PDBsum entry 4ret

Membrane protein, hydrolase/inhibitor

PDB id: 4ret

Contents

Protein chains

996 a.a.

290 a.a.

32 a.a.

Ligands

NAG-NAG

GLC-FRU ×2

CLR ×4

DGX ×2

17F ×3

NAG ×4

Metals

_MG ×6

Waters ×6

PDB id:

4ret

Name:

Membrane protein, hydrolase/inhibitor

Title:

Crystal structure of the na,k-atpase e2p-digoxin complex with bound magnesium

Structure:

Sodium/potassium-transporting atpase subunit alpha-1. Chain: a, c. Synonym: na(+)/k(+) atpase alpha-1 subunit, sodium pump subunit alpha-1. Sodium/potassium-transporting atpase subunit beta-1. Chain: b, d. Synonym: na(+),k)(+)-atpase beta-1 subunit, sodium/potassium- dependent atpase subunit beta-1. Na+/k+ atpase gamma subunit transcript variant a.

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organism_taxid: 9823

Resolution:

4.00Å R-factor: 0.223 R-free: 0.253

Authors:

J.L.Gregersen,M.Laursen,L.Yatime,P.Nissen,N.U.Fedosova

Key ref:

M.Laursen et al. (2015). Structures and characterization of digoxin- and bufalin-bound Na+,K+-ATPase compared with the ouabain-bound complex. Proc Natl Acad Sci U S A, 112, 1755-1760. PubMed id: 25624492 DOI: 10.1073/pnas.1422997112

Date:

23-Sep-14 Release date: 28-Jan-15

Protein chains

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

Seq: 1021 a.a.

Struc: 996 a.a.*

Protein chains

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

Seq: 303 a.a.

Struc: 290 a.a.

Protein chains

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

Seq: 65 a.a.

Struc: 32 a.a.

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

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) (Bound ligand (Het Group name = NAG) matches with 41.38% similarity) + Na(+)(out) + ADP + phosphate + H(+)

• Cofactor: Mg(2+)
• Enzyme class 3: Chains B, G, D, E: 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: 10.1073/pnas.1422997112

Proc Natl Acad Sci U S A 112:1755-1760 (2015)

PubMed id: 25624492

Structures and characterization of digoxin- and bufalin-bound Na+,K+-ATPase compared with the ouabain-bound complex.

M.Laursen, J.L.Gregersen, L.Yatime, P.Nissen, N.U.Fedosova.

ABSTRACT

Cardiotonic steroids (CTSs) are specific and potent inhibitors of the Na(+),K(+)-ATPase, with highest affinity to the phosphoenzyme (E2P) forms. CTSs are comprised of a steroid core, which can be glycosylated, and a varying number of substituents, including a five- or six-membered lactone. These functionalities have specific influence on the binding properties. We report crystal structures of the Na(+),K(+)-ATPase in the E2P form in complex with bufalin (a nonglycosylated CTS with a six-membered lactone) and digoxin (a trisaccharide-conjugated CTS with a five-membered lactone) and compare their characteristics and binding kinetics with the previously described E2P-ouabain complex to derive specific details and the general mechanism of CTS binding and inhibition. CTSs block the extracellular cation exchange pathway, and cation-binding sites I and II are differently occupied: A single Mg(2+) is bound in site II of the digoxin and ouabain complexes, whereas both sites are occupied by K(+) in the E2P-bufalin complex. In all complexes, αM4 adopts a wound form, characteristic for the E2P state and favorable for high-affinity CTS binding. We conclude that the occupants of the cation-binding site and the type of the lactone substituent determine the arrangement of αM4 and hypothesize that winding/unwinding of αM4 represents a trigger for high-affinity CTS binding. We find that the level of glycosylation affects the depth of CTS binding and that the steroid core substituents fine tune the configuration of transmembrane helices αM1-2.