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 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/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)). 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INORGANIC PYROPHOSPHATASE175Escherichia coliMutation(s): 0 
EC: 3.6.1.1
UniProt
Find proteins for P0A7A9 (Escherichia coli (strain K12))
Explore P0A7A9 
Go to UniProtKB:  P0A7A9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7A9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download Ideal Coordinates CCD File 
J [auth A]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description