PDBsum entry 1mo8

Hydrolase

PDB id: 1mo8

Contents

Protein chain

213 a.a. *

Ligands

ATP

* Residue conservation analysis

PDB id:

1mo8

Name:

Hydrolase

Title:

Atpase

Structure:

Sodium/potassium-transporting atpase alpha-1. Chain: a. Fragment: residues 383-595. Synonym: sodium pump, na+/k+ atpase 1. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

NMR struc:

20 models

Authors:

M.Hilge,G.Siegal,G.W.Vuister,P.Guentert,S.M.Gloor,J.P.Abrahams

Key ref:

M.Hilge et al. (2003). ATP-induced conformational changes of the nucleotide-binding domain of Na,K-ATPase. Nat Struct Biol, 10, 468-474. PubMed id: 12730684 DOI: 10.1038/nsb924

Date:

08-Sep-02 Release date: 10-Jun-03

Protein chain

P06685  (AT1A1_RAT) -  Sodium/potassium-transporting ATPase subunit alpha-1 from Rattus norvegicus

Seq: 1023 a.a.

Struc: 213 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.7.2.2.13 - Na(+)/K(+)-exchanging ATPase.
• Reaction: K⁺(out) + Na⁺(in) + ATP + H2O = K⁺(in) + Na(+)(out) + ADP + phosphate + H(+)

K(+)(out) (Bound ligand (Het Group name = ATP) corresponds exactly) + Na(+)(in) + ATP + H2O = K(+)(in) + Na(+)(out) + ADP + phosphate + H(+)

• Cofactor: Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nsb924

Nat Struct Biol 10:468-474 (2003)

PubMed id: 12730684

ATP-induced conformational changes of the nucleotide-binding domain of Na,K-ATPase.

M.Hilge, G.Siegal, G.W.Vuister, P.Güntert, S.M.Gloor, J.P.Abrahams.

ABSTRACT

The Na,K-ATPase hydrolyzes ATP to drive the coupled extrusion and uptake of Na+ and K+ ions across the plasma membrane. Here, we report two high-resolution NMR structures of the 213-residue nucleotide-binding domain of rat alpha1 Na,K-ATPase, determined in the absence and the presence of ATP. The nucleotide binds in the anti conformation and shows a relative paucity of interactions with the protein, reflecting the low-affinity ATP-binding state. Binding of ATP induces substantial conformational changes in the binding pocket and in residues located in the hinge region connecting the N- and P-domains. Structural comparison with the Ca-ATPase stabilized by the inhibitor thapsigargin, E2(TG), and the model of the H-ATPase in the E1 form suggests that the observed changes may trigger the series of events necessary for the release of the K+ ions and/or disengagement of the A-domain, leading to the eventual transfer of the gamma-phosphate group to the invariant Asp369.

Selected figure(s)

Figure 2.
Figure 2. ATP binding to the N-domain of NaK 1. (a) Titration curves for ATP (red), ADP (green) and MgATP (blue) giving K[d] values of 5.1, 24.2 and 25.1 mM, respectively, with standard deviations of 0.4, 5.3 and 8.6, respectively. (b) Mapping of chemical shift changes on the molecular surface of the N-domain of NaK 1. The color code reflects the normalized weighted average of the 1H and 15N chemical shifts calculated as (( 2[NH] + 2[N] / 25) / 2)1/2 / [max], where [max] is the maximum observed weighted shift difference in p.p.m.38. The most significant changes are in red and the moderate changes in yellow. (c) The ATP-binding pocket displaying one of the energy-minimized CYANA conformers with ATP and amino acids critical for ATP binding in ball-and-stick representation. (d) Stereo view of the conformational changes at the N and C termini in response to ATP binding. The ATP-bound form of the N-domain is colored blue; the native form of the protein is colored yellow. Binding of ATP (shown in ball and stick; carbon atoms, black; nitrogen, blue; oxygen, red; and phosphorons, magenta) causes a displacement of strands 1 and 6. The disordered loop between residues 391 -408 has been removed for clarity.

Figure 3.
Figure 3. Docking and superposition of the native (green) and ATP-bound (red) N-domain of NaK 1, the E2(TG) form of Ca-ATPase (violet) and E1 form of H-ATPase (blue). (a) Solution structure of the ATP-bound N-domain of NaK 1 and the crystal structure of the E2(TG) form of SERCA1a docked in the 11-Å Cryo-EM structure of Na,K-ATPase illustrating the relative positions of the three cytosolic domains, the TM-domain and the subunit, as well as the difference in positions of the N-domains. The surface corresponds to 75% of the expected molecular volume. (b) Enlarged view of the native and ATP-bound N-domains of NaK 1. (c) Superposition of native and ATP-bound N-domain with the E2(TG) form of Ca-ATPase. (d) Superposition of native and ATP-bound N-domain with the model for the E1 form of H-ATPase. Panels c and d focus on residues in the hinge region between the N- and P-domains.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 468-474) copyright 2003.

Figures were selected by an automated process.