1YPP

ACID ANHYDRIDE HYDROLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

  • DOI: 10.1111/j.1432-1033.1996.0220u.x
  • Structures With Same Primary Citation

  • 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: 
    • 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) Crystallogr Rep 41: 84
    • 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 D Biol Crystallogr 51: 399
    • 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
    • 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
    • Two Pathways of Pyrophosphate Hydrolysis and Synthesis by Yeast Inorganic Pyrophosphatase
      Baykov, A.A., Shestakov, A.S.
      (1992) Eur J Biochem 206: 463
    • 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) Кристаллография 36: 128
    • 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) Кристаллография 35: 1581
    • 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
    • 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
    • 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
    • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INORGANIC PYROPHOSPHATASE
A, B
286Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.1.1
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
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116α = 90
b = 106.2β = 90
c = 56.1γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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