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Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC

Author

Listed:
  • Jakob M. Silberberg

    (Goethe University Frankfurt)

  • Robin A. Corey

    (University of Oxford)

  • Lisa Hielkema

    (University of Groningen)

  • Charlott Stock

    (Goethe University Frankfurt
    Aarhus University)

  • Phillip J. Stansfeld

    (University of Warwick)

  • Cristina Paulino

    (University of Groningen)

  • Inga Hänelt

    (Goethe University Frankfurt)

Abstract

KdpFABC, a high-affinity K+ pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K+ limitation. Here, we apply a combination of cryo-EM, biochemical assays, and MD simulations to illuminate the mechanisms underlying transport and the coupling to ATP hydrolysis. We show that ions are transported via an intersubunit tunnel through KdpA and KdpB. At the subunit interface, the tunnel is constricted by a phenylalanine, which, by polarized cation-π stacking, controls K+ entry into the canonical substrate binding site (CBS) of KdpB. Within the CBS, ATPase coupling is mediated by the charge distribution between an aspartate and a lysine. Interestingly, individual elements of the ion translocation mechanism of KdpFABC identified here are conserved among a wide variety of P-type ATPases from different families. This leads us to the hypothesis that KdpB might represent an early descendant of a common ancestor of cation pumps.

Suggested Citation

  • Jakob M. Silberberg & Robin A. Corey & Lisa Hielkema & Charlott Stock & Phillip J. Stansfeld & Cristina Paulino & Inga Hänelt, 2021. "Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25242-x
    DOI: 10.1038/s41467-021-25242-x
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    Cited by:

    1. Grace D. Galles & Daniel T. Infield & Colin J. Clark & Marcus L. Hemshorn & Shivani Manikandan & Frederico Fazan & Ali Rasouli & Emad Tajkhorshid & Jason D. Galpin & Richard B. Cooley & Ryan A. Mehl &, 2023. "Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Jakob M. Silberberg & Sophie Ketter & Paul J. N. Böhm & Kristin Jordan & Marcel Wittenberg & Julia Grass & Inga Hänelt, 2024. "KdpD is a tandem serine histidine kinase that controls K+ pump KdpFABC transcriptionally and post-translationally," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    3. T. Bertie Ansell & Wanling Song & Claire E. Coupland & Loic Carrique & Robin A. Corey & Anna L. Duncan & C. Keith Cassidy & Maxwell M. G. Geurts & Tim Rasmussen & Andrew B. Ward & Christian Siebold & , 2023. "LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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