The structural basis for pyrophosphatase catalysis

Structure. 1996 Dec 15;4(12):1491-508. doi: 10.1016/s0969-2126(96)00155-4.


Background: Soluble inorganic pyrophosphatase (PPase), an essential enzyme central to phosphorus metabolism, catalyzes the hydrolysis of the phosphoanhydride bond in inorganic pyrophosphate. Catalysis requires divalent metal ions which affect the apparent pKas of the essential general acid and base on the enzyme, and the pKa of the substrate. Three to five metal ions are required for maximal activity, depending on pH and enzyme source. A detailed understanding of catalysis would aid both in understanding the nature of biological mechanisms of phosphoryl transfer, and in understanding the role of divalent cations. Without a high-resolution complex structure such a model has previously been unobtainable.

Results: We report the first two high-resolution structures of yeast PPase, at 2.2 and 2.0 A resolution with R factors of around 17%. One structure contains the two activating metal ions; the other, the product (MnPi)2 as well. The latter structure shows an extensive network of hydrogen bond and metal ion interactions that account for virtually every lone pair on the product phosphates. It also contains a water molecule/hydroxide ion bridging two metal ions and, uniquely, a phosphate bound to four Mn2+ ions.

Conclusions: Our structure-based model of the PPase mechanism posits that the nucleophile is the hydroxide ion mentioned above. This aspect of the mechanism is formally analogous to the "two-metal ion' mechanism of alkaline phosphatase, exonucleases and polymerases. A third metal ion coordinates another water molecule that is probably the required general acid. Extensive Lewis acid coordination and hydrogen bonds provide charge shielding of the electrophile and lower the pKa of the leaving group. This "three-metal ion' mechanism is in detail different from that of other phosphoryl transfer enzymes, presumably reflecting how ancient the reaction is.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alkaline Phosphatase / chemistry
  • Binding Sites
  • Crystallography, X-Ray
  • DNA-Directed DNA Polymerase / chemistry
  • Dimerization
  • Diphosphates / metabolism
  • Hydrogen Bonding
  • Hydroxides / chemistry
  • Hydroxides / metabolism
  • Inorganic Pyrophosphatase
  • Manganese / chemistry
  • Manganese / metabolism
  • Models, Chemical
  • Models, Molecular
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Pyrophosphatases / chemistry*
  • Pyrophosphatases / metabolism
  • Saccharomyces cerevisiae / enzymology*


  • Diphosphates
  • Hydroxides
  • Manganese
  • hydroxide ion
  • DNA-Directed DNA Polymerase
  • Alkaline Phosphatase
  • Pyrophosphatases
  • Inorganic Pyrophosphatase