PDBsum entry 3b8e

Hydrolase/transport protein

PDB id: 3b8e

Contents

Protein chains

998 a.a. *

46 a.a. *

29 a.a. *

Ligands

MF4 ×2

PC1 ×2

Metals

_MG ×2

_RB ×6

* Residue conservation analysis

PDB id:

3b8e

Name:

Hydrolase/transport protein

Title:

Crystal structure of the sodium-potassium pump

Structure:

Sodium/potassium-transporting atpase subunit alpha-1. Chain: a, c. Fragment: residues 19-1016. Synonym: sodium pump subunit alpha-1, na+, /k+, atpase alpha-1 subunit. Sodium/potassium-transporting atpase subunit beta-1. Chain: b, d. Fragment: residues 28-73. Synonym: sodium/potassium-dependent atpase beta-1 subunit, sodium

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Tissue: kidney. Tissue: kidney

Resolution:

3.50Å R-factor: 0.277 R-free: 0.313

Authors:

J.P.Morth,P.B.Pedersen,M.S.Toustrup-Jensen,T.L.M.Soerensen, J.Petersen,J.P.Andersen,B.Vilsen,P.Nissen

Key ref:

J.P.Morth et al. (2007). Crystal structure of the sodium-potassium pump. Nature, 450, 1043-1049. PubMed id: 18075585 DOI: 10.1038/nature06419

Date:

01-Nov-07 Release date: 18-Dec-07

Protein chains

P05024  (AT1A1_PIG) -  Sodium/potassium-transporting ATPase subunit alpha-1 from Sus scrofa

Seq: 1021 a.a.

Struc: 998 a.a.

Protein chains

P05027  (AT1B1_PIG) -  Sodium/potassium-transporting ATPase subunit beta-1 from Sus scrofa

Seq: 303 a.a.

Struc: 46 a.a.

Protein chains

Q58K79  (Q58K79_PIG) -  FXYD domain-containing ion transport regulator from Sus scrofa

Seq: 65 a.a.

Struc: 29 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, C: 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) + Na(+)(in) + ATP + H2O = K(+)(in) + Na(+)(out) + ADP + phosphate + H(+) (Bound ligand (Het Group name = PC1) matches with 41.67% similarity)

• Cofactor: Mg(2+)
• Enzyme class 3: Chains B, G, D, H: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1038/nature06419

Nature 450:1043-1049 (2007)

PubMed id: 18075585

Crystal structure of the sodium-potassium pump.

J.P.Morth, B.P.Pedersen, M.S.Toustrup-Jensen, T.L.Sørensen, J.Petersen, J.P.Andersen, B.Vilsen, P.Nissen.

ABSTRACT

The Na+,K+-ATPase generates electrochemical gradients for sodium and potassium that are vital to animal cells, exchanging three sodium ions for two potassium ions across the plasma membrane during each cycle of ATP hydrolysis. Here we present the X-ray crystal structure at 3.5 A resolution of the pig renal Na+,K+-ATPase with two rubidium ions bound (as potassium congeners) in an occluded state in the transmembrane part of the alpha-subunit. Several of the residues forming the cavity for rubidium/potassium occlusion in the Na+,K+-ATPase are homologous to those binding calcium in the Ca2+-ATPase of sarco(endo)plasmic reticulum. The beta- and gamma-subunits specific to the Na+,K+-ATPase are associated with transmembrane helices alphaM7/alphaM10 and alphaM9, respectively. The gamma-subunit corresponds to a fragment of the V-type ATPase c subunit. The carboxy terminus of the alpha-subunit is contained within a pocket between transmembrane helices and seems to be a novel regulatory element controlling sodium affinity, possibly influenced by the membrane potential.

Selected figure(s)

Figure 1.
Figure 1: Functional characterization of Na^+,K^+-ATPase used for crystallization. a, The reaction cycle of the Na^+,K^+-ATPase^2, ^3 showing in red the form crystallized. b, Demonstration of ^86Rb^+ occlusion in the MgF[4]^2--bound form of the pig renal Na^+,K^+-ATPase from outer medulla. The dissociation of ^86Rb^+ from membranous enzyme pre-incubated with ^86Rb^+ in the absence (lowest panel) or presence (middle panel) of MgF[4]^2-, and from C[12]E[8]-solubilized enzyme preincubated in the presence of MgF[4]^2- (uppermost panel), was followed at 25 °C. Error bars, s.e.m.; n = 3.

Figure 3.
Figure 3: Architecture of the Na^+,K^+-ATPase alpha-beta-bold gamma-complex and the K^+/Rb^+ sites. The cytoplasmic side is up in all panels. a, The -, - and -subunits are coloured blue, wheat and red, respectively. Helices are represented by cylinders and -strands by arrows. The -ectodomain is shown by surface representation of the experimental electron density. The transmembrane segments of the -subunit are numbered (yellow) starting with the most N-terminal. The small C-terminal helix (S, for switch) is light red. Mg^2+, MgF[4]^2- and Rb^+ ions are grey, orange and pink, respectively. b, The red mesh (anomalous difference Fourier map) and the green mesh (omit F[O]-F[C] electron density map) show the positions of Rb^+ and K^+ ions, respectively. Oxygen-containing side chains within and close to the coordination sphere are shown. c, Structural alignment of the Na^+,K^+-ATPase (blue) with SERCA (yellow; PDB 1WPG) in the E2⋅MgF[4]^2- forms. Yellow and magenta spheres represent water molecules in SERCA and K^+/Rb^+ ions in Na^+,K^+-ATPase, respectively. d, Interaction between Glu 327 ( M4) and Leu 97 ( M1)^17. The cyan mesh indicates the electron-density map (2F[O]-F[C]) of M1 contoured at 1.0 .

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 450, 1043-1049) copyright 2007.

Figures were selected by an automated process.