8B37

Crystal structure of Pyrobaculum aerophilum potassium-independent proton pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sulphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.290 

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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(+)-insensitive pyrophosphate-energized proton pump
A, B
729Pyrobaculum aerophilumMutation(s): 0 
Gene Names: hppAPAE1771
EC: 7.1.3.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8ZWI8 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2))
Explore Q8ZWI8 
Go to UniProtKB:  Q8ZWI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZWI8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2PN (Subject of Investigation/LOI)
Query on 2PN

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
IMIDODIPHOSPHORIC ACID
H5 N O6 P2
GNGSOPFGGKKDQP-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
O [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.290 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.19α = 90
b = 88.02β = 106.946
c = 116.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
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
Other governmentUniversity of Leeds 110th Anniversary Fellowship University of Leeds
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M021610/1
Academy of FinlandFinland1322609
Academy of FinlandFinland308105
Academy of FinlandFinland307775
German Research Foundation (DFG)GermanyEXC1074
German Research Foundation (DFG)GermanyEXC2056

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references