5GPJ

Crystal Structure of Proton-Pumping Pyrophosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism

Li, K.M.Wilkinson, C.Kellosalo, J.Tsai, J.Y.Kajander, T.Jeuken, L.J.Sun, Y.J.Goldman, A.

(2016) Nat Commun 7: 13596-13596

  • DOI: 10.1038/ncomms13596
  • Primary Citation of Related Structures:  

  • 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 di ...

    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.


    Organizational Affiliation

    Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrophosphate-energized vacuolar membrane proton pump
A, B, C, D
774Vigna radiata var. radiataMutation(s): 0 
EC: 7.1.3.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Membrane-Integral Pyrophosphatases (M-PPases)
Protein: 
H+-translocating M-PPase
Find proteins for P21616 (Vigna radiata var. radiata)
Go to UniProtKB:  P21616
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 225.703α = 90.00
b = 81.637β = 92.87
c = 264.845γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnolgyTaiwan101-2311-B-007-009-MY3 and 103-2627-M-007-008
Academia SinicaTaiwanAS-103-TP-B11

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release