6AFX

Proton pyrophosphatase - E225A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation.

Tsai, J.Y.Tang, K.Z.Li, K.M.Hsu, B.L.Chiang, Y.W.Goldman, A.Sun, Y.J.

(2019) J Mol Biol 431: 1619-1632

  • DOI: 10.1016/j.jmb.2019.03.009
  • Primary Citation of Related Structures:  
    6AFT, 6AFS, 6AFV, 6AFU, 6AFX, 6AFW, 6AFZ, 6AFY

  • 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

    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 i 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 i -, 2P i - 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 i -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.


    Organizational Affiliation

    Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan. Electronic address: yjsun@life.nthu.edu.tw.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrophosphate-energized vacuolar membrane proton pumpA, B766Vigna radiata var. radiataMutation(s): 1 
EC: 3.6.1.1 (PDB Primary Data), 7.1.3.1 (UniProt)
Find proteins for P21616 (Vigna radiata var. radiata)
Explore P21616 
Go to UniProtKB:  P21616
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PG
Query on 1PG

Download CCD File 
A, B
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.197α = 90
b = 88.321β = 125.14
c = 158.843γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Taiwan--

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references