Experimental Data Snapshot

  • Resolution: 2.4 Å

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate.

Harutyunyan, E.H.Kuranova, I.P.Vainshtein, B.K.Hohne, W.E.Lamzin, V.S.Dauter, Z.Teplyakov, A.V.Wilson, K.S.

(1996) Eur.J.Biochem. 239: 220-228

  • PubMed Abstract: 
  • The three-dimensional structure of the manganese-phosphate complex of inorganic pyrophosphatase from Saccharomyces cerevisiae has been refined to an R factor of 19.0% at 2.4-A resolution. X-ray data were collected from a single crystal using an imagi ...

    The three-dimensional structure of the manganese-phosphate complex of inorganic pyrophosphatase from Saccharomyces cerevisiae has been refined to an R factor of 19.0% at 2.4-A resolution. X-ray data were collected from a single crystal using an imaging plate scanner and synchrotron radiation. There is one dimeric molecule in the asymmetric unit. The upper estimate of the root-mean-square coordinate error is 0.4 A using either the delta A plot or the superposition of the two crystallographically independent subunits. The good agreement between the coordinates of the two subunits, which were not subjected to non-crystallographic symmetry restraints, provides independent validation of the structure analysis. The active site in each subunit contains four manganese ions and two phosphates. The manganese ions are coordinated by the side chains of aspartate and glutamate residues. The phosphate groups, which were identified on the basis of their local stereochemistry, interact either directly or via water molecules with manganese ions and lysine, arginine, and tyrosine side chains. The phosphates are bridged by two of the manganese ions. The outer phosphate is exposed to solvent. The inner phosphate is surrounded by all four manganese ions. The ion-binding sites are related to the order of binding previously established from kinetic studies. A hypothesis for the transition state of the catalytic reaction is put forward.

    Related Citations: 
    • Investigations of the Metal Ion-Binding Sites of Yeast Inorganic Pyrophosphatase
      Knight, W.B.,Dunaway-Mariano, D.,Ransom, S.C.,Villafranca, J.J.
      (1984) J.Biol.Chem. 259: 2886
    • Structure of Inorganic Pyrophosphatase from E. Coli and its Complex with a Mn2+ Ion at 2.2 Angstroms Resolution
      Harutyunyan, E.H.,Oganessyan, V.Yu.,Oganessyan, N.N.,Terzyan, S.S.,Popov, A.N.,Rubinskiy, S.V.,Vainshtein, B.K.,Nazarova, T.I.,Kurilova, S.A.,Vorobyova, N.N.,Avaeva, S.M.
      (1996) Crystallography reports 41: 84
    • Crystal Structure of Mnpi Complex of Yeast Inorganic Pyrophosphatase at 2.35 Angstroms Resolution (Russian)
      Chirgadze, N.Yu.,Kuranova, I.P.,Nevskaya, N.A.,Teplyakov, A.V.,Wilson, K.S.,Strokopytov, B.N.,Harutyunyan, E.H.,Hohne, W.E.
      (1991) Kristallografiya 36: 128
    • Inorganic Pyrophosphatase from Yeast at 3 A Resolution (Russian)
      Terzyan, S.S.,Voronova, A.A.,Smirnova, E.A.,Kuranova, I.P.,Nekrasov, Yu.V.,Harutyunyan, E.G.,Vainshtein, B.K.,Hohne, W.,Hansen, G.
      (1984) Bioorg.Khim. 10: 1469
    • The Structure of E.Coli Soluble Inorganic Pyrophosphatase at 2.7 A Resolution
      Kankare, J.,Neal, G.S.,Salminen, T.,Glumhoff, T.,Cooperman, B.S.,Lahti, R.,Goldman, A.
      (1994) Protein Eng. 7: 823
    • The Growing of Crystals of Inorganic Pyrophosphatase from Yeast with Metal Ions and Phosphate (Russian)
      Kuranova, I.P.,Smirnova, E.A.,Chirgadze, N.Yu.
      (1990) Kristallografiya 35: 1581
    • New Crystal Forms of Escherichia Coli and Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatases
      Heikineimo, P.,Salminen, T.,Lahti, R.,Cooperman, B.,Goldman, A.
      (1995) Acta Crystallogr.,Sect.D 51: 399
    • A Conformational Hypothesis of the Trans-Ligation of Metals which Activate Pyrophosphatase and Related Enzymes (Russian)
      Kuranova, I.P.,Sokolov, V.I.
      (1986) Bioorg.Khim. 12: 749
    • Crystal Structure of Inorganic Pyrophosphatase from Thermus Thermophilus
      Teplyakov, A.,Obmolova, G.,Wilson, K.S.,Ishii, K.,Kaji, H.,Samejima, T.,Kuranova, I.
      (1994) Protein Sci. 3: 1098
    • Two Pathways of Pyrophosphate Hydrolysis and Synthesis by Yeast Inorganic Pyrophosphatase
      Baykov, A.A.,Shestakov, A.S.
      (1992) Eur.J.Biochem. 206: 463
    • The Mechanism of Action of Yeast Inorganic Pyrophosphatase
      Cooperman, B.S.
      (1982) Methods Enzymol. 87: 526
    • Yeast Inorganic Pyrophosphatase: Studies on Metal Binding
      Baykov, A.A.,Avaeva, S.M.
      (1974) Eur.J.Biochem. 47: 57

    Organizational Affiliation

    Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A, B
286Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: IPP1 (PPA, PPA1)
Find proteins for P00817 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00817
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on MN

Download SDF File 
Download CCD File 
A, B
 Ligand Interaction
Query on PO4

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Download CCD File 
A, B
O4 P
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.4 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 116.000α = 90.00
b = 106.200β = 90.00
c = 56.100γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other