1IPW

INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI WITH THREE MAGNESIUM IONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic identification of metal-binding sites in Escherichia coli inorganic pyrophosphatase.

Kankare, J.Salminen, T.Lahti, R.Cooperman, B.S.Baykov, A.A.Goldman, A.

(1996) Biochemistry 35: 4670-4677

  • DOI: 10.1021/bi952637e

  • PubMed Abstract: 
  • We report refined crystal structures of the hexameric soluble inorganic pyrophosphatase from Escherichia coli (E-PPase) to R-factors of 18.3% and 17.1% at 2.2 and 2.3 angstroms, respectively. Both structures contain two independent monomers in the as ...

    We report refined crystal structures of the hexameric soluble inorganic pyrophosphatase from Escherichia coli (E-PPase) to R-factors of 18.3% and 17.1% at 2.2 and 2.3 angstroms, respectively. Both structures contain two independent monomers in the asymmetric unit of an R32 cell. The difference between the structures is that the latter contains 1.5 Mg2+ ions per monomer. One metal ion binds to the "tight" metal-binding site identified by equilibrium dialysis studies, and is coordinated to Asp65, Asp70, and Asp102. The other metal ion, shared between two monomers at a hitherto unidentified metal-binding site in the dyad interface between trimers, is coordinated through water molecules to Asp26s and Asn24s from two monomers. The hexamers with metal bound to them are more tightly associated than the ones without metal bound to them. Combined with our other mechanistic and structural data, the results suggest that, at high metal concentrations, E-PPase may bind at least 4.5 metals per monomer: two in the active site before binding substrate, two with substrate, and 0.5 in the dyad interface. Glu20 interacts via a water molecule with Asp70 and appears in the related yeast PPase structure (Heikinheimo, manuscript in preparation) to be involved in binding the second metal ion. Magnesium ion therefore stabilizes the hexamer form through both direct and indirect effects. The direct effect is by tighter association at the subunit interface; the indirect effect occurs because magnesium stabilizes the correct conformation of the loop between Glu20 and Ile32, a loop involved a trimer-trimmer interactions. Our results thus provide a structural explanation for the solution studies that show that the E20D variant is partially hexameric and that the hexamer form can be stabilized by binding magnesium ion.


    Related Citations: 
    • Structure of Escherichia Coli Inorganic Pyrophosphatase at 2.2 Angstroms Resolution
      Kankare, J.,Salminen, T.,Lahti, R.,Cooperman, B.S.,Baykov, A.A.,Goldman, A.
      () TO BE PUBLISHED --: --
    • New Crystal Forms of Escherichia Coli and Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase
      Heikinheimo, P.,Salminen, T.,Cooperman, B.,Lahti, R.,Goldman, A.
      (1995) Acta Crystallogr.,Sect.D 51: 399
    • Erratum. The Structure of E.Coli Soluble Inorganic Pyrophosphatase at 2.7 A Resolution
      Kankare, J.,Neal, G.S.,Salminen, T.,Glumoff, T.,Cooperman, B.S.,Lahti, R.,Goldman, A.
      (1994) Protein Eng. 7: 1173
    • The Structure of E.Coli Soluble Inorganic Pyrophosphatase at 2.7 A Resolution
      Kankare, J.,Neal, G.S.,Salminen, T.,Glumoff, T.,Cooperman, B.S.,Lahti, R.,Goldman, A.
      (1994) Protein Eng. 7: 823


    Organizational Affiliation

    Centre for Biotechnology, SF-20521 Turku, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SOLUBLE INORGANIC PYROPHOSPHATASE
A, B
175Escherichia coli (strain K12)Gene Names: ppa
EC: 3.6.1.1
Find proteins for P0A7A9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7A9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.171 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 109.400α = 90.00
b = 109.400β = 90.00
c = 154.300γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance