| Literature DB >> 30194725 |
Maria Martinez Molledo1, Esben M Quistgaard1,2, Christian Löw1,2.
Abstract
Proton-dependent oligopeptide transporters (POTs) are important for the uptake of di-/tripeptides in many organisms and for drug transport in humans. The binding mode of dipeptides has been well described. However, it is still debated how tripeptides are recognized. Here, we show that tripeptides of the sequence Phe-Ala-Xxx bind with similar affinities as dipeptides to the POT transporter from Streptococcus thermophilus (PepTS t ). We furthermore determined a 2.3-Å structure of PepTS t in complex with Phe-Ala-Gln. The phenylalanine and alanine residues of the peptide adopt the same positions as previously observed for the Phe-Ala dipeptide, while the glutamine side chain extends into a hitherto uncharacterized pocket. This pocket is adaptable in size and can likely accommodate a wide variety of peptide side chains.Entities:
Keywords: POTs; major facilitator superfamily (MFS); membrane protein crystallography; peptide binding; peptide transporters
Mesh:
Substances:
Year: 2018 PMID: 30194725 PMCID: PMC6221056 DOI: 10.1002/1873-3468.13246
Source DB: PubMed Journal: FEBS Lett ISSN: 0014-5793 Impact factor: 4.124
Crystallographic data processing and refinement statistics for PepTSt in complex with Phe‐Ala‐Xxx tripeptides. Numbers in parentheses refer to the highest resolution shell
| PepTSt[Phe‐Ala‐Gln] | PepTSt[Phe‐Ala‐Ala] | PepTSt[Phe‐Ala‐Thr] | |
|---|---|---|---|
| Data collection | |||
| Beamline |
PETRA III |
PETRA III |
PETRA III |
| Wavelength (Å) | 0.9143 | 0.9762 | 0.9762 |
| Space group | C2221 | C2221 | C2221 |
| Cell dimensions | |||
|
| 101.55, 108.22, 111.61 | 102.27, 108.99, 112.39 | 101.02, 108.05, 110.50 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Resolution (Å) | 48.69–2.26 (2.34–2.26) | 49.03–2.00 (2.07–2.00) | 48.53–2.10 (2.18–2.10) |
|
| 0.083 (0.811) | 0.073 (0.786) | 0.096 (1.708) |
|
| 19.44 (3.19) | 16.32 (2.23) | 12.29 (1.03) |
| CC1/2 | 0.999 (0.871) | 0.999 (0.776) | 1 (0.468) |
| Completeness (%) | 99.73 (99.79) | 99.74 (99.83) | 99.59 (98.49) |
| Total no. reflections | 299 776 (29 604) | 294 024 (29 583) | 241 819 (23 429) |
| Multiplicity | 10.3 (10.4) | 6.9 (7.0) | 6.9 (6.8) |
| Wilson | 40.59 | 34.54 | 46.82 |
| Refinement | |||
|
| 0.193/0.219 | 0.189/0.215 | 0.208/0.237 |
| No. atoms | |||
| Protein | 3529 | 3636 | 3527 |
| Bound tripeptide | 26 | 22 | 24 |
| HEPES/PEG/ions | 41 | 39 | 36 |
| Lipids | 308 | 264 | 264 |
| Water | 101 | 171 | 85 |
|
| |||
| Protein | 48.66 | 38.81 | 58.30 |
| Bound tripeptide | 51.94 | 49.07 | 84.81 |
| HEPES/PEG/ions | 96.49 | 79.05 | 95.88 |
| Lipids | 82.60 | 65.52 | 82.72 |
| Water | 53.04 | 46.08 | 56.94 |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.004 | 0.003 | 0.008 |
| Angles (°) | 0.75 | 0.62 | 0.82 |
| Ramachandran | |||
| Favored (%) | 98.89 | 98.92 | 98.66 |
| Outliers (%) | 0.00 | 0.00 | 0.00 |
| Clash score | 5.22 | 2.45 | 5.30 |
| PDB accession | 6GHJ | – | – |
Figure 1Binding of Phe‐Ala‐Xxx tripeptides as measured by nanoDSF and MST. (A) Thermostability data for PepT t measured by nanoDSF. Each Phe‐Ala‐Xxx tripeptide was measured at four different concentrations: 0.625, 1.25, 2.5, and 5 mm, as indicated on the x‐axis. Results for control samples, which did not contain any tripeptide, are shown as red bars (Ctrl is without DMSO, and Ctrl* is with 5% DMSO). For these samples, the transition midpoint (Tm) is further indicated by red dashed lines. Results for the tripeptides are shown as differently colored bars: Phe‐Ala‐Ala is light green, Phe‐Ala‐Leu is purple, Phe‐Ala‐Gln is light blue, Phe‐Ala‐Thr is orange, Phe‐Ala‐Asp is blue, and Phe‐Ala‐Phe is dark blue. Note that Phe‐Ala‐Phe should be compared to Ctrl* rather than Ctrl, since it was solubilized in DMSO. The average Tm value for each condition was calculated from three independent measurements. The error bars correspond to the standard deviation from these independent measurements. (B) MST binding curve for Phe‐Ala‐Ala. Error bars represent the standard deviation of two independent measurements. The estimated dissociation constant (K D) is indicated. (C) MST binding curve for Phe‐Ala‐Leu (shown as for panel B). (D) MST binding curve for Phe‐Ala‐Gln (shown as for panel B). (E) MST binding curve for Phe‐Ala‐Asp. Here, the binding was too weak to allow a K D value to be determined.
Figure 2Electron density maps for the bound Phe‐Ala‐Xxx tripeptides. (A) PepT t in complex with Phe‐Ala‐Ala (PepT t[Phe‐Ala‐Ala]). The peptide is shown with the 1‐σ 2Fo‐Fc simulated annealing composite omit map. (B) PepT t[Phe‐Ala‐Ala] with the 3‐σ Fo‐Fc map generated with the peptide omitted. (C) PepT t[Phe‐Ala‐Thr] with the 1‐σ 2Fo‐Fc simulated annealing composite omit map. (D) PepT t[Phe‐Ala‐Thr] with the 3‐σ Fo‐Fc peptide omit map. (E) PepT t[Phe‐Ala‐Gln] with the 1‐σ 2Fo‐Fc simulated annealing composite omit map. (F) PepT t[Phe‐Ala‐Gln] with the 3‐σ Fo‐Fc peptide omit map.
Figure 3Structural basis for binding of Phe‐Ala‐Gln to PepT t. (A) Peptide backbone configurations of bound Phe‐Ala‐Gln and Ala‐Leu. PepT t[Phe‐Ala‐Gln] is light green and PepT t[Ala‐Leu] is violet. The side chains of selected binding site residues and the backbones of the peptides are shown in sticks and labeled. Distances between the N terminus (nitrogen atom) and C terminus (carboxylate carbon atom) of each peptide are indicated. (B) Interactions with the peptide backbone and termini in PepT t[Phe‐Ala‐Gln]. Labels followed by an asterisk refer to residues in the peptide. (C) Interactions with the peptide glutamine side chain in PepT t[Phe‐Ala‐Gln]. (D) PepT t[Phe‐Ala‐Gln] in surface representation. The arrow indicates the accessibility to the binding cavity from the cytoplasmic side of the membrane (the protein is in the inward open conformation). (E) Binding pockets in PepT t. The protein is shown in a semitransparent surface representation, but with the residues forming the pockets also shown as sticks. Pocket 1 (P1) is colored purple, pocket 2 (P2) is salmon, pocket 3 (P3) is dark cyan, and Tyr‐68, which is part of both P2 and P3, is orange. The Phe‐Ala‐Gln peptide is shown as gray sticks. (F) LigPlot+ diagram for the binding of Phe‐Ala‐Gln to PepT t. The pockets are indicated by different background colors (using the same color scheme as in panel E). Hydrogen bonds and ionic interactions are indicated by green dashes, and the residues involved are labeled in green. Residues forming hydrophobic contacts to the peptide are labeled in black.