Although ABC transporters have a diverse transport mechanism, many of them share similar domain architectures. The core structure of ABC transporters are made up of a pair of ATP- binding domains, also known as nucleotide binding domain (NBD) and two sets of transmembrane domains (TMDs). Upon, dimerisation of the two TMDs, the translocation pathway is formed and the conformation of the TMDs is controlled by the NBDs through hydrolysis-induced separation and ATP-induced dimerisation (Dean et al., 2001; Higgins, 2001; Procko et al., 2009).
So far, based on TMDs folds, there are seven types of ABC transporters discovered (Figure 1.10), of which three can only transport substrates from outside to inside of the cells known as Type I and Type II importers, and energy coupling factor (ECF) transporters (Type III importers) (ter Beek et al., 2014; Rice et al., 2014; Lewinson et al., 2017). These ABC importers are only found in prokaryotes. While type IV and V ABC transporters are known as the ABC exporters which are found in both prokaryotes and eukaryotes (Locher, 2009; ter Beek et al., 2014) and type VI and VII are found in bacterial cells (Crow et al., 2017; Greene et al., 2018; Hicks et al., 2018).
Figure 1.10. Schematic diagram showing the available crystal structures of seven types of ABC transporters. The protein data bank identifiers are in bracket below the name of the
transporters. A single colour code present each protein chain. There are three types of importers (Type I, II and III (Energy coupling factor (ECF)) (Example: molybdate transporter (ModABC), vitamin B12 transporter (BtuCDF), folate importer (ECF-FolT) respectively). two types of exporters (Type IV and V) (Example: multidrug exporter (Sav1866) and sterol transporter (ABCG5/G8) repectively) and two types of mechanotransducers (Type VI and VII) (Example: lipopolysaccharide extractor (LptBFG) and, enterotoxin and macrolide transporter (MacB) respectively) (Greene et al., 2018).
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In prokaryotes, the two TMDs and the two NBDs of the ABC transporters are often assembled as separate protein subunits. Therefore, the two TMDs and NBDs can be identical or different proteins (Wilkens, 2015). Furthermore, where the TMDs differ to the NBDs, usually the two NBDs are similar in structure and in most cases the two TMDs are also similar in structure with the exception of the two TMDs in ECF transporters (Xu et al., 2013; ter Beek et al., 2014). In other cases, in particular in prokaryotic transporter have two and occasionally three protein domains fused together such as the fusion of the two NBDs and the fusion of the TMDs with the NBDs (ter Beek et al., 2014; Wilkens, 2015). See figure 1.11 for a schematic diagram of the different core structures of ABC transporters. On the other hand, type IV exporters either exist as a dimer of two polypeptides, each of which made up of a TMD and an NBD such as in the bacterial exporters (Dawson et al., 2006), or one polypeptide chain comprising all domains as in eukaryotic exporters (Locher, 2009 ter Beek et al., 2014) and type V exporters are known as ‘half transporters’ comprising of one NBD fused to one TMD to form a single polypepide chain consisting of six transmembrane helices (Lee et al., 2016; Taylor et al., 2017). The third group of ABC transporters are the mechanotransducers, type VI and VII.
Moreover, the Type I and II ABC importers require an additional substrate binding proteins (SBPs) are to help facilitate the transport of substrate by capturing the substrate on the trans- side and distributing it to the TMDs (Figure 1.11). The SBPs can either be found as a separate protein subunit or fused with a TMD to form a multidomain subunit (Higgins, 2001; Locher, 2009). Additionally, apart from the core domains many ABC transporters in prokaryotes and eukaryotes have additional subunits or domains such as extra TMDs or regulatory domains (Figure1.11) (Theodoulou et al., 2015).
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Figure 1.11. A schematic diagram of the different core structures of ABC transporters.
The ABC importers in prokaryotes (Example in Gram-negative bacteria) consist of two TMDs linked to two NBDs and a SBP subunit. The ECF transporters comprise of a substrate-specific integral membrane protein (S) and a transmembrane protein (T). The ABC exporters in all bacteria are homodimeric or heterodimeric, in which a TMD is fused with an NBD. In eukaryotes, the ABC transporters are divided into eight distinct subfamilies (A-H) (See section 1.6.4). Each subfamilies, has some representative of different arrangement of core and additional domains. However, subfamilies E, F and H are not present in plants, fungi and mammals (Theodoulou et al., 2015).
1.6.2.1 Nucleotide binding domain (NBD)
As mentioned earlier all ABC transporters have two NBDs which bind and hydrolyse ATP. A core of about 200 amino acids make each NBD which also consist of two subdomains, the
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RecA-like domain and the α-helical domain which is exclusive to ABC transporters. The NBDs consist of seven highly conserved motifs (Figure 1.12) (ter Beek et al., 2014; Wilkens, 2015).
Figure 1.12. A view along an axis perpendicular to the membrane plane from the trans- side onto the NBDs. The TMDs and SBP are not shown. A colour code show the different
highly conserved sequence motifs and domains: red, A-loop; magenta, Walker A; orange, Walker B; cyan, ABC motif; blue, D-loop; green, H-loop; yellow, Q-loop; faded grey, regulatory C-terminal domain; light blue, RecA-like domain; green, α-helical domain. The ATP analogue
Adenylyl-imidodiphosphate (AMP-PNP) is represented in sticks (ter Beek et al., 2014).
1.6.2.2 Transmembrane domain (TMD)
The TMDs of ABC transporters comprise a translocation pathway which facilitates the movement of substrates across the membrane (ter Beek et al., 2014).
Type I ABC importers consist of two TMDs each made up of five transmembrane (TM) helices. The TMDs are either homodimers or similar in structure. Furthermore, in many Type I importers there is an additional N-terminal helix thus making the total number of TM helices to 12 or 8 in some cases. The interface between the two TMDs produces the translocation pathway (Locher, 2009; ter Beek et al., 2014; Rice et al., 2014).
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Type II ABC importers consist of two similar TMDs each made up of 10 tightly packed TM helices. In addition the helices in one TMD do not cross over to the other TMD, rather the helices line up to each other in a TMD. Furthermore, in each TMD has two group of helices pack together to found two subdomains which are position in opposite direction with respect to the membrane. Thus the two TMDs form a translocation pathway at the interface (Locher, 2009; ter Beek et al., 2014; Rice et al., 2014).
ECF-type ABC importers, consist of two TMDs, termed the T-component (EcfT subunit) and the S-component. Their function and structure are not similar. The T-component has five TM helices and in other transporters may have between four to eight TM helices (Eitinger et al., 2011) while S-component usually has six TM helices and sometimes an additional N-terminal helix (Xu et al., 2013). The S-component has a high binding affinity for transported substrates (Berntsson et al., 2012). However, unlike the other ABC importers, the translocation pathway in ECF-type ABC importers rely on the S-component that uses another access mechanism (ter Beek et al., 2014).
Type IV ABC exporters consist of two TMDs each comprised of six TM helices. The two TMDs can either be similar in structure or identical, often the TMDs are fused with the NBDs and there is a crossover of two helices from each TMD to the other TMD. Moreover, both TMDs are embedded deep in the cytoplasm causing the NBDs to be located very far from the membrane. Therefore the translocation pathway is more likely to be located at the interface of the dimerisation of the TMDs (Higgins, 2001; Procko et al., 2009; ter Beek et al., 2014).
As mentioned above, type V ABC exporters are ‘half transporters’ in that they consist of only one TMD and one NBD. Example of a protein belonging to this group is ABCG2. The TMD is made up of six TM helices. Similar to other nucleotide-free ABC exporters and importers, type V ABC exporters have also adopted an inward conformation. Since they are ‘half transporters’ their functional form is a homodimer where by the TM helices from one subunit do not cross over to the TMD of the other ‘half transporter’. Moreover, the regions between TM helix 5 and TM helix 6 form distinct α-helical structures in the extracellular domain (ECD) (Lee et al., 2016; Taylor et al., 2017).
Type VI ABC transporters are lipopolysaccharide (LPS) exporters (Hicks et al., 2018). An LPS exporter is an oligomeric complex consisting of Lpt protein B, F, G and C subunits which are all bound to the inner membrane (IM) and Lpt D/E heterodimer which is bound in the out membrane (OM). The subunits in the IM are connected to the subunit in the OM by periplasmic LptA subunit thus form a teramer (Botos et al., 2016; Hicks et al., 2018).
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Type VII ABC transporters such MacB is a macrolide antibiotic-specific transporter in E. Coli. MacB consist of four TM helices, an N-terminal NBD and a large periplasmic domain linking TM helix 1 to TM helix 2 (Xu et al., 2009; Crow et al., 2017). MacB is a homodimeric protein binds MacA adaptor protein and ToIc exit duct to form a tripartite efflux pump to efflux antibiotics and heat-stable enterotoxin II (STII) out of the bacterial cell (Xu et al., 2009; Crow et al., 2017; Fitzpatrick et al., 2017; Greene et al., 2018)