2BQX

Inorganic Pyrophosphatase from the Pathogenic Bacterium Helicobacter pylori-Kinetic and Structural Properties


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kinetic and Structural Properties of Inorganic Pyrophosphatase from the Pathogenic Bacterium Helicobacter Pylori.

Chao, T.-C.Huang, H.Tsai, J.Y.Huang, C.Y.Sun, Y.-J.

(2006) Proteins 65: 670

  • DOI: 10.1002/prot.21093
  • Primary Citation of Related Structures:  2BQY

  • PubMed Abstract: 
  • Inorganic pyrophosphatase (PPase) catalyzes the hydrolysis of pyrophosphate (PPi) to orthophosphate (Pi) and controls the level of PPi in cells. PPase plays an essential role in energy conservation and provides the energy for many biosynthetic pathwa ...

    Inorganic pyrophosphatase (PPase) catalyzes the hydrolysis of pyrophosphate (PPi) to orthophosphate (Pi) and controls the level of PPi in cells. PPase plays an essential role in energy conservation and provides the energy for many biosynthetic pathways. The Helicobacter pylori pyrophosphatase (HpPPase) gene was cloned, expressed, purified, and found to have a molecular weight of 20 kDa. The K(m) and V (max) of HpPPase were determined as 214.4 microM and 594 micromol Pi min(-1) mg(-1), respectively. PPi binds Mg(2+) to form a true substrate that activates the enzyme. However, free PPi could be a potent inhibitor for HpPPase. The effects of the inhibitors NaF, ATP, iminodiphosphate, and N-ethylmaleimide on HpPPase activity were evaluated. NaF showed the highest inhibition of the enzyme. Crystal structures of HpPPase and the PPi-HpPPase complex were determined. HpPPase comprises three alpha-helices and nine beta-strands and folds as a barrel structure. HpPPase forms a hexamer in both the solution and crystal states, and each monomer has its own PPi-binding site. The PPi binding does not cause a significant conformational change in the PPi-HpPPase complex, which might represent an inhibition state for HpPPase in the absence of a divalent metal ion.


    Organizational Affiliation

    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan, Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INORGANIC PYROPHOSPHATASE
A
173Helicobacter pylori (strain ATCC 700392 / 26695)Gene Names: ppa
EC: 3.6.1.1
Find proteins for P56153 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56153
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.650α = 90.00
b = 102.650β = 90.00
c = 93.630γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance