7EFM

Crystal structure of the gastric proton pump K791S/E820D/Y340N in (BYK)E2BeF state

Summary for 7EFM

• Entry DOI: 10.2210/pdb7efm/pdb
• Descriptor: Sodium/potassium-transporting ATPase subunit alpha, Potassium-transporting ATPase subunit beta, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: cation pump, p-type atpase, gastric, proton pump, membrane protein
• Biological source: Sus scrofa (Pig); More
• Total number of polymer chains: 2
• Total formula weight: 140042.08

Authors

Abe, K.,Yamamoto, K.,Irie, K. (deposition date: 2021-03-22, release date: 2021-09-01, Last modification date: 2024-11-06)

Primary citation

Abe, K.,Yamamoto, K.,Irie, K.,Nishizawa, T.,Oshima, A.
Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations.
Nat Commun, 12:5709-5709, 2021

PubMed Abstract: The gastric H,K-ATPase mediates electroneutral exchange of 1H/1K per ATP hydrolysed across the membrane. Previous structural analysis of the K-occluded E2-P transition state of H,K-ATPase showed a single bound K at cation-binding site II, in marked contrast to the two K ions occluded at sites I and II of the closely-related Na,K-ATPase which mediates electrogenic 3Na/2K translocation across the membrane. The molecular basis of the different K stoichiometry between these K-counter-transporting pumps is elusive. We show a series of crystal structures and a cryo-EM structure of H,K-ATPase mutants with changes in the vicinity of site I, based on the structure of the sodium pump. Our step-wise and tailored construction of the mutants finally gave a two-K bound H,K-ATPase, achieved by five mutations, including amino acids directly coordinating K (Lys791Ser, Glu820Asp), indirectly contributing to cation-binding site formation (Tyr340Asn, Glu936Val), and allosterically stabilizing K-occluded conformation (Tyr799Trp). This quintuple mutant in the K-occluded E2-P state unambiguously shows two separate densities at the cation-binding site in its 2.6 Å resolution cryo-EM structure. These results offer new insights into how two closely-related cation pumps specify the number of K accommodated at their cation-binding site.

PubMed: 34588453
DOI: 10.1038/s41467-021-26024-1

Experimental method

X-RAY DIFFRACTION (3.2 Å)