7Z04 image
Entry Detail
PDB ID:
7Z04
Title:
10 mM Rb+ soak of beryllium fluoride inhibited Na+,K+-ATPase, E2-BeFx (rigid body model)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-02-22
Release Date:
2022-11-23
Method Details:
Experimental Method:
Resolution:
7.50 Å
R-Value Free:
0.33
R-Value Work:
0.30
R-Value Observed:
0.30
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Sodium/potassium-transporting ATPase subunit alpha-1
Chain IDs:A, D (auth: C)
Chain Length:1020
Number of Molecules:2
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Sodium/potassium-transporting ATPase subunit beta-1
Chain IDs:B, E (auth: D)
Chain Length:302
Number of Molecules:2
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:FXYD domain-containing ion transport regulator
Chain IDs:C (auth: G), F (auth: E)
Chain Length:64
Number of Molecules:2
Biological Source:Sus scrofa
Primary Citation
The Na + ,K + -ATPase in complex with beryllium fluoride mimics an ATPase phosphorylated state.
J.Biol.Chem. 298 102317 102317 (2022)
PMID: 35926706 DOI: 10.1016/j.jbc.2022.102317

Abstact

The Na+,K+-ATPase generates electrochemical gradients of Na+ and K+ across the plasma membrane via a functional cycle that includes various phosphoenzyme intermediates. However, the structure and function of these intermediates and how metal fluorides mimick them require further investigation. Here, we describe a 4.0 Å resolution crystal structure and functional properties of the pig kidney Na+,K+-ATPase stabilized by the inhibitor beryllium fluoride (denoted E2-BeFx). E2-BeFx is expected to mimic properties of the E2P phosphoenzyme, yet with unknown characteristics of ion and ligand binding. The structure resembles the E2P form obtained by phosphorylation from inorganic phosphate (Pi) and stabilized by cardiotonic steroids, including a low-affinity Mg2+ site near ion binding site II. Our anomalous Fourier analysis of the crystals soaked in Rb+ (a K+ congener) followed by a low-resolution rigid-body refinement (6.9-7.5 Å) revealed preocclusion transitions leading to activation of the dephosphorylation reaction. We show that the Mg2+ location indicates a site of initial K+ recognition and acceptance upon binding to the outward-open E2P state after Na+ release. Furthermore, using binding and activity studies, we find that the BeFx-inhibited enzyme is also able to bind ADP/ATP and Na+. These results relate the E2-BeFx complex to a transient K+- and ADP-sensitive E∗P intermediate of the functional cycle of the Na+,K+-ATPase, prior to E2P.

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