2.A.17 The Proton-dependent Oligopeptide Transporter (POT/PTR) Family

Proteins of the POT family (also called the PTR (peptide transport) family) consist of proteins from animals, plants, yeast, archaea and both Gram-negative and Gram-positive bacteria. Several of these organisms possess multiple POT family paralogues. The proteins are of about 450-600 amino acyl residues in length with the eukaryotic proteins in general being longer than the bacterial proteins. They exhibit 12 putative or established transmembrane α-helical spanners.  The plant homologues have been examined from phylogenetic standpoints (von Wittgenstein et al. 2014). 

Pairs of salt bridge interactions between transmembrane helices work in tandem to orchestrate alternating access transport within the PTR family (Newstead 2014). Key roles for residues conserved between bacterial and eukaryotic homologues suggest a conserved mechanism of peptide recognition and transport that in some cases has been subtly modified in individual species.  PepT1 and PepT2, mammalian members of this family, are responsible for the uptake of many pharmaceutically important drug molecules, including antibiotics and antiviral medications.  Thus, their promiscuity can be used for improving the oral bioavailability of poorly absorbed compounds (Newstead 2014).

While most members of the POT family catalyze peptide transport, one is a nitrate permease and one can transport histidine as well as peptides. A nitrate permease of Arabidopsis, Chl1 (TC #2.A.17.3.1), exhibits dual affinity. When phosphorylated at threonine-101, it exhibits high affinity (50 μM) for nitrate, but when not phosphorylated, it exhibits low affinity (~5 mM) (Liu and Tsay, 2003). Some of the peptide transporters can also transport antibiotics. They function by proton symport, but the substrate:H+ stoichiometry is variable: the high affinity rat PepT2 carrier catalyzes uptake of 2 and 3H+ with neutral and anionic dipeptides, respectively, while the low affinity PepT1 carrier catalyzes uptake of one H+ per neutral peptide. In eukaryotes, some of these transporters may be in organellar membranes such as the lysosomes.

Di- and tripeptide transporters of the POT/PTR/NRT1 family are localized either to the tonoplast (TP) or plasma membrane (PM). A 7 amino acid fragment of the hydrophilic N-terminal region of Arabidopsis PTR2, PTR4 and PTR6 is required for TP localization and sufficient to redirect not only PM-localized PTR1 or PTR5, but also sucrose transporter SUC2 to the tonopolast (Komarova et al., 2012). L(11) and I(12) of PTR2 are essential for TP targeting, while only one acidic amino acid at position 5, 6 or 7 is required, revealing a dileucine (LL or LI) motif with at least one upstream acidic residue. Similar dileucine motifs could be identified in other plant TP transporters. Targeting to the PM required the loop between transmembrane domains 6 and 7 of PTR1 or PTR5. Deletion of either PM or TP targeting signals resulted in retention in internal membranes, indicating that PTR trafficking to these destination membranes requires distinct signals and is in both cases not by default (Komarova et al., 2012).

Both proton and ligand significantly change the conformational free-energy landscape of PepT (Batista et al. 2019). In the absence of ligand and protonation, only transitions involving inner facing (IF) and occluded (OC) states are allowed. After protonation of residue Glu300, the wider free-energy well  indicates a greater conformational variability relative to the apo system, and outward facing (OF) conformations become accessible. For the Glu300 protonated holo-PepT, the presence of a second free-energy minimum suggests that OF conformations are accessible and stable. Thus, the differences in the free-energy profiles suggest that transitions toward outward-facing conformations occur only after protonation, which is likely the first step in the mechanism of peptide transport.

The generalized transport reaction catalyzed by the proteins of the POT family is:

Substrate (out) nH (out) → substrate (in) nH+ (in)

This family belongs to the MFS Superfamily.



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TC#NameOrganismal TypeExample

Di- or tripeptide:H+ symporter of 497 aas and 13 or 14 TMSs. DtpT is specific for di- and tripeptides, with the highest affinities for peptides with at least one hydrophobic residue. The effect of the hydrophobicity, size, or charge of the amino acid was different for the amino- and carboxyl-terminal positions of dipeptides. Free amino acids, omega-amino fatty acidss, and peptides with more than three amino acid residues do not interact with DtpT. For high-affinity interaction, the peptides need to have free amino and carboxyl termini, amino acids in the L configuration, and trans-peptide bonds. Comparison of the specificity of DtpT with those of the eukaryotic homologues PepT(1) and PepT(2) showed that the bacterial transporter is more restrictive in its substrate recognition. (Fang et al. 2000). 


DtpT of Lactococcus lactis (P0C2U2)


The di/tripeptide:H+ symport permease, TppB (DtpA or YdgR) (transports di and tripeptides and peptidomimetics such as aminocephalosporins (Weitz et al., 2007).  The transporter has two alternate conformations, one of which is promoted by inhbitor binding (Bippes et al. 2013).


TppB of E. coli (P77304)

2.A.17.1.3The dipeptide/tripeptide:H+ symport permease, DtpB (YhiP) (transports glycyl-sarcosine (Gly-Sar) with low affinity (6mM) and the toxic dipeptide, alafosfalin (Harder et al., 2008)BacteriaDtpB of E. coli (P36837)

DtpD (YbgH) peptide transporter.  A projection structure at 19 Å resolution and a high resolution x-ray structure are available; Casagrande et al., 2009; Zhao et al. 2014). Glu21 is the only conserved proton-titratable amino acyl residue (among POTs) that is located in the central cavity, and it is critical for in vivo transport (Zhao et al. 2014).


DtpD of E. coli (P75742)


Peptide transporter, YjdL (preference for di-peptides) (Ernst et al., 2009; Gabrielsen et al., 2011; Jensen et al., 2011).  The motif, ExxERFxxYY has been shown to be involved in proton translocation, and the nearby K117 may play a dual role in protonation and substrate binding (Jensen et al. 2014).


YjdL of E. coli (P39276)


POT famiy di- and tri-peptide porter, DtpT. 3-d structures (PDB:24APS; 5MMT: 5D58' 5D59) are available for an inward open conformation. A hinge-like movement in the C-terminal half facilitates opening of an intracellular gate controlling access to a central peptide binding site. Salt bridges may orchestrate alternating access (Solcan et al., 2012; Quistgaard et al. 2017).


Peptide porter, DtpT of Streptococcus thermophilus (Q5M4H8)


Peptide uptake transporter of 496 aas, POT.  The 3-d structure has been determined to 1.9Å resolution leading to a proposed mechanism (Doki et al. 2013).  Glu310 first may bind the carboxyl group of the peptide substrate. Then deprotonation of Glu310 in the inward open state triggers the release of the bound peptide toward the intracellular space, and salt bridge formation between Glu310 and Arg43 induces the transition state to the occluded conformation.


POT of Geobacillus kaustophilus


Proton-coupled oligopeptide uptake transporter of 485 aas and 14 TMSs, DtpT or Pot.  Expression of the encoded gene is upregulated upon infection. Transports di- and tripeptides but can not accumulate peptides with a positively charged residue in the C-terminal position.  An aromatic residue patch in the active site of the transporter may be responsible for it's unusual specificity (Sharma et al. 2016).

DtpT of Neisseria meningitidis


TC#NameOrganismal TypeExample
2.A.17.2.1Peptide:H+ symporter Plants PTR2-A of Arabidopsis thaliana

Peptide:H+ symporter (dipeptides and tripeptides preferred (Cai et al., 2007). Substrate preference is altered by mutations in the fifth TMS of Ptr2p (Hauser et al. 2013).


PTR2 of Saccharomyces cerevisiae


Dipeptide uptake porter, Ptr2.  Transports dipeptides such as Ala-Leu, Ala-Tyr and Tyr-Ala (Belmondo et al. 2014).


Ptr2 of Rhizophagus irregularis (Arbuscular mycorrhizal fungus) (Glomus intraradices)


Di- and tripeptide uptake transporter, Ptr2 of 577 aas and 12 TMSs. The ptr2 gene showed increased expression upon interaction with the plant-pathogenic fungus Botrytis cinerea, suggesting that it is involved in the mycoparasitic process. Its expression was triggered by nitrogen starvation (Vizcaíno et al. 2006).

Ptr2 of Trichoderma harzianum (Hypocrea lixii)


Oligopeptide transporter of 576 aas and 12 TMSs, PTR22. Transports a variety of peptides as well as derivatives of antifungal agents, such as chlorotetaine and lysyl-cholortetaine (Liu et al. 2018).

PTR22 of Candida albicans (Yeast)


TC#NameOrganismal TypeExample

Dual affinity Nitrate/Chlorate symporter, Nrt1.1; CHL1 (Martin et al., 2008).  The low affinity form is a homo-dimer and has Thr101 in the non-phosphorylated form; the high affinty form (0.1 micromolar Km) is a monomer and has Thr101 phosphorylated (Sun and Zheng 2015).


Ntr1.1/CHL1 of Arabidopsis thaliana


solute carrier family 15, member 5.  Function unknown as of 1/17, but probably a di- and tri-peptide uptake porter (Verri et al. 2016). The tissue expression profile has been reported (Sreedharan et al. 2011).



SLC15A5 of Homo sapiens


Solute carrier family 15 member 4 (Peptide transporter 4) (Peptide/histidine transporter 1) (hPHT1) present in immune cells (Verri et al. 2016).


SLC15A4 of Homo sapiens

2.A.17.3.12Putative peptide/nitrate transporter At3g25280PlantsAt3g25280 of Arabidopsis thaliana
2.A.17.3.13Probable peptide transporter At1g52190PlantsAt1g52190 of Arabidopsis thaliana
2.A.17.3.14Nitrate transporter 1.6PlantsNRT1.6 of Arabidopsis thaliana
2.A.17.3.15Nitrate transporter 1.7PlantsNRT1.7 of Arabidopsis thaliana

Nitrate transporter 1.2 (Nitrate transporter NTL1).  Low-affinity proton-dependent nitrate transporter involved in constitutive nitrate uptake but not histidine or dipeptides transport. Involved in (+)-abscisic acid (ABA) transport, but not in gibberellin, indole-3-acetic acid or jasmonic acid import (Kanno et al. 2013).


NRT1.2 of Arabidopsis thaliana


Transporter for glucosinolates (aliphatic but not indole glucosinolates such as 4-methylthiobutyl glucosinolate, major defence compounds, translocated to seeds on maturation) as well as gibberellic acid and jasmonoyl-L-isoleucine, GTR1 or NPF2.10, of 636 aas and 12 TMSs (Nour-Eldin et al. 2012; Ishimaru et al. 2017). Regulated at the transcriptional level, but also postranslationally.  Dimerization of GTR1, possibly induced by dephosphorylation of a Thr residue, regulates its plasma membrane localization, leading to increased transport of glucosinolates and gibberellic acid (Ishimaru et al. 2017). Homologues have been found and characterized in Chinese kale (Jiang et al. 2019).


GTR1 of Arabidopsis thaliana

2.A.17.3.18Nitrate transporter 1.4PlantsNRT1.4 of Arabidopsis thaliana
2.A.17.3.19Nitrate transporter 1.5PlantsNRT1.5 of Arabidopsis thaliana
2.A.17.3.2Histidine or peptide:H+ symporter Plants PTR2-B (NTR1) of Arabidopsis thaliana

High-affinity, proton-dependent glucosinolate-specific transporter-2, GTP2 or NPF2.11. Involved in apoplasmic phloem-loading of glucosinolates and in bidirectional long-distance transport of aliphatic but not indole glucosinolates. May be involved in removal of glucosinolates from the xylem in roots (Nour-Eldin et al. 2012; Andersen et al. 2013).


GTR2 of Arabidopsis thaliana


Low affinity nitrate transporter, Nrt1, of 584 aas and 13 putative TMSs.  Two splice variants, Ntr1.1a and Ntr1.1b, have been identified.  Under low nitrogen condition, Nrt1.1b accumulates more nitrogen in plants and improves rice growth, but Ntr1.1a had no such effect (Fan et al. 2015).

Ntr1 of Oryza sativa (Rice)


Uncharacterized peptide transport protein of 609 aas and 12 TMSs, PTR3-A.


aof Aegilops tauschii (Tausch's goatgrass) (Aegilops squarrosa)

2.A.17.3.3Nitrate (chlorate) or histidine:H+ symporter Plants RCH2 of Brassica napus
2.A.17.3.4Peptide transporter, PTR3-A (induced by histidine, leucine and phenylalanine in cotyledons and lower leaves; involved in stress tolerance in seeds during germination and in defense against virulent bacterial pathogens) (Karim et al., 2007; Karim et al., 2005)PlantsPTR3-A of Arabidopsis thaliana (Q9FNL7)
2.A.17.3.5The nitrate excretion transporter1, NaxT1 (in the plasma membranes of plant cells)PlantsNaxT1 of Arabidopsis thaliana (Q9M1E2)
2.A.17.3.6Chloroplast nitrite uptake system, Nitr1-L (Sugiura et al., 2007)PlantsNitr1-L of Arabidopsis thaliana (Q9SX20)

The root dipeptide/tripeptide transporter, PTRI (Komarova et al., 2008). Transport is electrogenic and dependent on protons. Leak currents are inhibited by Phe-Ala when this peptide binds at the active site with high affinity (Hammes et al., 2010).


PTR1 of Arabidopsis thaliana (Q9M390)


The germinating pollen dipeptide/tripeptide transporter, PTR5 (Komarova et al., 2008). Transport is electrogenic and dependent on protons. Leak currents are inhibited by Phe-Ala when this peptide binds at the active site with high affinity (Hammes et al., 2010).


PTR5 of Arabidopsis thaliana (Q0WR84)


solute carrier family 15, member 3, di- and tri-peptide uptake transporter in immune cells (Verri et al. 2016).


SLC15A3 of Homo sapiens


TC#NameOrganismal TypeExample

Peptide:H+ symporter (transports cationic, neutral and anionic dipeptides including glycylsarcosine (gly-sar) (Søndergaard et al., 2008) as well as anserine (β-alanyl-1-N-methyl-L-histidine) and carnosine (β-alanyl-L-histidine) (Geissler et al., 2010); also transports β-lactam antibiotics, the antitumor agent, bestatin, and various protease inhibitors). It is competitively inhibited by L-4,4'-biphenylalanyl-L-proline (Bip-Pro) with ~10-20µM affinity. Inhibitors/substrates include cefadroxil, Ala-4-nitroanilide and δ-aminolevulinic acid (Knutter et al., 2007). The intracellular loop linking transmembrane domains 6 and 7 of the human dipeptide transporter hPEPT1 includes two amphipathic alpha-helices, with net positive and negative charges which interact and influence conformational changes of hPEPT1 during and after glycylsarcosine transport (Xu et al., 2010).  The rabbit orthologue provides the main pathway for dietary nitrogen uptake. Five tyrosyl residues are important for function and/or substrate binding (Pieri et al. 2009).  Human PepT1 is modified by N-glycosylation, and all six asparagine residues in the large extracellular loop between transmembrane domains 9 and 10 are subject to N-glycosylation (Chan et al. 2016).


PepT1 of Rattus norvegicus

2.A.17.4.10Peptide transporter 3 (Oligopeptide transporter 3)WormPept-3 of Caenorhabditis elegans

Peptide transporter, Pep1, also called CptB, Opt-2 and Pep-2.  It is of 835 aas and 11 TMSs.  It transports di-, tri- and tetra-peptides including phenylalanylmethionylarginylphenylalaninamide (FMRFamide) and N-acetylaspartylglutamate, both neuropeptides found throughout the animal kingdom. In contrast to CptA (TC# 2.A.17.4.3), CptB has low-affinity for its substrates (Fei et al. 1998).

CptB of Caenorhabditis elegans

2.A.17.4.2Oligopeptide transporter 1 Animals Oligopeptide transporter of Drosophila melanogaster

High affinity oligopeptide transporter, CPTA. It transports di-, tri- and tetra peptides with low specificity. Neuropeptides (FMRF-amide and N-acetyl-Asp-Glu) are also transported (Fei et al. 1998).


CPTA of Caenorhabditis elegans


The renal brush-border electrogenic, proton-coupled, broad specificity, high affinity, peptide transporter, PepT2 (Rubio-Aliaga et al., 2000). It is competitively inhibited by L-4,4'-Biphenylalanyl-L-Proline (Bip-Pro) with ~10-20µM affinity. Inhibitor/substrates includes cefadroxil, Ala-4-nitroanilide and delta-aminolevulinic acid (Knutter et al., 2007).  It transports the fluorescent tracer-dipeptide beta-Ala-Lys-Nepsilon-7-amino-4-methyl-coumarin-3-acetic acid (Ala-Lys-AMCA). Whole-mount preparations from mouse, rat, and guinea pig stomach and small and large intestine were incubated with Ala-Lys-AMCA in the presence or absence of the uptake-inhibitors L-histidine, D-phenylalanyl-L-alanine (D-Phe-Ala), glycyl-L-sarcosine (Gly-Sar), glycyl-L-glutamine (Gly-Gln), benzylpenicillin, and cefadroxil. Fluorescence microscopy revealed that Ala-Lys-AMCA specifically accumulated in both ganglionic layers of the enteric nervous system (ENS) in all regions and species studied (Rühl et al. 2005). This could be inhibited by Gly-Sar, D-Phe-Ala, Gly-Gln, and cefadroxil, but not by free histidine and benzylpenicillin, indicating uptake via PEPT2. Accordingly, dipeptide uptake was completely abolished in PEPT2-deficient mice.


PepT2 of Mus musculus (Q9ES07)

2.A.17.4.5The high affinity, low capacity, peptide transporter, PepT2 (SLC15A2) [affinity for glycyl-L-glutamine=18μM] (Romano et al., 2006)AnimalsPepT2 of Danio rerio (NP_0010349)

Oligopeptide transporter, PepT1 (Slc15A1b) (Bucking and Schulte, 2012) (expressed in freshwater acclimated fish)


PepT1b of Fundulus heteroclitus (H2DJV9)


Di-/Tri-peptide porter. 3-d structure (PDB: 2XUT) known revealing a probable alternating access mechanism of transport (Newstead et al., 2011).  A second structure shows the protein in an inward open conformation with the peptidommetic, alafosfalin, bound (Guettou et al. 2013). Appears to take up glutathione (Deutschbauer et al. 2011).


Di-/Tri-peptide permease of Shewanella oneidensis (Q8EKT7)


Solute carrier family 15 member 2 (Kidney H+:peptide cotransporter) (Oligopeptide transporter, kidney isoform) (Peptide transporter 2, PEPT2) (Verri et al. 2016). Transports opioid peptides (Ganapathy and Miyauchi 2005).


SLC15A2 of Homo sapiens


Solute carrier family 15 member 1 (Intestinal H+:peptide cotransporter) (Oligopeptide transporter, small intestine isoform) (Peptide transporter 1, PepT1).  Takes up oligopeptides of 2 to 4 amino acids with a preference for dipeptides, a major route for the absorption of protein digestion end-products. PepT1 is modified by N-glycosylation, and all six asparagine residues in the large extracellular loop between TMSs 9 and 10 are subject to N-glycosylation.  This allows proper association with the plasma membrane and/or stabilization (Chan et al. 2016). Transports opioid peptides (Ganapathy and Miyauchi 2005), can serve as a druh importer and plays a role in inflammatory bowel diseases (Viennois et al. 2018).


PepT1 of Homo sapiens