1I6T

STRUCTURE OF INORGANIC PYROPHOSPHATASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 

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This is version 1.3 of the entry. See complete history. 


Literature

The structures of Escherichia coli inorganic pyrophosphatase complexed with Ca(2+) or CaPP(i) at atomic resolution and their mechanistic implications.

Samygina, V.R., Popov, A.N., Rodina, E.V., Vorobyeva, N.N., Lamzin, V.S., Polyakov, K.M., Kurilova, S.A., Nazarova, T.I., Avaeva, S.M.

(2001) J Mol Biol 314: 633-645

  • DOI: 10.1006/jmbi.2001.5149
  • Primary Citation of Related Structures:  
    1I40, 1I6T

  • PubMed Abstract: 

    • Two structures of Escherichia coli soluble inorganic pyrophosphatase (EPPase) complexed with calcium pyrophosphate (CaPP(i)-EPPase) and with Ca(2+) (Ca(2+)-EPPase) have been solved at 1.2 and 1.1 A resolution, respectively. In the presence of Mg(2+), this enzyme cleaves pyrophosphate (PP(i)) into two molecules of orthophosphate (P(i)) ...

    Two structures of Escherichia coli soluble inorganic pyrophosphatase (EPPase) complexed with calcium pyrophosphate (CaPP(i)-EPPase) and with Ca(2+) (Ca(2+)-EPPase) have been solved at 1.2 and 1.1 A resolution, respectively. In the presence of Mg(2+), this enzyme cleaves pyrophosphate (PP(i)) into two molecules of orthophosphate (P(i)). This work has enabled us to locate PP(i) in the active site of the inorganic pyrophosphatases family in the presence of Ca(2+), which is an inhibitor of EPPase.Upon PP(i) binding, two Ca(2+) at M1 and M2 subsites move closer together and one of the liganded water molecules becomes bridging. The mutual location of PP(i) and the bridging water molecule in the presence of inhibitor cation is catalytically incompetent. To make a favourable PP(i) attack by this water molecule, modelling of a possible hydrolysable conformation of PP(i) in the CaPP(i)-EPPase active site has been performed. The reasons for Ca(2+) being the strong PPase inhibitor and the role in catalysis of each of four metal ions are the mechanistic aspects discussed on the basis of the structures described.

    Organizational Affiliation: 

    A.V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninski pr. 59, Moscow, 117333, Russia.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INORGANIC PYROPHOSPHATASE A175Escherichia coliMutation(s): 0 
EC: 3.6.1.1
Find proteins for P0A7A9 (Escherichia coli (strain K12))
Explore P0A7A9 
Go to UniProtKB:  P0A7A9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.356α = 90
b = 109.356β = 90
c = 75.582γ = 120
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description