CoChat
Sign Up
Cited by 29Drug Transport and Resistance MechanismsProtein Structure and DynamicsAmino Acid Enzymes and Metabolism

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Extracellular domain of PepT1 interacts with TM1 to facilitate substrate transport

Open access
Shen, Jiemin, Hu, Miaohui, Fan, Xiao, Ren, Zhenning, Portioli, Corinne, Yan, Xiuwen, Rong, Mingqiang, Zhou, Ming·2022·Structure
DOI 10.1016/j.str.2022.04.011PMC PMC10404463

Published version of a preprint

Open this paper in CoChat — free account

Abstract

Mammalian peptide transporters, PepT1 and PepT2, mediate uptake of small peptides and are essential for their absorption. PepT also mediates absorption of many drugs and prodrugs to enhance their bioavailability. PepT has twelve transmembrane (TM) helices that fold into an N-terminal domain (NTD, TM1-6) and a C-terminal domain (CTD, TM7-12) and has a large extracellular domain (ECD) between TM9-10. It is well recognized that peptide transport requires movements of the NTD and CTD, but the role of the ECD in PepT1 remains unclear. Here we report the structure of horse PepT1 encircled in lipid nanodiscs and captured in the inward-open apo conformation. The structure shows that the ECD bridges the NTD and CTD by interacting with TM1. Deletion of ECD or mutations to the ECD-TM1 interface impairs the transport activity. These results demonstrate an important role of ECD in PepT1 and enhance our understanding of the transport mechanism in PepT1.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.str.2022.04.011

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 47

  1. Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. Section D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925 · DOI · Paper page
  2. Asarnow, 2020, UCSF pyem v0. 5., Zenodo (2019).
  3. Autzen, 2018, Structure of the human TRPM4 ion channel in a lipid nanodisc, Science, 359, 228, 10.1126/science.aar4510 · DOI
  4. Barad, 2015, EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy, Nat. Methods, 12, 943, 10.1038/nmeth.3541 · DOI · Paper page
  5. Beale, 2015, Crystal structures of the extracellular domain from PepT1 and PepT2 provide novel insights into mammalian peptide transport, Structure, 23, 1889, 10.1016/j.str.2015.07.016 · DOI
  6. Boggavarapu, 2015, Role of electrostatic interactions for ligand recognition and specificity of peptide transporters, BMC Biol., 13, 58, 10.1186/s12915-015-0167-8 · DOI
  7. Chen, 1999, Stoichiometry and kinetics of the high-affinity H+-coupled peptide transporter PepT2, J. Biol. Chem., 274, 2773, 10.1074/jbc.274.5.2773 · DOI
  8. Daniel, 2004, The proton oligopeptide cotransporter family SLC15 in physiology and pharmacology, Pflugers Arch., 447, 610, 10.1007/s00424-003-1101-4 · DOI
  9. Doki, 2013, Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT, Proc. Natl. Acad. Sci. U S A., 110, 11343, 10.1073/pnas.1301079110 · DOI
  10. Drew, 2021, Structures and general transport mechanisms by the major facilitator superfamily (MFS), Chem. Rev., 121, 5289, 10.1021/acs.chemrev.0c00983 · DOI
  11. Emsley, 2010, Features and development of coot, Acta Crystallogr. Section D Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493 · DOI · Paper page
  12. Guettou, 2014, Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2, Nat. Struct. Mol. Biol., 21, 728, 10.1038/nsmb.2860 · DOI
  13. Guettou, 2013, Structural insights into substrate recognition in proton-dependent oligopeptide transporters, EMBO Rep., 14, 804, 10.1038/embor.2013.107 · DOI
  14. Kamal, 2009, Influence of genetic knockout of Pept2 on the in vivo disposition of endogenous and exogenous carnosine in wild-type and Pept2 null mice, Am. J. Physiol. Regul. Integr. Comp. Physiol., 296, R986, 10.1152/ajpregu.90744.2008 · DOI
  15. Killer, 2021, Structural snapshots of human PepT1 and PepT2 reveal mechanistic insights into substrate and drug transport across epithelial membranes, Sci. Adv., 7, eabk3259, 10.1126/sciadv.abk3259 · DOI · Paper page
  16. Kimanius, 2016, Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2, Elife, 5, e18722, 10.7554/eLife.18722 · DOI
  17. Lyons, 2014, Structural basis for polyspecificity in the POT family of proton-coupled oligopeptide transporters, EMBO Rep., 15, 886, 10.15252/embr.201338403 · DOI
  18. Martens, 2016, Lipids modulate the conformational dynamics of a secondary multidrug transporter, Nat. Struct. Mol. Biol., 23, 744, 10.1038/nsmb.3262 · DOI
  19. Martinez Molledo, 2018, Multispecific substrate recognition in a proton-dependent oligopeptide transporter, Structure, 26, 467, 10.1016/j.str.2018.01.005 · DOI
  20. Martinez Molledo, 2018, Tripeptide binding in a proton-dependent oligopeptide transporter, FEBS Lett., 592, 3239, 10.1002/1873-3468.13246 · DOI
  21. Mastronarde, 2005, Automated electron microscope tomography using robust prediction of specimen movements, J. Struct. Biol., 152, 36, 10.1016/j.jsb.2005.07.007 · DOI
  22. Matthews, 1983, Intestinal absorption of peptides, Biochem. Soc. Trans., 11, 808, 10.1042/bst0110808 · DOI
  23. Minhas, 2019, Structural basis for prodrug recognition by the SLC15 family of proton-coupled peptide transporters, Proc. Natl. Acad. Sci. U S A., 116, 804, 10.1073/pnas.1813715116 · DOI
  24. Newstead, 2017, Recent advances in understanding proton coupled peptide transport via the POT family, Curr. Opin. Struct. Biol., 45, 17, 10.1016/j.sbi.2016.10.018 · DOI
  25. Newstead, 2011, Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2, EMBO J., 30, 417, 10.1038/emboj.2010.309 · DOI
  26. Pan, 2020, Structural basis of ion transport and inhibition in ferroportin, Nat. Commun., 11, 5686, 10.1038/s41467-020-19458-6 · DOI · Paper page
  27. Parker, 2021, Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals, Sci. Adv., 7, eabh3355, 10.1126/sciadv.abh3355 · DOI
  28. Parker, 2017, Proton movement and coupling in the POT family of peptide transporters, Proc. Natl. Acad. Sci. U S A., 114, 13182, 10.1073/pnas.1710727114 · DOI
  29. Pettersen, 2004, UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 · DOI
  30. Pettersen, 2021, UCSF ChimeraX: structure visualization for researchers, educators, and developers, Protein Sci., 30, 70, 10.1002/pro.3943 · DOI
  31. Punjani, 2017, cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination, Nat. Methods, 14, 290, 10.1038/nmeth.4169 · DOI · Paper page
  32. Punjani, 2020, Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction, Nat. Methods, 17, 1214, 10.1038/s41592-020-00990-8 · DOI
  33. Qandeel, 2009, Diurnal expression and function of peptide transporter 1 (PEPT1), J. Surg. Res., 156, 123, 10.1016/j.jss.2009.03.052 · DOI
  34. Quistgaard, 2017, Structure determination of a major facilitator peptide transporter: inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121, PLoS One, 12, e0173126, 10.1371/journal.pone.0173126 · DOI
  35. Ramamoorthy, 1995, Proton/peptide cotransporter (PEPT 2) from human kidney: functional characterization and chromosomal localization, Biochim. Biophys. Acta, 1240, 1, 10.1016/0005-2736(95)00178-7 · DOI
  36. Rosenthal, 2003, Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy, J. Mol. Biol., 333, 721, 10.1016/j.jmb.2003.07.013 · DOI · Paper page
  37. Sanchez-Garcia, 2021, DeepEMhancer: a deep learning solution for cryo-EM volume post-processing, Commun. Biol., 4, 874, 10.1038/s42003-021-02399-1 · DOI
  38. Scheres, 2012, RELION: implementation of a Bayesian approach to cryo-EM structure determination, J. Struct. Biol., 180, 519, 10.1016/j.jsb.2012.09.006 · DOI · Paper page
  39. Scheres, 2015, Semi-automated selection of cryo-EM particles in RELION-1.3, J. Struct. Biol., 189, 114, 10.1016/j.jsb.2014.11.010 · DOI
  40. Shen, 1999, Localization of PEPT1 and PEPT2 proton-coupled oligopeptide transporter mRNA and protein in rat kidney, Am. J. Physiol., 276, F658
  41. Steel, 1997, Stoichiometry and pH dependence of the rabbit proton-dependent oligopeptide transporter PepT1, J. Physiol., 498, 563, 10.1113/jphysiol.1997.sp021883 · DOI
  42. Terada, 2004, Genetic variant Arg57His in human H+/peptide cotransporter 2 causes a complete loss of transport function, Biochem. Biophys. Res. Commun., 316, 416, 10.1016/j.bbrc.2004.02.063 · DOI
  43. Ural-Blimke, 2019, Structure of prototypic peptide transporter DtpA from E. coli in Complex with Valganciclovir provides insights into drug binding of human PepT1, J. Am. Chem. Soc., 141, 2404, 10.1021/jacs.8b11343 · DOI
  44. Xu, 2009, Mutagenesis and cysteine scanning of transmembrane domain 10 of the human dipeptide transporter, Pharm. Res., 26, 2358, 10.1007/s11095-009-9952-9 · DOI
  45. Zhang, 2016, Gctf: real-time CTF determination and correction, J. Struct. Biol., 193, 1, 10.1016/j.jsb.2015.11.003 · DOI
  46. Zhang, 2013, Prodrug design targeting intestinal PepT1 for improved oral absorption: design and performance, Curr. Drug Metab., 14, 675, 10.2174/1389200211314060004 · DOI
  47. Zheng, 2017, MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy, Nat. Methods, 14, 331, 10.1038/nmeth.4193 · DOI

Metadata

Authors
Shen, J., Hu, M., Fan, X., Ren, Z., Portioli, C., Yan, X., Rong, M., & Zhou, M.
Affiliations
  • Baylor College of Medicine (US)
  • Princeton University (US)
Corresponding author
  • Fan, Xiao
  • Zhou, Ming
ORCID
Venue
Structure
Publisher
Elsevier BV
Published
2022-07
Volume
30
Issue
7
Pages
1035-1041.e3
ISSN
0969-2126 (ISSN-L)
DOI
10.1016/j.str.2022.04.011
PMC
PMC10404463
OpenAlex
W4280558405
Cited by
29
References
1
Citations by year
2026: 6 · 2025: 3 · 2024: 14 · 2023: 4 · 2022: 2
FWCI
2.41
Type
journal article
Language
en
Open access
Licence
Locations
  • Structure (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Digital Commons-TMC (Texas Medical Center) (submittedVersion)
Funders
  • National Institutes of Health (DK122784, GM145416, HL086392, GM098878)
  • Cancer Prevention and Research Institute of Texas (R1223)
  • National Science Foundation
  • Princeton Center for Complex Materials
  • Materials Research Science and Engineering Center, Harvard University (DMR-1420541)
Topics
  • Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Amino Acid Enzymes and Metabolism
Keywords
PepT1, peptide transporters, extracellular domain, transmembrane helices, peptide absorption, drug absorption, apo conformation, lipid nanodiscs, transporter structure, transport mechanisms, horses
MeSH terms
Peptide Transporter 1, Animals, Biological Transport, Horses, Mammals, Molecular Conformation, Peptides, Symporters

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review