6AFX

Proton pyrophosphatase - E225A

Summary for 6AFX

• Entry DOI: 10.2210/pdb6afx/pdb
• Descriptor: Pyrophosphate-energized vacuolar membrane proton pump, PHOSPHATE ION, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: hydrolase, proton pumping, vigna radiata, membrane protein
• Biological source: Vigna radiata var. radiata (Mung bean)
• Total number of polymer chains: 2
• Total formula weight: 162536.86

Authors

Tsai, J.-Y.,Tang, K.-Z.,Sun, Y.-J. (deposition date: 2018-08-08, release date: 2019-04-10, Last modification date: 2024-10-23)

Primary citation

Tsai, J.Y.,Tang, K.Z.,Li, K.M.,Hsu, B.L.,Chiang, Y.W.,Goldman, A.,Sun, Y.J.
Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation.
J. Mol. Biol., 431:1619-1632, 2019

PubMed Abstract: Membrane-embedded pyrophosphatase (M-PPase) hydrolyzes pyrophosphate to drive ion (H and/or Na) translocation. We determined crystal structures and functions of Vigna radiata M-PPase (VrH-PPase), the VrH-PPase-2P complex and mutants at hydrophobic gate (residue L555) and exit channel (residues T228 and E225). Ion pore diameters along the translocation pathway of three VrH-PPases complexes (P-, 2P- and imidodiphosphate-bound states) present a unique wave-like profile, with different pore diameters at the hydrophobic gate and exit channel, indicating that the ligands induced pore size alterations. The 2P-bound state with the largest pore diameter might mimic the hydrophobic gate open. In mutant structures, ordered waters detected at the hydrophobic gate among VrH-PPase imply the possibility of solvation, and numerous waters at the exit channel might signify an open channel. A salt-bridge, E225-R562 is at the way out of the exit channel of VrH-PPase; E225A mutant makes the interaction eliminated and reveals a decreased pumping ability. E225-R562 might act as a latch to regulate proton release. A water wire from the ion gate (R-D-K-E) through the hydrophobic gate and into the exit channel may reflect the path of proton transfer.

PubMed: 30878480
DOI: 10.1016/j.jmb.2019.03.009

Experimental method

X-RAY DIFFRACTION (2.301 Å)