5GPJ

Crystal Structure of Proton-Pumping Pyrophosphatase

Summary for 5GPJ

• Entry DOI: 10.2210/pdb5gpj/pdb
• Descriptor: Pyrophosphate-energized vacuolar membrane proton pump, PHOSPHATE ION, MAGNESIUM ION (3 entities in total)
• Functional Keywords: vigna radiata, proton-pumping, phosphate-bound, hydrolase
• Biological source: Vigna radiata var. radiata (Mung bean)
• Cellular location: Vacuole membrane ; Multi- pass membrane protein : P21616
• Total number of polymer chains: 4
• Total formula weight: 324957.82

Authors

Li, K.M.,Tsai, J.Y.,Sun, Y.J. (deposition date: 2016-08-03, release date: 2016-12-28, Last modification date: 2024-10-16)

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 (3.5 Å)