5KSD

Crystal Structure of a Plasma Membrane Proton Pump

「3B8C」から置き換えられました

5KSD の概要

• エントリーDOI: 10.2210/pdb5ksd/pdb
• 分子名称: ATPase 2, plasma membrane-type, MAGNESIUM ION, POTASSIUM ION, ... (5 entities in total)
• 機能のキーワード: p-type atpase proton transport, transport protein
• 由来する生物種: Arabidopsis thaliana (Mouse-ear cress)
• 細胞内の位置: Cell membrane ; Multi-pass membrane protein : P19456
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 184825.28

構造登録者

Croll, T.,Pedersen, B.P.,Nissen, P. (登録日: 2016-07-08, 公開日: 2016-08-10, 最終更新日: 2024-05-08)

主引用文献

Focht, D.,Croll, T.I.,Pedersen, B.P.,Nissen, P.
Improved Model of Proton Pump Crystal Structure Obtained by Interactive Molecular Dynamics Flexible Fitting Expands the Mechanistic Model for Proton Translocation in P-Type ATPases.
Front Physiol, 8:202-202, 2017

PubMed Abstract: The plasma membrane H-ATPase is a proton pump of the P-type ATPase family and essential in plants and fungi. It extrudes protons to regulate pH and maintains a strong proton-motive force that energizes e.g., secondary uptake of nutrients. The only crystal structure of a H-ATPase (AHA2 from ) was reported in 2007. Here, we present an improved atomic model of AHA2, obtained by a combination of model rebuilding through interactive molecular dynamics flexible fitting (iMDFF) and structural refinement based on the original data, but using up-to-date refinement methods. More detailed map features prompted local corrections of the transmembrane domain, in particular rearrangement of transmembrane helices 7 and 8, and the cytoplasmic N- and P-domains, and the new model shows improved overall quality and reliability scores. The AHA2 structure shows similarity to the Ca-ATPase E1 state, and provides a valuable starting point model for structural and functional analysis of proton transport mechanism of P-type H-ATPases. Specifically, Asp684 protonation associated with phosphorylation and occlusion of the E1P state may result from hydrogen bond interaction with Asn106. A subsequent deprotonation associated with extracellular release in the E2P state may result from an internal salt bridge formation to an Arg655 residue, which in the present E1 state is stabilized in a solvated pocket. A release mechanism based on an in-built counter-cation was also later proposed for Zn-ATPase, for which structures have been determined in Zn released E2P-like states with the salt bridge interaction formed.

PubMed: 28443028
DOI: 10.3389/fphys.2017.00202

実験手法

X-RAY DIFFRACTION (3.5 Å)