5LZQ

Crystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sodium ion

Summary for 5LZQ

• Entry DOI: 10.2210/pdb5lzq/pdb
• Descriptor: K(+)-stimulated pyrophosphate-energized sodium pump, MAGNESIUM ION, IMIDODIPHOSPHORIC ACID, ... (5 entities in total)
• Functional Keywords: pyrophosphatase, imidodiphosphate, transport protein
• Biological source: Thermotoga maritima MSB8
• Cellular location: Cell membrane ; Multi-pass membrane protein : Q9S5X0
• Total number of polymer chains: 2
• Total formula weight: 157431.27

Authors

Wilkinson, C.,Kellosalo, J.,Kajander, T.,Goldman, A. (deposition date: 2016-10-01, release date: 2016-12-14, Last modification date: 2024-01-17)

Primary citation

Li, K.M.,Wilkinson, C.,Kellosalo, J.,Tsai, J.Y.,Kajander, T.,Jeuken, L.J.,Sun, Y.J.,Goldman, A.
Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism.
Nat Commun, 7:13596-13596, 2016

PubMed Abstract: Membrane-bound pyrophosphatases (M-PPases), which couple proton/sodium ion transport to pyrophosphate synthesis/hydrolysis, are important in abiotic stress resistance and in the infectivity of protozoan parasites. Here, three M-PPase structures in different catalytic states show that closure of the substrate-binding pocket by helices 5-6 affects helix 13 in the dimer interface and causes helix 12 to move down. This springs a 'molecular mousetrap', repositioning a conserved aspartate and activating the nucleophilic water. Corkscrew motion at helices 6 and 16 rearranges the key ionic gate residues and leads to ion pumping. The pumped ion is above the ion gate in one of the ion-bound structures, but below it in the other. Electrometric measurements show a single-turnover event with a non-hydrolysable inhibitor, supporting our model that ion pumping precedes hydrolysis. We propose a complete catalytic cycle for both proton and sodium-pumping M-PPases, and one that also explains the basis for ion specificity.

PubMed: 27922000
DOI: 10.1038/ncomms13596

Experimental method

X-RAY DIFFRACTION (3.495 Å)