5Y0B

PIG GASTRIC H+,K+ - ATPASE IN COMPLEX with BYK99


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 6.70 Å

wwPDB Validation 3D Report Full Report



Literature

The cryo-EM structure of gastric H(+),K(+)-ATPase with bound BYK99, a high-affinity member of K(+)-competitive, imidazo[1,2-a]pyridine inhibitors

Abe, K.Shimokawa, J.Naito, M.Munson, K.Vagin, O.Sachs, G.Suzuki, H.Tani, K.Fujiyoshi, Y.

(2017) Sci Rep 7: 6632-6632

  • DOI: 10.1038/s41598-017-06698-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The gastric proton pump H + ,K + -ATPase acidifies the gastric lumen, and thus its inhibitors, including the imidazo[1,2-a]pyridine class of K + -competitive acid blockers (P-CABs), have potential application as acid- ...

    The gastric proton pump H + ,K + -ATPase acidifies the gastric lumen, and thus its inhibitors, including the imidazo[1,2-a]pyridine class of K + -competitive acid blockers (P-CABs), have potential application as acid-suppressing drugs. We determined the electron crystallographic structure of H + ,K + -ATPase at 6.5 Å resolution in the E2P state with bound BYK99, a potent P-CAB with a restricted ring structure. The BYK99 bound structure has an almost identical profile to that of a previously determined structure with bound SCH28080, the original P-CAB prototype, but is significantly different from the previously reported P-CAB-free form, illustrating a common conformational change is required for P-CAB binding. The shared conformational changes include a distinct movement of transmembrane helix 2 (M2), from its position in the previously reported P-CAB-free form, to a location proximal to the P-CAB binding site in the present BYK99-bound structure. Site-specific mutagenesis within M2 revealed that D137 and N138, which face the P-CAB binding site in our model, significantly affect the inhibition constant (K i ) of P-CABs. We also found that A335 is likely to be near the bridging nitrogen at the restricted ring structure of the BYK99 inhibitor. These provide clues to elucidate the binding site parameters and mechanism of P-CAB inhibition of gastric acid secretion.


    Organizational Affiliation

    CeSPIA Inc., 2-1-1, Otemachi, Chiyoda, Tokyo, 100-0004, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase alpha chain 1A1034Sus scrofaMutation(s): 0 
Gene Names: ATP4A
EC: 3.6.3.10 (PDB Primary Data), 7.2.2.19 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
gastric H+,K+-ATPase with bound BYK99
Find proteins for P19156 (Sus scrofa)
Explore P19156 
Go to UniProtKB:  P19156
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase subunit betaB290Sus scrofaMutation(s): 0 
Gene Names: ATP4B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
gastric H+,K+-ATPase with bound BYK99
Find proteins for P18434 (Sus scrofa)
Explore P18434 
Go to UniProtKB:  P18434
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 6.70 Å
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.6α = 90
b = 112β = 90
c = 320γ = 90

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release