5ksd

From Proteopedia

Crystal Structure of a Plasma Membrane Proton Pump

PDB ID 5ksd

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Structural highlights

5ksd is a 2 chain structure with sequence from Arabidopsis thaliana. This structure supersedes the now removed PDB entry 3b8c. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.5Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PMA2_ARATH The plasma membrane H(+) ATPase of plants and fungi generates a proton gradient that drives the active transport of nutrients by H(+)-symport. The resulting external acidification and/or internal alkinization may mediate growth responses.

Publication Abstract from PubMed

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 Arabidopsis thaliana) 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 Ca2+-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 Zn2+-ATPase, for which structures have been determined in Zn2+ released E2P-like states with the salt bridge interaction formed.

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.,Focht D, Croll TI, Pedersen BP, Nissen P Front Physiol. 2017 Apr 11;8:202. doi: 10.3389/fphys.2017.00202. eCollection, 2017. PMID:28443028^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Focht D, Croll TI, Pedersen BP, 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. 2017 Apr 11;8:202. doi: 10.3389/fphys.2017.00202. eCollection, 2017. PMID:28443028 doi:http://dx.doi.org/10.3389/fphys.2017.00202