2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily

2.A.7.1.3 - 1S7B

References:

Examples:

SMR family pumps are prokaryotic transport systems consisting of homodimeric or heterodimeric structures (Chung and Saier, 2001). The subunits of these systems are of 100-120 amino acid residues in length and span the membrane as α-helices four times. Functionally characterized members of the SMR family catalyze multidrug efflux driven drug:H⁺ antiport where the proton motive force provides the driving force for drug efflux. The drugs transported are generally cationic, and a simple cation antiport mechanism involving the conserved Glu-14 has been proposed (Yerushalmi and Schuldiner, 2000). This mechanism suggests a requisite, mutually exclusive occupancy of Glu-14, providing a simple explanation for coupling the movement of two positively charged molecules. One system (YdgEF of E. coli; TC# 2.A.7.1.8) is reported to confer resistance to anionic detergents (Nishino and Yamaguchi, 2001). A low resolution (7 Å) 3-dimensional structure has been reported for EmrE showing it to be an asymmetric dimer with one substrate that binds in the middle of the dimer (Ubarretxena-Belandia et al., 2003). A 3.8 Å resolution structure shows a tetramer comprised of two conformational heterodimers related by a two-fold symmetry axis perpendicular to the cell membrane (Ma and Chang, 2004). A dimer of dimers has also been suggested from crosslinking studies (Elbaz et al., 2004).

The BAT family consists of 5 TMS proteins from bacteria and archaea. None of these proteins is functionally characterized.

The DME family is a large family of integral membrane proteins with sizes ranging from 287 to 310 amino acyl residues and exhibiting 10 putative α-helical transmembrane spanners (TMSs). These proteins are derived from phylogenetically divergent bacteria and archaea, and B. subtilis, E. coli, S. coelicolor and A. fulgidus have multiple paralogues. Distant eukaryotic homologues are more closely related to DME family members than to other DM superfamily members can be found (i.e., the Riken gene product of the mouse (BAC31006)).

Proteins of the DME family evidently arose by an internal gene duplication event as the first halves of these proteins are homologous to the second halves. One of these prokaryotic proteins, YdeD, is functionally characterized and exports cysteine metabolites in E. coli. Another, RhtA of E. coli, exports threonine and homoserine. A third, Sam of Rickettsia prowazekii, takes up S-adenosylmethionine (TC #3.A.7.3.7; Tucker et al., 2003). In addition, several members of the DME family have been implicated in solute transport. Thus, the MttP protein of the archaeon, Methanosarcina barkeri, may transport methylamine (Ferguson and Krzycki, 1997); MadN is encoded within the malonate utilization operon of Malonomonas rubra and may be an acetate efflux pump, and PecM is encoded within a locus of Erwinia chrysanthemi controlling pectinase, cellulase and blue pigment production and might export the pigment indigoidine, produced by gene products encoded in the pecM operon. The PecM protein has been shown experimentally to exhibit a 10 TMS topology (Rouanet and Nasser, 2001).

The P-DME family is a large subset of the DME family. All of these proteins are derived from plants, and they cluster loosely together on a phylogenetic tree that includes all members of the DME and P-DME families. All of these proteins appear to have 10 TMSs. If this suggestion proves to be correct, then the two halves of these proteins will have opposite orientation in the membrane. Hydropathy plots suggest that families 2.A.7.3-2.A.7.14 all exhibit 10 putative TMSs. No member of the P-DME family is functionally characterized, although one of these proteins, Nodulin 21 of M. truncatula, may be involved in bacterial nodulation.

The glucose/ribose uptake (GRU) family includes two functionally characterized members, a glucose uptake permease of Staphylococcus xylosus, and a probable ribose uptake permease of Lactobacillus sakei. Both proteins probably function by H⁺ symport.

The RhaT family includes only 2 proteins, the rhamnose:H⁺ symporters of E. coli and Salmonella typhimurium, both of which have been functionally characterized. The RhaT proteins of both species are 344 aas long with 10 putative TMSs.

No member of the RarD family is functionally characterized. Members of the family are from Gram-negative bacteria, Gram-positive bacteria and possibly archaea. They vary in size from 250-300 residues. They exhibit 10 TMSs.

The CEO family is a small family of 6 paralogues encoded within the genome of C. elegans. None of these proteins is functionally characterized.

Functionally characterized members of the former TPT family are derived from the inner envelope membranes of chloroplasts and nongreen plastids of plants. However, homologues are also present in yeast. Saccharomyces cerevisiae has three functionally uncharacterized TPT paralogues encoded within its genome. Under normal physiological conditions, chloroplast TPTs mediate a strict antiport of substrates, frequently exchanging an organic three carbon compound phosphate ester for inorganic phosphate (P_i). Normally, a triose-phosphate, 3-phosphoglycerate, or another phosphorylated C₃ compound made in the chloroplast during photosynthesis, exits the organelle into the cytoplasm of the plant cell in exchange for P_i. These transporters are members of a subfamily, the TPT subfamily within the TPT family. Experiments with reconstituted translocators in artificial membranes indicate that transport can also occur by a channel-like uniport mechanism with up to 10-fold higher transport rates. Channel opening may be induced by a membrane potential of large magnitude and/or by high substrate concentrations. Nongreen plastid and chloroplast carriers, such as those from maize endosperm and root membranes, mediate transport of C₃ compounds phosphorylated at carbon atom 2, particularly phosphoenolpyruvate, in exchange for P_i. These are the phosphoenolpyruvate:P_i antiporters (the PPT subfamily). Glucose-6-P has also been shown to be a substrate of some plastid translocators (the GPT subfamily). These three subfamilies of proteins (TPT, PPT and GPT) are divergent in sequence as well as substrate specificity, but their substrate specificities overlap.

Each TPT family protein consists of about 400-450 amino acyl residues with 5-8 putative transmembrane α-helical spanners TMSs). The actual number has been proposed to be 6 for the plant proteins as for mitochondrial carriers (TC# 2.A.29) and members of several other transporter families. However, proteins of the TPT family do not exhibit significant sequence similarity with the latter proteins, and there is no evidence for an internal repeat sequence. TPT proteins may exist as homodimers in the membrane.

The generalized reaction catalyzed by the proteins of the TPT family is:

organic phosphate ester (in) + P_i (out) organic phosphate ester (out) + P_i (in).

Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as C. elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter.

NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterized. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids. Comparable transport proteins exist for ATP which phosphorylates proteins, and phosphoadenosine phosphosulfate (PAPS) which is used as a percursor for protein sulfation. It is not known if these transport proteins are members of the DMT superfamily.

The sequenced NSTs are generally of about 320-340 amino acyl residues in length and exhibit 8-12 putative transmembrane α-helical spanners. An 8 TMS model has been presented by Kawakita et al. (1998) for the human UDP galactose transporter 1.

The generalized reaction catalyzed by NSTs is:

nucleotide-sugar (cytoplasm) + nucleotide (lumen) nucleotide-sugar (lumen) + nucleotide (cytoplasm)

Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as C. elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter.

NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterized. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids. Comparable transport proteins exist for ATP which phosphorylates proteins, and phosphoadenosine phosphosulfate (PAPS) which is used as a percursor for protein sulfation. It is not known if these transport proteins are members of the DMT superfamily.

The sequenced NSTs are generally of about 320-340 amino acyl residues in length and exhibit 8-12 putative transmembrane α-helical spanners. An 8 TMS model has been presented by Kawakita et al. (1998) for the human UDP galactose transporter 1.

The generalized reaction catalyzed by NSTs is:

nucleotide-sugar (cytoplasm) + nucleotide (lumen) nucleotide-sugar (lumen) + nucleotide (cytoplasm)

Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as C. elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter.

NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterized. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids. Comparable transport proteins exist for ATP which phosphorylates proteins, and phosphoadenosine phosphosulfate (PAPS) which is used as a percursor for protein sulfation. It is not known if these transport proteins are members of the DMT superfamily.

The sequenced NSTs are generally of about 320-340 amino acyl residues in length and exhibit 8-12 putative transmembrane α-helical spanners. An 8 TMS model has been presented by Kawakita et al. (1998) for the human UDP galactose transporter 1.

The generalized reaction catalyzed by NSTs is:

nucleotide-sugar (cytoplasm) + nucleotide (lumen) nucleotide-sugar (lumen) + nucleotide (cytoplasm)

The yeast VRG4 protein, also called "vanidate resistance protein", is a GDP-mannose transporter with the same size and topology as the other NSTs, but it shows very little sequence similarity with them. Only with the PSI-BLAST program with one iteration do these proteins exhibit apparent similarity. VRG4 is most similar to proteins in C. elegans, Leishmania donovani, Arabidopsis thaliana, and another S. cerevisiae protein reported to be of 249 aas (spP40027).

A single member of the POP family (AtPUP1) has been functionally characterized. It has been shown to transport adenine and cytosine with high affinity. Evidence concerning energy coupling suggested an H⁺ symport mechanism. Purine derivatives (e.g., hypoxanthine), phytohormones (e.g., zeatin and kinetin) and alkaloids (e.g., caffeine) proved to be competitive inhibitors suggesting that they may be transport substrates. The order of inhibition of adenine uptake by a variety of purine derivatives, phytohormones and alkaloids was reported to be: adenine, kinetin, caffeine, cytosine, zeatin, hypoxanthine, cytidine, nicotine, kinetin riboside, adenosine, zeatin riboside and thymine (Williams and Miller, 2001). At least 15 members of this family have been sequenced from A. thaliana. Thus, AtPUP1 may be a broad specificity organocation transporter. Other family members have been reported to exhibit different affinities for nucleobases.

The generalized transport reaction probably catalyzed by AtPUP1 is:

Organocation (out) + H⁺ (out) → Organocation (in) + H⁺ (in)

The PE family is a small family of proteobacterial proteins with 10 putative TMSs and sizes and sequences that most resemble the proteins of the DME family (2.A.7.3) within the DMT superfamily. One member of this family, YddG of Salmonella typhimurium (closely related [>95% identical] to YddG of E. coli), has been functionally characterized (Santiviago et al., 2002). It is an efflux pump for paraquat (methyl viologen) which is a hydrophilic, doubly charged, quaternary ammonium compound that can participate in a redox cycle that generates oxygen free radicals in the bacterial cell under aerobic conditions. YddG cannot pump out acriflavin, showing that it is fairly specific. Therefore, it may not be a multidrug resistance pump. Paraquat resistance is also dependent on the major Salmonella porin, OmpD. Thus, YddG and OmpD are believed to function together in exporting paraquat to the external medium, but it is not known if this occurs in one or two steps (Santiviago et al., 2002).

The overall reaction catalyzed by YddG is:

Paraquat (in) → Paraquat (out).

A single functionally characterized secondary transporter, LicB of Haemophilus influenzae defines the LicB-T family (Fan et al., 2003). It has 292 aas and 10 putative TMSs.

LicB is a high-affinity choline permease that takes up choline under choline-limiting conditions. It is required for the use of exogenous choline for the synthesis of phosphorylcholine which is incorporated into the bacterium's lipopolysaccharide (LPS). It does not play a role in osmoprotection. Phosphorylcholine derivatized LPS contributes to H. influenzae's pathogenesis by mimicry of host cell molecules (Fan et al., 2003).

The overall reaction catalyzed by LicB is probably:

choline (out) + H⁺ (out) → choline (in) + H⁺ (in).