Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters

Thijs W. Ettema; Satomi Inaba-Inoue; Chancievan Thangaratnarajah; Leticia Alves da Silva; Nikas Senning; Amy Clarke; Piotr Stepien; Anokhi Shah; Yue Ma; Katie Hardman; Sophia David; Hassane El Mkami; Jonathan G. Heddle; Norimichi Nomura; Satoshi Ogasawara; So Iwata; Dmitry Ghilarov; Christos Pliotas; Thomas Stockner; Dirk J. Slotboom; Konstantinos Beis

doi:10.1038/s41467-026-71633-3

Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters

Thijs W. Ettema
, Satomi Inaba-Inoue
, Chancievan Thangaratnarajah
, Leticia Alves da Silva
, Nikas Senning
, Amy Clarke
, Piotr Stepien
, Anokhi Shah
, Yue Ma
, Katie Hardman
, Sophia David
, Hassane El Mkami
, Jonathan G. Heddle
, Norimichi Nomura
, Satoshi Ogasawara
, So Iwata
, Dmitry Ghilarov^*
, Christos Pliotas^*
, Thomas Stockner^*
, Dirk J. Slotboom^*

Konstantinos Beis^*

^*Corresponding author for this work

School of Physics and Astronomy

Research output: Contribution to journal › Article › peer-review

Abstract

SbmA is a membrane transporter from Escherichia coli that imports antimicrobial peptides. SbmA belongs to the SbmA-like peptide transporter (SLiPT) family. Although the protein is a secondary active transporter that is energized by the proton gradient, it is structurally related to the transmembrane domain (TMD) of ATP-binding cassette (ABC) transporters. SbmA therefore bridges the structural divide between primary and secondary transporters. However, it remains unclear, if SbmA also shares the mechanism of alternating access with ABC transporters, because only a single (outward-open) state is resolved. Here, we show by sequence analysis that SbmA is likely evolved from the TMD of an early ancestor of the ABC transporter YddA. We determine the cryogenic electron microscopy structures of SbmA in occluded and inward-facing states. These conformations closely resemble equivalent states found in ABC transporters, indicating a shared structural mechanism of transport. In contrast to ABC transporters, where nucleotide binding, hydrolysis and release steer conformational changes necessary for substrate translocation, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations reveal how pH changes induce conformational transitions in SbmA, consistent with a mechanism of substrate internalization that utilizes the transmembrane proton gradient.

Original language	English
Article number	5619
Number of pages	14
Journal	Nature Communications
Volume	17
DOIs	https://doi.org/10.1038/s41467-026-71633-3
Publication status	Published - 29 Jun 2026

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Enabling Shaped Pulse Capability: Enabling Shaped Pulse Capability for Superior Biological Structural Determination Using EPR Spectroscopy.
Lovett, J. (PI), Bode, B. (CoI), Penedo, C. (CoI), Pitt, S. J. (CoI), Schwarz-Linek, U. (CoI), Smith, G. (CoI), Watson, A. (CoI) & White, M. (CoI)
Biotechnology and Biological Sciences Research Council
1/10/20 → 30/09/21
Project: Standard
Cryogen-free arbitrary waveform EPR: Cryogen-free arbitrary waveform EPR for structural Biology and Biophysics
Bode, B. (PI), Lovett, J. (CoI), Pliotas, C. (CoI), Schwarz-Linek, U. (CoI), Smith, G. (CoI), Stewart, A. J. (CoI) & White, M. (CoI)
1/05/18 → 30/04/19
Project: Standard
State of the art pulse EPR instrumentati: State of the art pulse EPR instrumentation for long range distance measurements in biomacromolecules
Smith, G. (PI), Bode, B. (CoI), Naismith, J. (CoI), Schiemann, O. (CoI) & White, M. (CoI)
The Wellcome Trust
1/09/12 → 31/08/17
Project: Standard

Simulation data related to the shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters
Alves da Silva, L. (Creator), Clarke, A. (Creator), Senning, N. (Creator), Stockner, T. (Creator), Konstantinos, B. (Creator) & Slotboom, D. (Creator), Zenodo, Dec 2025
DOI: 10.5281/zenodo.17544057
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Ettema, T. W., Inaba-Inoue, S., Thangaratnarajah, C., Alves da Silva, L., Senning, N., Clarke, A., Stepien, P., Shah, A., Ma, Y., Hardman, K., David, S., El Mkami, H., Heddle, J. G., Nomura, N., Ogasawara, S., Iwata, S., Ghilarov, D., Pliotas, C., Stockner, T., ... Beis, K. (2026). Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters. Nature Communications, 17, Article 5619. https://doi.org/10.1038/s41467-026-71633-3

@article{0612f108f87c46e789aa70b445008e99,

title = "Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters",

abstract = "SbmA is a membrane transporter from Escherichia coli that imports antimicrobial peptides. SbmA belongs to the SbmA-like peptide transporter (SLiPT) family. Although the protein is a secondary active transporter that is energized by the proton gradient, it is structurally related to the transmembrane domain (TMD) of ATP-binding cassette (ABC) transporters. SbmA therefore bridges the structural divide between primary and secondary transporters. However, it remains unclear, if SbmA also shares the mechanism of alternating access with ABC transporters, because only a single (outward-open) state is resolved. Here, we show by sequence analysis that SbmA is likely evolved from the TMD of an early ancestor of the ABC transporter YddA. We determine the cryogenic electron microscopy structures of SbmA in occluded and inward-facing states. These conformations closely resemble equivalent states found in ABC transporters, indicating a shared structural mechanism of transport. In contrast to ABC transporters, where nucleotide binding, hydrolysis and release steer conformational changes necessary for substrate translocation, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations reveal how pH changes induce conformational transitions in SbmA, consistent with a mechanism of substrate internalization that utilizes the transmembrane proton gradient.",

author = "Ettema, \{Thijs W.\} and Satomi Inaba-Inoue and Chancievan Thangaratnarajah and \{Alves da Silva\}, Leticia and Nikas Senning and Amy Clarke and Piotr Stepien and Anokhi Shah and Yue Ma and Katie Hardman and Sophia David and \{El Mkami\}, Hassane and Heddle, \{Jonathan G.\} and Norimichi Nomura and Satoshi Ogasawara and So Iwata and Dmitry Ghilarov and Christos Pliotas and Thomas Stockner and Slotboom, \{Dirk J.\} and Konstantinos Beis",

note = "Funding: Funding for this work was provided by: Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/H01778X/1 (K.B.), Japan Society for the Promotion of Science Overseas Fellowship and Grants-in-Aid for Scientific Research KAKENHI grants 24K08708 (S.I.-I.), the Bill \& Melinda Gates Foundation (investment number INV-025280) (S.D.), Joint Usage/Research Center Program of the Institute for Life and Medical Sciences at Kyoto University (N.N.), AMED Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS, JP24ama121007) (N.N. and S.I.), Team program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund TEAM/2016-3/23 (J.G.H. and P.S.). As part of the COFUND project oLife, C.T. acknowledges funding from the European Union{\textquoteright}s Horizon 2020 research and innovation program under the Grant Agreement 847675. D.J.S. acknowledges funding from the Dutch Research Council: NWO TOP grant 714.018.003. EPR spectroscopy sample preparation and measurements were supported by BBSRC (BB/T006048/1, BB/S018069/1) awarded to C.P. and BB/W019795/1 awarded to C.P. and K.B. HEM thanks the Wellcome Trust for multi-user equipment grant (099149/Z/12/Z), and the equipment funding by BBSRC (BB/T017740/1) and BB/R013780/1). D.G. is a recipient of the Sir Henry Dale fellowship (221868/Z/20/Z) jointly funded by the Wellcome Trust and the Royal Society; work in his lab is also supported by the BBSRC-funded Institute Strategic Programme {\textquotedblleft}Harnessing Biosynthesis for Sustainable Food and Health{\textquotedblright} (HBio) (grant number BB/X01097X/1). T.S. has received funding from the Austrian Science Fund (FWF) stand-alone grants P32017 and P34670 and from the European Union{\textquoteright}s Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie grant agreement no: 860954.",

year = "2026",

month = jun,

day = "29",

doi = "10.1038/s41467-026-71633-3",

language = "English",

volume = "17",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

}

Ettema, TW, Inaba-Inoue, S, Thangaratnarajah, C, Alves da Silva, L, Senning, N, Clarke, A, Stepien, P, Shah, A, Ma, Y, Hardman, K, David, S, El Mkami, H, Heddle, JG, Nomura, N, Ogasawara, S, Iwata, S, Ghilarov, D, Pliotas, C, Stockner, T, Slotboom, DJ & Beis, K 2026, 'Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters', Nature Communications, vol. 17, 5619. https://doi.org/10.1038/s41467-026-71633-3

TY - JOUR

T1 - Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters

AU - Ettema, Thijs W.

AU - Inaba-Inoue, Satomi

AU - Thangaratnarajah, Chancievan

AU - Alves da Silva, Leticia

AU - Senning, Nikas

AU - Clarke, Amy

AU - Stepien, Piotr

AU - Shah, Anokhi

AU - Ma, Yue

AU - Hardman, Katie

AU - David, Sophia

AU - El Mkami, Hassane

AU - Heddle, Jonathan G.

AU - Nomura, Norimichi

AU - Ogasawara, Satoshi

AU - Iwata, So

AU - Ghilarov, Dmitry

AU - Pliotas, Christos

AU - Stockner, Thomas

AU - Slotboom, Dirk J.

AU - Beis, Konstantinos

N1 - Funding: Funding for this work was provided by: Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/H01778X/1 (K.B.), Japan Society for the Promotion of Science Overseas Fellowship and Grants-in-Aid for Scientific Research KAKENHI grants 24K08708 (S.I.-I.), the Bill & Melinda Gates Foundation (investment number INV-025280) (S.D.), Joint Usage/Research Center Program of the Institute for Life and Medical Sciences at Kyoto University (N.N.), AMED Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS, JP24ama121007) (N.N. and S.I.), Team program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund TEAM/2016-3/23 (J.G.H. and P.S.). As part of the COFUND project oLife, C.T. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Grant Agreement 847675. D.J.S. acknowledges funding from the Dutch Research Council: NWO TOP grant 714.018.003. EPR spectroscopy sample preparation and measurements were supported by BBSRC (BB/T006048/1, BB/S018069/1) awarded to C.P. and BB/W019795/1 awarded to C.P. and K.B. HEM thanks the Wellcome Trust for multi-user equipment grant (099149/Z/12/Z), and the equipment funding by BBSRC (BB/T017740/1) and BB/R013780/1). D.G. is a recipient of the Sir Henry Dale fellowship (221868/Z/20/Z) jointly funded by the Wellcome Trust and the Royal Society; work in his lab is also supported by the BBSRC-funded Institute Strategic Programme “Harnessing Biosynthesis for Sustainable Food and Health” (HBio) (grant number BB/X01097X/1). T.S. has received funding from the Austrian Science Fund (FWF) stand-alone grants P32017 and P34670 and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no: 860954.

PY - 2026/6/29

Y1 - 2026/6/29

N2 - SbmA is a membrane transporter from Escherichia coli that imports antimicrobial peptides. SbmA belongs to the SbmA-like peptide transporter (SLiPT) family. Although the protein is a secondary active transporter that is energized by the proton gradient, it is structurally related to the transmembrane domain (TMD) of ATP-binding cassette (ABC) transporters. SbmA therefore bridges the structural divide between primary and secondary transporters. However, it remains unclear, if SbmA also shares the mechanism of alternating access with ABC transporters, because only a single (outward-open) state is resolved. Here, we show by sequence analysis that SbmA is likely evolved from the TMD of an early ancestor of the ABC transporter YddA. We determine the cryogenic electron microscopy structures of SbmA in occluded and inward-facing states. These conformations closely resemble equivalent states found in ABC transporters, indicating a shared structural mechanism of transport. In contrast to ABC transporters, where nucleotide binding, hydrolysis and release steer conformational changes necessary for substrate translocation, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations reveal how pH changes induce conformational transitions in SbmA, consistent with a mechanism of substrate internalization that utilizes the transmembrane proton gradient.

AB - SbmA is a membrane transporter from Escherichia coli that imports antimicrobial peptides. SbmA belongs to the SbmA-like peptide transporter (SLiPT) family. Although the protein is a secondary active transporter that is energized by the proton gradient, it is structurally related to the transmembrane domain (TMD) of ATP-binding cassette (ABC) transporters. SbmA therefore bridges the structural divide between primary and secondary transporters. However, it remains unclear, if SbmA also shares the mechanism of alternating access with ABC transporters, because only a single (outward-open) state is resolved. Here, we show by sequence analysis that SbmA is likely evolved from the TMD of an early ancestor of the ABC transporter YddA. We determine the cryogenic electron microscopy structures of SbmA in occluded and inward-facing states. These conformations closely resemble equivalent states found in ABC transporters, indicating a shared structural mechanism of transport. In contrast to ABC transporters, where nucleotide binding, hydrolysis and release steer conformational changes necessary for substrate translocation, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations reveal how pH changes induce conformational transitions in SbmA, consistent with a mechanism of substrate internalization that utilizes the transmembrane proton gradient.

U2 - 10.1038/s41467-026-71633-3

DO - 10.1038/s41467-026-71633-3

M3 - Article

C2 - 41986346

SN - 2041-1723

VL - 17

JO - Nature Communications

JF - Nature Communications

M1 - 5619

ER -

Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters

Abstract

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Enabling Shaped Pulse Capability: Enabling Shaped Pulse Capability for Superior Biological Structural Determination Using EPR Spectroscopy.

Cryogen-free arbitrary waveform EPR: Cryogen-free arbitrary waveform EPR for structural Biology and Biophysics

State of the art pulse EPR instrumentati: State of the art pulse EPR instrumentation for long range distance measurements in biomacromolecules

Datasets

Simulation data related to the shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters

Cite this