Inhibited KdpFABC transitions into an E1 off-cycle state
Abstract
KdpFABC is a high-affinity prokaryotic K+ uptake system that forms a functional chimera between a channel-like subunit (KdpA) and a P-type ATPase (KdpB). At high K+ levels, KdpFABC needs to be inhibited to prevent excessive K+ accumulation to the point of toxicity. This is achieved by a phosphorylation of the serine residue in the TGES162 motif in the A domain of the pump subunit KdpB (KdpBS162-P). Here, we explore the structural basis of inhibition by KdpBS162 phosphorylation by determining the conformational landscape of KdpFABC under inhibiting and non-inhibiting conditions. Under turnover conditions, we identified a new inhibited KdpFABC state that we termed E1P tight, which is not part of the canonical Post-Albers transport cycle of P-type ATPases. It likely represents the biochemically described stalled E1P state adopted by KdpFABC upon KdpBS162 phosphorylation. The E1P tight state exhibits a compact fold of the three cytoplasmic domains and is likely adopted when the transition from high-energy E1P states to E2P states is unsuccessful. This study represents a structural characterization of a biologically relevant off-cycle state in the P-type ATPase family and supports the emerging discussion of P-type ATPase regulation by such states.
Data availability
The three-dimensional cryo-EM densities and corresponding modelled coordinates generated have been deposited in the Electron Microscopy Data Bank and the Protein Data Bank under the accession numbers summarized in Table 4. The depositions include maps calculated with higher b-factors, both half-maps and the mask used for the final FSC calculation.
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KdpFABC WT (KdpB-Ser162-P) in an E1·ATPearly state under turnover conditionsPDB-ID: 7ZRG, EMDB-ID: EMD-14913; EMPIAR: EMPIAR-11232.
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KdpFABC WT (KdpB-Ser162-P) in an E1P·ADP state under turnover conditionsPDB-ID: 7ZRK, EMDB-ID: EMD-14917; EMPIAR: EMPIAR-11232.
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KdpFABC WT (KdpB-Ser162-P) in an E1P-tight state under turnover conditionsPDB-ID: 7ZRE, EMDB-ID: EMD-14912; EMPIAR: EMPIAR-11232.
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KdpFABC WT (KdpB-Ser162-P) in an E1P-tight state in presence of orthovanadatePDB-ID: 7ZRD, EMDB-ID: EMD-14911; EMPIAR: EMPIAR-11230.
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KdpFAB(Ser162-P,D307N)C in an E1 apo tight statePDB-ID: 7ZRH, EMDB-ID: EMD-14914; EMPIAR: EMPIAR-11229.
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KdpFAB(Ser162-P,D307N)C in an E1 apo open 1 statePDB-ID: 7ZRI, EMDB-ID: EMD-14915; EMPIAR: EMPIAR-11229.
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KdpFAB(Ser162-P,D307N)C in an E1 apo open 2 statePDB-ID: 7ZRJ, EMDB-ID: EMD-14916; EMPIAR: EMPIAR-11229.
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KdpFAB(S162A) in an E1P·ADP state under turnover conditionsPDB-ID: 7ZRM, EMDB-ID: EMD-14919; EMPIAR: EMPIAR-11231.
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KdpFABC WT (KdpB-Ser162-P) in an E2P state under turnover conditionsPDB-ID: 7ZRL, EMDB-ID: EMD-14918; EMPIAR: EMPIAR-11231.
Article and author information
Author details
Funding
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Veni grant 722.017.001)
- Cristina Paulino
Biotechnology and Biological Sciences Research Council (BB/R002517/1)
- Phillip J Stansfeld
Biotechnology and Biological Sciences Research Council (BB/S003339/1)
- Phillip J Stansfeld
State of Hesse (LOEWE Schwerpunkt TRABITA)
- Jakob M Silberberg
Wellcome Trust (208361/Z/17/Z)
- Robin A Corey
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Start-Up grant 740.018.016)
- Cristina Paulino
Deutsche Forschungsgemeinschaft (Emmy Noether grant HA6322/3-1)
- Inga Hänelt
Deutsche Forschungsgemeinschaft (Heisenberg program HA6322/5-1)
- Inga Hänelt
Aventis Foundation (Life Science Bridge Award)
- Inga Hänelt
Uniscientia Foundation
- Inga Hänelt
Wellcome Trust (208361/Z/17/Z)
- Phillip J Stansfeld
Medical Research Council (MR/S009213/1)
- Phillip J Stansfeld
Biotechnology and Biological Sciences Research Council (BB/P01948X/1)
- Phillip J Stansfeld
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Silberberg et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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