8B23

Time-resolved structure of K+-dependent Na+-PPase from Thermotoga maritima 600-seconds post reaction initiation with Na+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.334 
  • R-Value Observed: 0.336 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases.

Strauss, J.Wilkinson, C.Vidilaseris, K.de Castro Ribeiro, O.M.Liu, J.Hillier, J.Wichert, M.Malinen, A.M.Gehl, B.Jeuken, L.J.Pearson, A.R.Goldman, A.

(2024) EMBO Rep 25: 853-875

  • DOI: https://doi.org/10.1038/s44319-023-00037-x
  • Primary Citation of Related Structures:  
    8B21, 8B22, 8B23, 8B24, 8B37

  • PubMed Abstract: 

    Membrane-bound pyrophosphatases (M-PPases) are homodimeric primary ion pumps that couple the transport of Na + - and/or H + across membranes to the hydrolysis of pyrophosphate. Their role in the virulence of protist pathogens like Plasmodium falciparum makes them an intriguing target for structural and functional studies. Here, we show the first structure of a K + -independent M-PPase, asymmetric and time-dependent substrate binding in time-resolved structures of a K + -dependent M-PPase and demonstrate pumping-before-hydrolysis by electrometric studies. We suggest how key residues in helix 12, 13, and the exit channel loops affect ion selectivity and K + -activation due to a complex interplay of residues that are involved in subunit-subunit communication. Our findings not only explain ion selectivity in M-PPases but also why they display half-of-the-sites reactivity. Based on this, we propose, for the first time, a unified model for ion-pumping, hydrolysis, and energy coupling in all M-PPases, including those that pump both Na + and H + .


  • Organizational Affiliation

    Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
K(+)-stimulated pyrophosphate-energized sodium pump
A, B
735Thermotoga maritimaMutation(s): 2 
Gene Names: hppATM_0174
Membrane Entity: Yes 
UniProt
Find proteins for Q9S5X0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9S5X0 
Go to UniProtKB:  Q9S5X0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S5X0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.334 
  • R-Value Observed: 0.336 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.327α = 90
b = 111.552β = 109.05
c = 106.217γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union722687
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M021610/1
Academy of FinlandFinland1322609 and 308105

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references