2.A.66 The Multidrug/Oligosaccharidyl-lipid/Polysaccharide (MOP) Flippase Superfamily
The MOP flippase superfamily includes eight distantly related families, five for which functional data are available: One ubiquitous family (MATE) specific for drugs, one (PST) specific for polysaccharides and/or their lipid-linked precursors in prokaryotes, one (OLF) specific for lipid-linked oligosaccharide precursors of glycoproteins in eukaryotes, one (AgnG) which includes a single functionally characterized member that extrudes the antibiotic, Agrocin 84, and one (MVI) of unknown transport function. The OLF family is found in the endoplasmic reticular membranes of eukaryotes. All functionally characterized members of the MOP superfamily catalyze efflux of their substrates, presumably by cation antiport. Members of this family have been reported to have the MATE fold (Ferrada and Superti-Furga 2022).
2.A.66.1 The Multi Antimicrobial Extrusion (MATE) Family
The MATE family includes a functionally characterized multidrug efflux system from Vibrio parahaemolyticus NorM, and several homologues from other closely related bacteria that function by a drug:Na+ antiport mechanism, a putative ethionine resistance protein of Saccharomyces cerevisiae, a cationic drug efflux pump in A. thaliana and the functionally uncharacterized DNA damage-inducible protein F (DinF) of E. coli. The bacterial proteins are of about 450 amino acyl residues in length and exhibit 12 putative TMS. They arose by an internal gene duplication event from a primordial 6 TMS encoding genetic element. The yeast proteins are larger (up to about 700 residues) and exhibit about 12 TMSs. A conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na+ in ion-coupled drug efflux (Castellano et al. 2021).
Human MATE1 (hMATE1) is an electroneutral H+/organic cation (OC) exchanger responsible for the final excretion step of structurally unrelated toxic organic cations in kidney and liver. Glu273, Glu278, Glu300 and Glu389 are conserved in the transmembrane regions. Substitution with alanine or aspartate reduced export of tetraethylammonium (TEA) and cimetidine, and several had altered substrate affinities (Matsumoto et al., 2008). Thus, all of these glutamate residues are involved in binding and/or transport of TEA and cimetidine, but their roles are different.
There are 59 MATE transporters in grapes (Vitis vinifera) (Watanabe et al. 2022). Group 1 may transport toxic compounds and alkaloids; Group 2 may transport polyphenolic compounds; Group 3 may transport organic acids, and Group 4 may transport plant hormones related to signal transduction. In addition to the known anthocyanin transporters, VvMATE37 and VvMATE39, a novel anthocyanin transporter, VvMATE38 in Group 2, was suggested as a key transporter for anthocyanin accumulation in grape berry skin. VvMATE46, VvMATE47, and VvMATE49 in Group 3 may contribute to Al3+ detoxification and Fe2+/Fe3+ translocation via organic acid transport (Watanabe et al. 2022).
The family includes hundreds of functionally uncharacterized but sequenced homologues from bacteria, archaea, and all eukaryotic kingdoms (Kuroda and Tsuchiya, 2009). A comprehensive review of the classes of efflux pump inhibitors from various sources, highlighting their structure-activity relationships, which can be useful for medicinal chemists in the pursuit of novel efflux pump inhibitors has appeared (Durães et al. 2018). A whole-body physiologically based pharmacokinetic study has characterized the interplay of OCTs (TC# 2.A.1.19) and MATEs in intestine, liver and kidney, predicting drug-drug interactions of metformin with perpetrators (Yang et al. 2021).
The probable transport reaction catalyzed by NorM, and possibly by other proteins of the MATE family is:
Antimicrobial (in) + nNa+ (out) → Antimicrobial (out) + nNa+ (in).
2.A.66.2 The Polysaccharide Transport (PST) Family
The protein members of the PST family are generally of 400-500 amino acyl residues in size and traverse the membrane as putative α-helical spanners twelve times. Analyses conducted in 1997 showed that they formed two major clusters. One is concerned with lipopolysaccharide O-antigen (undecaprenol pyrophosphate-linked O-antigen repeat unit) export (flipping from the cytoplasmic side to the periplasmic side of the inner membranes) in Gram-negative bacteria. On the periplasmic side, polymerization occurs catalyzed by Wzy. The other is concerned with exopolysaccharide or capsular polysaccharide export in both Gram-negative and Gram-positive bacteria. However, arachaeal and eukaryotic homologues are now recognized. The mechanism of energy coupling is not established, but homology with the MATE family suggests that they are secondary carriers. A review of Wzx undecaprenyl pyrophosphate (UndPP)-linked polysaccharide repeat units occurs by a substrate:product antiport mechanism (Islam and Lam 2012). These transporters may function together with auxiliary proteins that allow passage across just the cytoplasmic membrane or both membranes of the Gram-negative bacterial envelope. They may also regulate transport. Thus, each Gram-negative bacterial PST system specific for an exo- or capsular polysaccharide functions in conjunction with a cytoplasmic membrane-periplasmic auxiliary (MPA) protein with a cytoplasmic ATP-binding domain (MPA1-C; TC #3.C.3) as well as an outer membrane auxiliary protein (OMA; TC #3.C.5). Each Gram-positive bacterial PST system functions in conjunction with a homologous MPA1 + C pair of proteins equivalent to an MPA1-C proteins of Gram-negative bacteria. The C-domain has been shown to possess tyrosine protein kinase activity, so it may function in a regulatory capacity. The lipopolysaccharide exporters may function specifically in the translocation of the lipid-linked O-antigen side chain precursor from the inner leaflet of the cytoplasmic membrane to the outer leaflet (Islam and Lam 2012). In this respect they correlate in function with the members of the oligosaccharidyl-lipid flippase (OLF) family of the MOP flippase superfamily.
The generalized transport reaction catalyzed by PST family proteins is:
Polysaccharide (in) + energy → Polysaccharide (out).
2.A.66.3 The Oligosaccharidyl-lipid Flippase (OLF) Family
N-linked glycosylation in eukaryotic cells follows a conserved pathway in which a tetradecasaccharide substrate (Glc3Man9GlcNAc2) is initially assembled in the ER membrane as a dolichylpyrophosphate (Dol-PP)-linked intermediate before being transferred to an asparaginyl residue in a lumenal protein. An intermediate, Man5GlcNAc2-PP-Dol is made on the cytoplasmic side of the membrane and translocated across the membrane so that the oligosaccharide chain faces the ER lumen where biosynthesis continues to completion.
The flippase that catalyzes the translocation step is dependent on the Rft1 protein of S. cerevisiae (Helenius et al., 2002). Homologues are found in plants, animals and fungi including C. elegans, D. melanogaster, H. sapiens, A. thaliana, S. cerevisiae and S. pombe. The yeast protein, called the nuclear division Rft1 protein, is 574 aas with 12 putative TMSs. The homologue in A. thaliana is 401 aas in length with 8 or 9 putative TMSs while that in C. elegans is 522 aas long with 11 putative TMSs. These proteins are distantly related to MATE and PST family members and therefore are probably secondary carriers.
2.A.66.4 The Mouse Virulence Factor (MVF) Family
A single member of the MVF family, MviN of Salmonella typhimurium, has been shown to be an important virulence factor for this organism when infecting the mouse (Kutsukake et al., 1994). In several bacteria, mviN genes occur in operons including glnD genes that encode the uridylyl transferase that participates in the regulation of nitrogen metabolism (Rudnick et al., 2001). Nothing more is known about the function of this protein or any other member of the MVF family. However, these proteins are related to members of the PST and MATE families (>9 S.D.), and the greatest sequence similarity is found with members of the PST family. It is therefore possible that MVF family members are functionally related to PST family members and catalyze efflux by a cation antiport mechanism.
2.A.66.5 The Agrocin 84 Antibiotic Exporter (AgnG) Family
Agrocin 84 is a disubstituted adenine nucleotide antibiotic made by and specific for Agrobacteria. It is encoded by the pAgK84 plasmid of A. tumefaciens (Kim et al., 2006) and targets a tRNA synthetase (Reader et al., 2005). The agnG gene encodes a protein of 496 aas with 12-13 putative TMSs and a short hydrophilic N-terminal domain of 80 residues. AgnG is distantly related to members of the Mop superfamily, but is so distant, that it does not retrieve any such members in a TC BLAST search. Nevertheless, an NCBI BLAST search retrieves proteins of the PST and MVI families without iterations. agnG null mutants accumulate agrocin 84 intracellularly and do not export it (Kim et al., 2006).
The reaction catalyzed by AgnG is:
agrocin (in) agrocin (out)
2.A.66.6 The Putative Exopolysaccharide Exporter (EPS-E) Family
2.A.66.7 Putative O-Unit Flippase (OUF) Family
2.A.66.8 Unknown MOP-1 (U-MOP1) Family
2.A.66.9 The Progressive Ankylosis (Ank) Family
Craniometaphyseal dysplasia (CMD) is a bone dysplasia characterized by overgrowth and sclerosis of the craniofacial bones and abnormal modeling of the metaphyses of the tubular bones. Hyperostosis and sclerosis of the skull may lead to cranial nerve compressions resulting in hearing loss and facial palsy. An autosomal dominant form of the disorder has been linked to chromosome 5p15.2-p14.1 within a region harboring the human homolog (ANKH) of the mouse progressive ankylosis (ank) gene. The ANK protein spans the cell membrane and shuttles inorganic pyrophosphate (PPi), a major inhibitor of physiologic and pathologic calcification, bone mineralization and bone resorption (Nurnberg et al., 2001).
The ANK protein has 12 membrane-spanning helices with a central channel permitting the passage of PPi. Mutations occur at highly conserved amino acid residues presumed to be located in the cytosolic portion of the protein. The PPi channel ANK is concerned with bone formation and remodeling (Nurnberg et al., 2001).
2.A.66.10 LPS Precursor Flippase (LPS-F) Family
2.A.66.11 Uncharacterized MOP-11 (U-MOP11) Family
2.A.66.12 Uncharacterized MOP-12 (U-MOP12) Family
Drug:Na+ antiporter (norfloxacin, ethidium, kanamycin, ciprofloxin, streptomycin efflux pump), NorM. Transport is dependent on Na+, and several essential residiues have been identified. Specifically, Asp32, Glu251, and Asp367 are involved in the Na+-dependent drug transport process. (Otsuka et al. 2005).
NorM of Vibrio parahaemolyticus (O82855)
Na -dependent cationic drug (ethidium, acriflavine, 2-N-methyl ellipticinium, berberine, norfloxacin, ciprofloxacin, rhodamine 6G, crystal violet, doxorubicin, novobiocin, enoxacin, and tetraphenylphosphonium chloride) efflux pump, NorM (Long et al. 2008). 3-d structures of the N. gonorrheae NorM transporter (96% identical to the N. miningitidis protein) have been solved complexed with three different substrates in a multidrug cavity and Cs (4HUN; Lu et al. 2013). Lu et al. an identified an uncommon cation-π interaction in the Na+-binding site located outside the drug-binding cavity and validated the biological relevance of both the substrate- and cation-binding sites by conducting drug resistance and transport assays. Additionally, they observed a potential rearrangement of at least two transmembrane helices upon Na+-induced drug export. They suggested that Na+ triggers multidrug extrusion by inducing protein conformational changes rather than by directly competing for the substrate-binding amino acids. However, see 2.A.66.1.32 where the opposite was concluded for a homologue that functions by drug:H+ antiport.
NorM of Neisseria meningitidis
The Enhanced Disease Susceptibility Protein (EDS5), also called the Salicylate Induction Deficient (Sid1) protein; a chloroplast isochorismate exporter that exports isochorismate from the plastid to the cytosol (Rekhter et al. 2019).
EDS5 of Arabidopsis thaliana chloroplasts
Drug (monovalent and divalent biocides; fluoroquinolones including norfloxacin and ciprofloxacin) efflux pump, SvrA (MepA) (Kaatz et al., 2006). Also exports tigecycline (McAleese et al., 2005).
SvrA of Staphylococcus aureus (Q2G140)
Human MATE1 electroneutral organocation:H antiporter (transports tetraethylammonium, TEA, and cimetidine as well as cisplatin and oxaliplatin) (Yonezawa et al., 2006). MATE1 also exports chloroquine across the luminal membrane (Müller et al., 2011). It has an established 13 TMS topology with the "extra" TMS in an extracellular C-terminal region that is not essential for function (Zhang et al., 2012). Also exports 1-methyl-4-phenylpyridinium (MPP), N-methylnicotinamide (NMN), metformin, creatinine, guanidine, procainamide, topotecan, estrone sulfate, acyclovir, cimetidine, ganciclovir and the zwitterionic cephalosporin, cephalexin and cephradin (Nigam 2015). Seems to also play a role in the uptake of oxaliplatin (a platinum anticancer agent). Able to transport paraquat (PQ or N,N-dimethyl-4-4'-bipiridinium); a widely used herbicid. Responsible for the secretion of cationic drugs across the brush border membranes (Tanihara et al. 2007).
SLC47A1 of Homo sapiens
MATE-1 of Rattus norvegicus (Q5I0E9)
MATE2 of Mus musculus (Q3V050)
MATE efflux pump, MatE
MatE of Tetrahymena thermophila
MATE1b of Mus musculus (Q8K0H1)
JAT1 of Nicotiana tabacum (B7ZGMO)
Drug:Na+ antiporter, VcmA (exports norfloxacin, ciprofloxacin, ofloxacin, daunomycin, doxorubicin, streptomycin, kanamycin, ethidium, 4',6'-diamidino-2-phenylindole, Hoechst 33342 and acriflavin). The 3-d x-ray structure (3.65Å resolution) is available (He et al., 2010). Ion binding and internal hydration have been studied by molecular dynamics simulations (Vanni et al., 2012). NorM simultaneously couples drug export to the sodium-motive force and the proton-motive force. Residues involved and protein regions that play important roles in Na+ or H+ binding have been identified (Jin et al. 2014). Na+- and H+-driven conformational changes are facilitated by a network of polar residues in the N-terminal domain cavity, whereas conserved carboxylates buried in the C-terminal domain are critical for stabilizing the drug-bound state. These results establish the role of ion-coupled conformational dynamics in the functional cycle and implicate H+ in the doxorubicin release mechanism (Claxton et al. 2018).
VcmA (NorM) of Vibrio cholerae non-01
Multidrug and Toxin Extrusion Protein 2, MATE-2 (catalyzes drug:H+ antiport; broad specificity, low affinity (50-3000 μM) for organic cationic and anionic compounds (Tanihara et al., 2007)).
H+-coupled multidrug efflux pump, AbeM (most like 2.A.66.1.2, NorM of Vibrio cholerae) (Su et al., 2005). Exports norfloxacin, ciprofloxacin, DAPI, acriflavin, Hoechst 33342, daunorubicin, doxorubicin, and ethidium (Su et al., 2005) as well as carbapenem (AlQumaizi et al. 2022).
AbeM of Acinetobacter baumannii (Q5FAM9)
Quinolone:H+ antiporter, EmmdR. Substates include benzalkonium chloride, norfloxacin, ciprofloxacin, levofloxacin, ethidium bromide, acriflavine, rhodamine 6G and trimethoprim.
EmmdR of Enterobacter cloacae (D5CJ69)
MDR efflux pump, YeeO (NorA) (81.8% identical to 2.A.66.1.22). Transports dipeptides (see 2.A.1.2.55) (Hayashi et al., 2010). Also exports both flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). However, significant amounts of flavins were trapped intracellularly when YeeO was produced. Wild-type E. coli secretes 3 flavins (riboflavin, FMN, and FAD), so it must have additional flavin transporters (McAnulty and Wood 2014).
YeeO of E. coli (P76352)
FRD3 efflux pump for citrate; involved in iron homeostasis. Localized to the pericycle and vascular cylinder of roots; loads citrate into xylem tissues facilitating iron transport from the roots to the shoots; null mutants are sterile (Green and Rogers 2004; Roschzttardtz et al., 2011; Durrett et al., 2007).
FRD3 of Arabidopsis thaliana (Q9SFB0)
Probable multidrug resistance protein YoeA
YoeA of Bacillus subtilis
NorM of Caulobacter crescentus
NorM of Thermotoga maritima
MATE exporter protein
MATE exporter protein of Myxococcus xanthus
Multidrug-resistance efflux pump, NorM (MdtK, NorE or YdhE) (Nishino and Yamaguchi 2001). Exports chloramphenicol, norfloxacin, enoxacin, phosphomycin, doxorubicin, trimethoprim, ethidium, deoxycholate, etc (Long et al., 2008). May also export signals for cell-cell communication (Yang et al., 2006).
NorM (YdhE) of E. coli
Ciprofloxacin export permease, AbeM2
AbeM2 of Acinetobacter baumannii
Ciprofloxacin efflux pump, AbeM4 (Eijkelkamp et al. 2011).
AbeM4 of Acinetobacter baumannii
Multidrug:proton antiporter of the DinF subfamily. The structure has been solved to 3.2 Å resolution with and without the substrate, Rhodamine 6 G. The 12 TMSs show asymmetry with a membrane-embedded substrate-binding chamber. Direct competition between the H+ and the substrate during transport was suggested (Lu et al. 2013). However, the opposite was suggested for a sodium antiporter (see TC# 2.A.66.1.10).
DinF-like MDR pump of Bacillus halodurans
MDR efflux pump for quinolones (moxifloxacin, ciprofloxacin and levofloxacin) of 456 aas, DinF (Tocci et al. 2013).
DinF of Streptococcus pneumoniae
MATE MDR exporter of 411 aas, SP2065 (Tocci et al. 2013). Exports novobiocin.
SP2065 of Streptococcus pneumoniae
Citrate-specific transporter of 538 aas, MATE1. Necessary for iron supply to the nodule infection zone (Takanashi et al. 2013).
MATE1 of Lotus japonicus
Multidrug exporter, DinF, of 457 aas. Exports various toxic compounds, including antibiotics, phytoalexins, and detergents. Mutants are less virulent on the tomato plant than the wild-type strain (Brown et al. 2007).
DinF of Ralstonia solanacearum (Pseudomonas solanacearum)
Multidrug resistance protein, CdeA of 441 aas. Exports ethidium bromide, fluoroquinolone and acriflavin but had no effect on susceptibility to the following antibiotics: norfloxacin, ciprofloxacin, gentamicin, erythromycin, tetracyclin, and chloramphenicol (Dridi et al. 2004). May be a Na+ antiporter.
CdeA of Clostridium difficile
CdeA of Clostridium difficile
Homologue of Mte1 of Tricholomp vaccinum of 588 aas which mediates detoxification of xenobiotics and metal ions such as Cu, Li, Al, and Ni, as well as secondary plant metabolites (Schlunk et al. 2015).
Mte1 homologue of Moniliophthora roreri (Cocoa frosty pod rot fungus) (Crinipellis roreri)
Jasmonate-inducible alkaloid transporter-2, JAT2.Transports nicotine and other alkaloids into the tonoplast vacuole for sequestration (Chen et al. 2015; Shitan et al. 2014).
JAT2 of Nicotiana tabacum
DNA damage-inducible protein F, DinF. Protects against oxidative stress and bile salts, possibly by pumping relevant compounds out of the cytoplasm (Rodríguez-Beltrán et al. 2012).
DinF of E. coli
Putative MDR or polysaccharide exporter of 514 aas and 12 TMSs
Exporter of Treponema succinifaciens
Na+-coupled multidrug efflux pump, PdrM (Hashimoto et al. 2013). Confers resistance to several antibacterial agents including norfloxacin, acriflavine, and 4',6-diamidino-2-phenylindole (DAPI).
PdrM of Streptococcus pneumoniae
Paralytic shellfish toxin (PST; including saxitoxin (STX)) exporter, SxtM, of 464 aas (Soto-Liebe et al. 2013). These toxins, which block Na+ channels, are produced by cyanobacteria and dinoflagellates, and >30 such natural alkaloids are known (Soto-Liebe et al. 2012).
SxtM of Cylindrospermopsis raciborskii
MATE1 of 563 aas and 12 TMSs. Involved in aluminum resistance (Maron et al. 2013).
MATE1 of Zea mays (Maize)
Transparent Testa 12 (TT12), also called Protein DETOXIFICATION, is a valuolar transporter of proanthocyanidins (PAs). It transports these compounds from the cytoplasm into the vacuolar lumen (Gao et al. 2015).
TT12 of Gossypium hirsutum (Upland cotton) (Gossypium mexicanum)
Damage inducible multidrug resistance protein F, DinF of 455 aas and 12 TMSs. An x-ray structure is available (Radchenko et al. 2015).
DinF of Pyrococcus furiosus
Saxitoxin, STX, exporter, SxtF; also exports fluoroquinolone, suggesting it is an MDR pump (Ongley et al. 2016).
SxtF of Cylindrospermopsis raciborskii
Saxitoxin, STX, exporter, SxtM; also exports fluoroquinolone, suggesting it is an MDR pump (Ongley et al. 2016).
SxtM of Aphanizomenon sp. NH-5 (Anabaena circinalis)
MATE transporter. ClbM, of 479 aas and 12 TMSs, ClbM. Exports precolibactin, a genotoxin made by a polyketide complex in E. coli, that generates double strand breaks in the DNA (Mousa et al. 2016). The 3-d structure is available (PDB# 4Z3N).
ClbM of E. coli
MATE family transporter of 475 aas and 12 TMSs in a 6 + 6 TMS pseudosymmetic arrangement. The 3-d structure has been determined at 2.9 Å resolution (Tanaka et al. 2017). The protein possesses a negatively charged internal pocket with an outward-facing shape. This structure was determined for the C. sativa orthologue of the C. rubella protein, the sequence of which is 94% identical to the one provided here.
CasMATE of Capsella rubella
Ethionine resistance protein, ERC1, of 581 aas and 11 TMSs in a 6 + 5 TMS arrangement. It catalyzes S-adenosyl methionine (SAM) accumulation in Sake yeast (Kanai et al. 2017).
ERC1 (YHR032w) of Saccharomyces cerevisiae
Detoxification protein, DTX35, of 614 aas and 12 TMSs, also called FLOWER FLAVONOID TRANSPORTER (FFT), encodes a MATE family transporter in Arabidopsis thaliana. FFT (AtDTX35) is highly transcribed in floral tissues, the transcript being localized to epidermal guard cells, including those of the anthers, stigma, siliques and nectaries (Thompson et al. 2010). The absence of FFT affects flavonoid levels in the plant. Moreover, root growth, seed development and germination, and pollen development, release and viability are all affected (Thompson et al. 2010). Also functions as a chloride channel, which, together with DTX33, is essential for turgor regulation (Zhang et al. 2017). Involved in floral development (Song et al. 2017).
DTX35 of Arabidopsis thaliana
Multidrug resistance efflux pump, Detoxification 48, DTX48. Functions as a multidrug and toxin extrusion transporter. Contributes to iron homeostasis during stress responses and senescence (Seo et al. 2012). Overexpression of DTX48 alters shoot developmental programs leading to a loss of apical dominance phenotype (Wang et al. 2015).
DTX48 of Arabidopsis thaliana (Mouse-ear cress)
Detoxification protein 14, DTX14, of 485 aas and 12 TMSs. This MATE family (MOP superfamily) proter extrduces xenobiotics from the cell. It's 3-d structure is known to 2.6 Å resolution (Miyauchi et al. 2017). Its carboxy-terminal lobe (C-lobe) contains an extensive hydrogen-bonding network with well-conserved acidic residues, as demonstrated by structure-based mutational analyses. The analyses suggest that the transport mechanism involves a structural change of transmembrane helix 7, induced by the formation of a hydrogen-bonding network upon the protonation of the conserved acidic residue in the C-lobe (Miyauchi et al. 2017).
DTX14 of Arabidopsis thaliana
Citrate exporter, MATE1 or DETOXIFICATION, of 553 aas and 12 probable TMSs. It's activity gives rise to aluminum (Al3+) tolerance (Garcia-Oliveira et al. 2014). 98% identical to the rye and barley orthologs (Zhou et al. 2013).
MATE1 of Tritium aestivum (Wheat)
MATE2 or Detoxification 47 (DTX47) of 543 aas and 12 TMSs. The orthologs from several plants have been sequenced and characterized (i.e., wheat; potato) (Li et al. 2018). This protein may be a citrate and salicylate exporter and promote resistance to aluminum (Al3+) (Garcia-Oliveira et al. 2018).
MATE2 of Arabidopsis thaliana
MATE drug:sodium symporter of 461 aas and 12 TMSs. Several crystal structures are known (3VVO, 3VVP, 3VVR, 3VVS, 6FHZ, 6GWH) in several distinct apo-form conformations, and in complexes with a derivative of the antibacterial drug norfloxacin and three in vitro selected thioether-macrocyclic peptides, at 1.8 - 3.0 Å resolutions. The structures, combined with functional analyses, show that the protonation of Asp 41 on the N-terminal lobe induces the bending of TMS1, which in turn collapses the N-lobe cavity, thereby extruding the substrate drug to the extracellular space. Moreover, the macrocyclic peptides bind the central cleft in distinct manners, which correlate with their inhibitory activities (Tanaka et al. 2013). The Na+-binding site, in the N-lobe of this transporter, is selective against K+, weakly specific against H+, and broadly conserved among prokaryotic MATEs (Ficici et al. 2018). The inward-facing state was obtained after crystallization in the presence of native lipids (Zakrzewska et al. 2019). The transition from the outward-facing state to the inward-facing state involves rigid body movements of TMSs 2-6 and 8-12 to form an inverted V, facilitated by a loose binding of TMS1 and TMS7 to their respective bundles and their conformational flexibility. The inward-facing structure of PfMATE in combination with the outward-facing one supports an alternating access mechanism for MATE family transporters ()Zakrzewska et al. 2019.
MOP superfamily transporter of Pyrococcus furiosus
MATE transporter,DETOXIFICATION 4, DTX4 or At2g04070, of 476 aas and 12 TMSs. May transport alkaloids, heavy metals, bile salts, organic acids amd organic amines (Li et al. 2018).
DTX4 of Arabidopsis thaliana (Mouse-ear cress)
DETOXIFICATION 41, DTX41, TDS3, TT12 of 507 aas and 12 TMSs. Acts as a flavonoid/H+-antiporter that controls the vacuolar sequestration of flavonoids in the seed coat endothelium (Debeaujon et al. 2001; Marinova et al. 2007). May also transport the anthocyanin cyanidin-3-O-glucoside (Marinova et al. 2007) and epicatechin 3'-O-glucoside (Zhao and Dixon 2009).
DTX41 of Arabidopsis thaliana (Mouse-ear cress)
Detoxification-50, DTX50, of 505 aas and 12 TMSs. It catalyzes abscisic acid efflux and modulates ABA sensitivity as well as drought tolerance (Zhang et al. 2014). It may also function in heavy metal ion export (Sailer et al. 2018).
DTX50 of Arabidopsis thaliana
The Activated Disease Susceptibility 1, ADS1 (DTX51, ABS3, ADP1, NIC4), putative exporter of 532 aas and 12 TMSs. ADS1 negatively regulates the accumulation of the plant immune activator salicylic acid as well as cognate Pathogenesis-Related 1 (PR1) gene expression which influences microbial pathogenesis (Sun et al. 2011). It may be a salicylate exporter.
ADS1 of Arabidopsis thaliana
Drug (norfloxacin, ciprofoxacin, ethidium, tetramethylammonium, pyrrolidinone, polyvinylpyrrolidone) resistance pump, Alf5 or DTOXIFICATION 19, DTX19, of 427 aas and 12 TMSs. Note: A. thaliana has 56 MATE transporters (Takanashi et al. 2013).
Alf5 of Arabidopsis thaliana
Probable multidrug resistence efflux pump of 452 aas and 12 TMSs in a 6 + 6 TMS arrangement.
MDR pump of Candidatus Prometheoarchaeum syntrophicum
Vacuolar nicotine exporter (from the cytoplasm into the vacuole), the NtMATE2 transporter, also designated the DETOXIFICATION 40-like protein, of 500 aas and 12 TMSs in a 6 + 6 TMS arrangement. NtMATE2 is located in the vacuole membrane of the tobacco plant root and is involved in the transport of nicotine, a secondary or specialized metabolic compound in Solanaceae ((Shoji et al. 2009). The crystal structures of NtMATE2 in its outward-facing forms have been determined (Tanaka et al. 2021). The overall structure has a bilobate V-shape with pseudo-symmetrical assembly of the N- and C-lobes. In one crystal structure, the C-lobe cavity of NtMATE2 interacts with an unidentified molecule that may mimic a substrate. NtMATE2-specific conformational transitions imply that an unprecedented movement of the transmembrane alpha-helix 7 (TMS7) is related to the release of the substrate into the vacuolar lumen (Tanaka et al. 2021).
NtMATE2 of Nicotiana tabacum (common tobacco)
Cationic drug (4',6'-diamidino-2-phenylindole (DAPI), tetraphenylphosphonium (TPP), acriflavin, ethidium):Na+ antiporter, VmrA of 447 aas and 12 TMSs.
VmrA of Vibrio parahaemolyticus
Plasma membrane efflux pump, AtDTX1, for plant alkaloids, drugs (e.g., norfloxacin), antibiotics and Cd2+ (Li et al. 2002).
AtDTX1 of Arabidopsis thaliana
Drug (norfloxacin, polymyxin B) resistance efflux pump, NorM, of 462 aas and 12 TMSs.
NorM of Burkholderia vietnamiensis
Wzx isoprenoid-linked O-antigen precursor glycan translocase. A 12 TMS topology with N- and C-termini in the cytoplasm has been established, and functionally important residues have been identified (Marolda et al. 2010). A substrate:proton antiport mechanism has been established (Islam et al. 2013).
Wzx of E. coli O157:H7 str 1125
Uncharacterized protein of Streptomyces coelicolor
Uncharacterized protein of Beggiatoa alba
Uncharacterized MOP superfamily member of 506 aas and 14 TMSs. Subfamily 2.A.66.12 may be most closely related to 2.A.66.2, suggesting that these proteins are glycolipid flippases.
U-MOP family 12 member-1 of Myxococcus xanthus
Uncharacterized protein of 452 aas and 12 TMSs.
UP of Parvularcula oceani
Uncharacterized putative flippase of 496 aas and 14 TMSs.
UP of Cyclobacterium lianum
Exopolysaccharide flippase, Wzxeps (MXAN_7416) of 490 aas and 14 TMSs in a 6 + 2 + 6 TMS arrangement. The gene encoding this transporter is adjacent to two genes encoding EpsZ (MXAN_7415; TC# 9.B.18.1.6), a glycosyl transferase that initiates repeat unit synthesis, and an outer membrane exopolysaccharide export protein, Opx or EpsY (MXAN_7417; TC# 1.B.18.3.9) (Pérez-Burgos et al. 2020).
Wzxeps of Myxococcus xanthus
Uncharacterized MOP superfamily member of 1049 aas and 14 or 15 TMSs
U-MOP family 12 member-2
Uncharacterized MOP superfamily member of 489 aas and 14 TMSs
U-MOP family 12 member-3
Uncharacterized MOP superfamily member of 487 aas and 14 TMSs
U-MOP superfamily protein
Uncharacterized MOP superfamily of 488 aas and 14 TMSs
U-MOP superfamily member
Putative polysaccharide exporter of 449 aas, YghQ.
YghQ of E. coli
The succinoglycan biosynthesis transporter homologue, Mth342
Mth342 of Methanobacterium thermoautotrophicum (O26442)
Putative Wzx flippase of 499 aas and 14 TMSs (Hug et al. 2016).
Wzx of Candidatus Peribacter riflensis
Uncharacterized flippase of 516 aas and 14 TMSs
UP of Cuniculiplasma divulgatum
Isoprenoid lipid sugar glycan flippase, Wzx (note: Wzx forms a complex with Wzy and Wzz for assembly of periplasmic O-antigen) (Marolda et al., 2006). Wzx has a 12 TMS topology (Cunneen and Reeves, 2008). WzyE (450aas; 12 TMSs; TC#9.B.128.1.1; B614D1) is called the enterobacterial common antigen (ECA) polysaccharide chain elongation polymerase (Marolda et al., 2006). The structure of Wzz has been determined by cryoEM (Collins et al. 2017).
Wzx of E. coli (Q1L811)
The 14 TMS SpoVB protein (possibly catalyzes lipid-linked oligosaccharide transport across the cytoplasmic membrane; required for proper cell wall biosynthesis) (Vasudevan et al., 2009).
The SpoVB protein of Bacillus subtilis (Q00758)
Anionic O-antigen (undecaprenyl pyrophosphate-linked anionic O-Ag) subunit flippase, Wzx. Translocates from the inner to the outer leaflets of the inner membrane. The topology has been studied (Ormazabal et al. 2010).
Wzx of Pseudomonas aeruginosa (G3XD19)
Capsular polysaccharide exporter, CpsU (428aas; 12 TMSs).
CpsU of Streptococcus thermophilus (Q8KUK6)
Sporulation protein YkvU
YkvU of Bacillus subtilis
O-antigen transmembrane translocase, Wzx (Franklin et al. 2011). In S. enterica groups B, D2 and E, Wzx translocation exhibits specificity for the repeat-unit structure, as variants with single sugar differences are translocated with lower efficiency, and little long-chain O antigen is produced. It appears that Wzx translocases are specific for their O antigen for normal levels of translocation (Hong et al. 2012).
Wzx of Salmonella enterica subsp. enterica
O-antigen transmembrane translocase, Wzx (Franklin et al. 2011). For S. enterica groups B, D2 and E, Wzx translocation exhibits specificity for the repeat-unit structure, as variants with single sugar differences are translocated with lower efficiency, and little long-chain O antigen is produced. It appears that Wzx translocases are specific for their O antigen for normal levels of translocation (Hong et al. 2012).
Wzx of Salmonella typhimurium subsp. houtenae
PST family homologue of 14 TMSs
Hypothetical protein of Parachlamydia acanthamoebae
Putative polysaccharide transporter
Putative polysaccharide transporter of Leptospira interrogans
Choline-derivatized teichoic acid exporter (flippase), TacF of495 aas. TacF is responsible for the choline dependent growth phenotype (Damjanovic et al. 2007).
TacF of Streptococcus pneumoniae
Xanthan precursor exporter of 499 aas and 14 TMSs, GumJ (Bianco et al. 2014).
GumJ of Xanthomonas campestris
Putative polysaccharide exporter of 471 aas and 14 TMSs
UP of E. coli
Polysaccharide export protein of 572 aas and 12 TMSs.
PS exporter of Candidatus Beckwithbacteria bacterium
Uncharacterized MOP superfamily member of 456 aas and 12 TMSs.
UP of Parvularcula oceani
Putative flippase of 416 aas and 12 TMSs.
Flippase of Candidatus Marithrix sp. Canyon 246
Uncharacterized protein of 435 aas and 13 TMSs.
UP of Bacillus wiedmannii
Uncharacterized polysaccharide precursor flippase of 476 aas and 14 TMSs.
UP of Clostridium botulinum
Undecaprenol-pyrophosphate O-antigen flippase WzxE
WzxE of E. coli (P0AAA7)
Uncharacterized putative carbohydrate-lipid flippase of 486 aas and 14 TMSs in a 6 + 2 + 6 arrangement.
UP of Bacteroides timonensis
Uncharacterized protein of 455 aas and 14 TMSs.
UP of Exiguobacterium sp. KRL4
Probable polysaccharide biosynthesis transport proteinof 433 aas and 12 TMSs [Candidatus Amesbacteria bacterium
PS transporter of Candidatus Amesbacteria bacterium
Exopolysaccharide (Amylovoran) exporter, AmsL
AmsL of Erwinia amylovora
The OLF (Rft1 protein) of Saccharomyces cerevisiae. May play a role in phospholipid flipping from the inner leaflet of the plasma membrane to the outer leaflet (Chauhan et al. 2016).
Rft1 of Saccharomyces cerevisiae
Uncharacterized protein, RFT1 homologue, of 469 aas and 14 TMSs.
RFT1 homologue of Paramecium tetraurelia (A0D5K0)
The mouse virulence factor, MviN. (May flip the Lipid II peptidoglycan precursor from the cytoplasmic side of the inner membrane to the periplasmic surface) (Vasudevan et al., 2009). MviN, a putative lipid flippase (Fay and Dworkin, 2009). In E. coli, MviN is an essential protein which when defective results in the accumulation of polyprenyl diphosphate-N-acetylmuramic acid-(pentapeptide)-N-acetyl-glucosamine. This may be the peptidoglycan intermediated exported via MviN (Inoue et al. 2008). It is essential for the growth of several bacteria.
MviN of Salmonella typhimurium (P37169)
Peptidoglycan biosynthesis protein MurJ (Ruiz 2008). A 3-d structural model showed a solvent-exposed cavity within the plane of the membrane (Butler et al. 2013). MurJ has 14 TMSs, and specific charged residues localized in the central cavity are essential for function. This structural homology model suggests that MurJ functions as an essential transporter in PG biosynthesis (Butler et al. 2013). Based on an in vivo assay, MurJ is a flippase for the lipid-linked cell wall precursors, polyisoprenoid-linked disaccharide-peptapeptides (Sham et al. 2014). There is controversy about the role of this porter and FtsW/RodA which on the basis of an in vitro assay, were thought to be flippases for the same intermediate (Young 2014). MurJ, the bacterial lipid II flippase, functions by an alternating-access mechanism (Kumar et al. 2019). The crystal structure of MurJ in a "squeezed" form, distinct from its inward- and outward-facing forms, has been published (Kohga et al. 2022). These authors reported two crystal structures of inward-facing forms from Arsenophonus endosymbiont MurJ and a crystal structure of E. coli MurJ in a "squeezed" form, which lacks a cavity to accommodate the substrate, mainly because of the increased proximity of transmembrane helices 2 and 8. Molecular dynamics simulations support the hypothesis that the squeezed form is an intermediate conformation (Kohga et al. 2022).
MurJ of Escherichia coli
MviN. Essential for peptidoglycan biosynthesis (Gee et al. 2012).
MviN of Mycobacterium tuberculosis
MviN; LuxO regulated for induction during the early logarithmic and stationary phase of growth (Cao et al. 2010).
MviN of Vibrio alginolyticus
UP of E. coli
Probable peptidoglycan-lipid II flippase, MurJ or MviN; essential for cell wall synthesis and viability (Mohamed and Valvano 2014).
MurJ of Burkholderia cenocepacia
MurJ (MviV) of 475 aas and 14 TMSs. Kuk et al. 2016 presented a crystal structure of MurJ from Thermosipho africanus in an inward-facing conformation at 2.0-A resolution. A hydrophobic groove is formed by two C-terminal transmembrane helices, which leads into a large central cavity that is mostly cationic. Their results suggest that alternating access is important for MurJ function, which may be applicable to other MOP superfamily transporters (Kuk et al. 2016).
MurJ of Thermosipho africanus
AgnG homologue 2 (448aas; 12TMSs; (2)6. Probable polysaccharide exporter.
AgnG homologue 2 of Lyngbya sp. PCC8106 (A0YL48)
Putative exopolysaccharide transporter with two subunits, PelFG (PelF has 507 aas and 1 N-terminal TMS, while PelG has 456 aas and 12 TMSs) (Vasseur et al., 2007)
PelFG of Pseudomonas aeruginosa (Q02PM3)
Hypothetical protein (598aas with 12-14TMSs; probably 14 with the central 2 being of low hydrokphobicity) The topologies and sequence similarities of subfamily 8 is like that of subfamily 3.
Hypothetical protein of Trypanosoma brucei (Q383B3)
The progressive ankylosis (ANK) protein (AnkH; SLC62A1) gives rise to craniometaphyseal bone dysplasia in man. This 12 TMS protein was reported to transport pyrophosphate, but a more recent report suggests it transports ATP instead of pyrophosphate (Szeri et al. 2022). It is expressed in the primary ciliary/basal body complex of kidney and bone tissues (Nürnberg et al., 2001; Carr et al. 2009). It is critical for the regulation of pyrophosphate, and gain of function ANK mutations are associated with calcium pyrophosphate deposition disease (Mitton-Fitzgerald et al. 2016).
AnkH of Homo sapiens (Q9HCJ1)
Hypothetical protein, Pcar_0400
Pcar_0400 of Pelobacter carbinolicus (Q3A7I4)