Gene family
The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.
ABC transporters often consist of multiple subunits, one or two of which are transmembrane proteins and one or two of which are membrane-associated AAA ATPases. The ATPase subunits utilize the energy of adenosine triphosphate (ATP) binding and hydrolysis to provide the energy needed for the translocation of substrates across membranes, either for uptake or for export of the substrate.
Most of the uptake systems also have an extracytoplasmic receptor, a solute binding protein. Some homologous ATPases function in non-transport-related processes such as translation of RNA and DNA repair. ABC transporters are considered to be an ABC superfamily based on the similarities of the sequence and organization of their ATP-binding cassette (ABC) domains, even though the integral membrane proteins appear to have evolved independently several times, and thus comprise different protein families. Like the ABC exporters, it is possible that the integral membrane proteins of ABC uptake systems also evolved at least three times independently, based on their high resolution three-dimensional structures. ABC uptake porters take up a large variety of nutrients, biosynthetic precursors, trace metals and vitamins, while exporters transport lipids, sterols, drugs, and a large variety of primary and secondary metabolites. Some of these exporters in humans are involved in tumor resistance, cystic fibrosis and a range of other inherited human diseases. High level expression of the genes encoding some of these exporters in both prokaryotic and eukaryotic organisms (including human) result in the development of resistance to multiple drugs such as antibiotics and anti-cancer agents.
Hundreds of ABC transporters have been characterized from both prokaryotes and eukaryotes. ABC genes are essential for many processes in the cell, and mutations in human genes cause or contribute to several human genetic diseases. Forty eight ABC genes have been reported in humans. Among these, many have been characterized and shown to be causally related to diseases present in humans such as cystic fibrosis, adrenoleukodystrophy, Stargardt disease, drug-resistant tumors, Dubin–Johnson syndrome, Byler's disease, progressive familiar intrahepatic cholestasis, X-linked sideroblastic anemia, ataxia, and persistent and hyperinsulimenic hypoglycemia. ABC transporters are also involved in multiple drug resistance, and this is how some of them were first identified. When the ABC transport proteins are overexpressed in cancer cells, they can export anticancer drugs and render tumors resistant.
Function.
ABC transporters utilize the energy of ATP binding and hydrolysis to transport various substrates across cellular membranes. They are divided into three main functional categories. In prokaryotes, "importers" mediate the uptake of nutrients into the cell. The substrates that can be transported include ions, amino acids, peptides, sugars, and other molecules that are mostly hydrophilic. The membrane-spanning region of the ABC transporter protects hydrophilic substrates from the lipids of the membrane bilayer thus providing a pathway across the cell membrane. Eukaryotes do not possess any importers. "Exporters" or "effluxers", which are present both in prokaryotes and eukaryotes, function as pumps that extrude toxins and drugs out of the cell. In gram-negative bacteria, exporters transport lipids and some polysaccharides from the cytoplasm to the periplasm. The third subgroup of ABC proteins do not function as transporters, but are rather involved in translation and DNA repair processes.
Prokaryotic.
Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity. Iron ABC uptake systems, for example, are important effectors of virulence. Pathogens use siderophores, such as Enterobactin, to scavenge iron that is in complex with high-affinity iron-binding proteins or erythrocytes. These are high-affinity iron-chelating molecules that are secreted by bacteria and reabsorb iron into iron-siderophore complexes. The chvE-gguAB gene in "Agrobacterium tumefaciens" encodes glucose and galactose importers that are also associated with virulence. Transporters are extremely vital in cell survival such that they function as protein systems that counteract any undesirable change occurring in the cell. For instance, a potential lethal increase in osmotic strength is counterbalanced by activation of osmosensing ABC transporters that mediate uptake of solutes. Other than functioning in transport, some bacterial ABC proteins are also involved in the regulation of several physiological processes.
In bacterial efflux systems, certain substances that need to be extruded from the cell include surface components of the bacterial cell (e.g. capsular polysaccharides, lipopolysaccharides, and teichoic acid), proteins involved in bacterial pathogenesis (e.g. hemolysis, heme-binding protein, and alkaline protease), heme, hydrolytic enzymes, S-layer proteins, competence factors, toxins, antibiotics, bacteriocins, peptide antibiotics, drugs and siderophores. They also play important roles in biosynthetic pathways, including extracellular polysaccharide biosynthesis and cytochrome biogenesis.
Eukaryotic.
Although most eukaryotic ABC transporters are effluxers, some are not directly involved in transporting substrates. In the cystic fibrosis transmembrane regulator (CFTR) and in the sulfonylurea receptor (SUR), ATP hydrolysis is associated with the regulation of opening and closing of ion channels carried by the ABC protein itself or other proteins.
Human ABC transporters are involved in several diseases that arise from polymorphisms in ABC genes and rarely due to complete loss of function of single ABC proteins. Such diseases include Mendelian diseases and complex genetic disorders such as cystic fibrosis, adrenoleukodystrophy, Stargardt disease, Tangier disease, immune deficiencies, progressive familial intrahepatic cholestasis, Dubin–Johnson syndrome, Pseudoxanthoma elasticum, persistent hyperinsulinemic hypoglycemia of infancy due to focal adenomatous hyperplasia, X-linked sideroblastosis and anemia, age-related macular degeneration, familial hypoapoproteinemia, Retinitis pigmentosum, cone rod dystrophy, and others. The human ABCB (MDR/TAP) family is responsible for multiple drug resistance (MDR) against a variety of structurally unrelated drugs. ABCB1 or MDR1 P-glycoprotein is also involved in other biological processes for which lipid transport is the main function. It is found to mediate the secretion of the steroid aldosterone by the adrenals, and its inhibition blocked the migration of dendritic immune cells, possibly related to the outward transport of the lipid platelet activating factor (PAF). It has also been reported that ABCB1 mediates transport of cortisol and dexamethasone, but not of progesterone in ABCB1 transfected cells. MDR1 can also transport cholesterol, short-chain and long-chain analogs of phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), sphingomyelin (SM), and glucosylceramide (GlcCer). Multispecific transport of diverse endogenous lipids through the MDR1 transporter can possibly affect the transbilayer distribution of lipids, in particular of species normally predominant on the inner plasma membrane leaflet such as PS and PE.
More recently, ABC-transporters have been shown to exist within the placenta, indicating they could play a protective role for the developing fetus against xenobiotics. Evidence has shown that placental expression of the ABC-transporters P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) are increased in preterm compared to term placentae, with P-gp expression further increased in preterm pregnancies with chorioamnionitis. To a lesser extent, increasing maternal BMI also associated with increased placental ABC-transporter expression, but only at preterm.
Structure.
All ABC transport proteins share a structural organization consisting of four core domains. These domains consist of two trans-membrane (T) domains and two cytosolic (A) domains. The two T domains alternate between an inward and outward facing orientation, and the alternation is powered by the hydrolysis of adenosine triphosphate or ATP. ATP binds to the A subunits and it is then hydrolyzed to power the alternation, but the exact process by which this happens is not known. The four domains can be present in four separate polypeptides, which occur mostly in bacteria, or present in one or two multi-domain polypeptides. When the polypeptides are one domain, they can be referred to as a full domain, and when they are two multi-domains they can be referred to as a half domain. The T domains are each built of typically 10 membrane spanning alpha helices, through which the transported substance can cross through the plasma membrane. Also, the structure of the T domains determines the specificity of each ABC protein. In the inward facing conformation, the binding site on the A domain is open directly to the surrounding aqueous solutions. This allows hydrophilic molecules to enter the binding site directly from the inner leaflet of the phospholipid bilayer. In addition, a gap in the protein is accessible directly from the hydrophobic core of the inner leaflet of the membrane bilayer. This allows hydrophobic molecules to enter the binding site directly from the inner leaflet of the phospholipid bilayer. After the ATP powered move to the outward facing conformation, molecules are released from the binding site and allowed to escape into the exoplasmic leaflet or directly into the extracellular medium.
The common feature of all ABC transporters is that they consist of two distinct domains, the "transmembrane domain (TMD)" and the "nucleotide-binding domain (NBD)". The TMD, also known as membrane-spanning domain (MSD) or integral membrane (IM) domain, consists of alpha helices, embedded in the membrane bilayer. It recognizes a variety of substrates and undergoes conformational changes to transport the substrate across the membrane. The sequence and architecture of TMDs is variable, reflecting the chemical diversity of substrates that can be translocated. The NBD or ATP-binding cassette (ABC) domain, on the other hand, is located in the cytoplasm and has a highly conserved sequence. The NBD is the site for ATP binding. In most exporters, the N-terminal transmembrane domain and the C-terminal ABC domains are fused as a single polypeptide chain, arranged as TMD-NBD-TMD-NBD. An example is the "E. coli" hemolysin exporter HlyB. Importers have an inverted organization, that is, NBD-TMD-NBD-TMD, where the ABC domain is N-terminal whereas the TMD is C-terminal, such as in the "E. coli" MacB protein responsible for macrolide resistance.
The structural architecture of ABC transporters consists minimally of two TMDs and two NBDs. Four individual polypeptide chains including two TMD and two NBD subunits, may combine to form a "full transporter" such as in the "E. coli" BtuCD importer involved in the uptake of vitamin B12. Most exporters, such as in the multidrug exporter Sav1866 from "Staphylococcus aureus", are made up of a homodimer consisting of two "half transporters" or monomers of a TMD fused to a nucleotide-binding domain (NBD). A full transporter is often required to gain functionality. Some ABC transporters have additional elements that contribute to the regulatory function of this class of proteins. In particular, importers have a high-affinity "binding protein (BP)" that specifically associates with the substrate in the periplasm for delivery to the appropriate ABC transporter. Exporters do not have the binding protein but have an "intracellular domain (ICD)" that joins the membrane-spanning helices and the ABC domain. The ICD is believed to be responsible for communication between the TMD and NBD.
Transmembrane domain (TMD).
Most transporters have transmembrane domains that consist of a total of 12 α-helices with 6 α-helices per monomer. Since TMDs are structurally diverse, some transporters have varying number of helices (between six and eleven). The TM domains are categorized into three distinct sets of folds: "type I ABC importer", "type II ABC importer" and "ABC exporter" folds. The classification of importer folds is based on detailed characterization of the sequences.
The type I ABC importer fold was originally observed in the ModB TM subunit of the molybdate transporter. This diagnostic fold can also be found in the MalF and MalG TM subunits of MalFGK2 and the Met transporter MetI. In the MetI transporter, a minimal set of 5 transmembrane helices constitute this fold while an additional helix is present for both ModB and MalG. The common organization of the fold is the "up-down" topology of the TM2-5 helices that lines the translocation pathway and the TM1 helix wrapped around the outer, membrane-facing surface and contacts the other TM helices.
The type II ABC importer fold is observed in the twenty TM helix-domain of BtuCD and in Hi1471, a homologous transporter from "Haemophilus influenzae". In BtuCD, the packing of the helices is complex. The noticeable pattern is that the TM2 helix is positioned through the center of the subunit where it is surrounded in close proximity by the other helices. Meanwhile, the TM5 and TM10 helices are positioned in the TMD interface. The membrane spanning region of ABC exporters is organized into two "wings" that are composed of helices TM1 and TM2 from one subunit and TM3-6 of the other, in a domain-swapped arrangement. A prominent pattern is that helices TM1-3 are related to TM4-6 by an approximate twofold rotation around an axis in the plane of the membrane.
The exporter fold is originally observed in the Sav1866 structure. It contains 12 TM helices, 6