | reaction center and cytochrome b6f complex of Rhodobacter sphaeroides |
b Substrates of single transporters within a family are separated by commas; substrates transported by different protein members of the family are separated by semicolons. When various solutes serve as transported substrates, they are separated by a slash; when two different solutes are transported in a symport fashion, they are separated by a comma; when two or more substrates are transported in an antiport fashion they are separated by a colon.
c Size range (in number of amino acid residues) when a single type of subunit is present, or for the entire complex when several types of subunits are present. In some cases the individual subunits in multisubunit systems are indicated separately.
d Number of (putative) transmembrane a-helical segments, TMS, (or b-strands in section 1.B) in a polypeptide chain. Underlined numbers indicate that the number is established by X-ray chrystallographic data or that substantial experimental evidence suggests the proposed topology, usually as a result of the use of gene fusion technology. If not underlined, numbers indicate the number of TMS predicted on the basis of hydropathy analysis using available programs such as WHAT and AveHAS see the Web site at (http://www.biology.ucsd.edu/~yzhai/biotools.html). In some cases, the numbers of predicted TMS is zero, and hence a "0" is entered. In many such cases, the actual TMS is (are) amphipathic, and hence the program does not predict the number correctly. Subscripts refer to the number of polypeptide chains in the complex when known; n indicates an oligomeric structure of unknown or poorly defined number of subunits. If alternative structures are found for different transporters within a single family, these are separated by semicolons.
e Abbreviations used for types of organisms, organelles and viruses are as follows: B, Bacteria; A, Archaea; E, Eucarya; G-, Gram-negative bacteria; G+, Gram-positive bacteria; Y, yeasts; Fu, fungi; Pr, protozoans; Pl, plants; An, animals; Mito, mitochondria; Chloro, chloroplasts; ER, endoplasmic reticulum; Bp, bacteriophage; V, virus
f The numbers represent the order of magnitude of members in this family as of November 2001. 0: between 1 and 5; 1: between 6 and 49; 2: between 50 and 499; 3: more than 500.