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A proficient enzyme

A Radzicka1, R Wolfenden

  • 1Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill 27599.

Science (New York, N.Y.)
|January 6, 1995
PubMed
Summary

Spontaneous decarboxylation of orotic acid and hydrolysis of phosphodiester bonds occur over millions of years. Enzymes dramatically accelerate these reactions, with orotidine 5'-phosphate decarboxylase showing exceptional catalytic efficiency.

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Area of Science:

  • Biochemistry
  • Chemical Kinetics
  • Molecular Biology

Background:

  • Spontaneous chemical reactions, such as orotic acid decarboxylation and phosphodiester bond hydrolysis, are fundamental processes in biological systems.
  • Understanding the rates of these uncatalyzed reactions provides a baseline for evaluating enzyme catalysis.
  • Previous studies have established slow rates for various biochemical reactions under physiological conditions.

Purpose of the Study:

  • To determine the spontaneous reaction rates of orotic acid decarboxylation and phosphodiester bond hydrolysis.
  • To compare the range of spontaneous rate constants with those of enzyme-catalyzed reactions.
  • To investigate the catalytic efficiency of orotidine 5 omino-phosphate decarboxylase.

Main Methods:

  • Orotic acid decarboxylation was studied in quartz tubes at elevated temperatures to extrapolate rates at room temperature.
  • Spontaneous hydrolysis of dimethyl phosphate was measured to determine phosphodiester bond lability.
  • Enzyme kinetics, specifically the second-order rate constant (kcat/Km) and dissociation constant (Kd), were analyzed for orotidine 5 omino-phosphate decarboxylase.

Main Results:

  • Orotic acid decarboxylation has a half-time (t1/2) of 78 million years in neutral aqueous solution at room temperature.
  • Dimethyl phosphate hydrolysis has a t1/2 of 130,000 years, indicating slow spontaneous phosphodiester bond cleavage.
  • These spontaneous rates span over 14 orders of magnitude, contrasting with the narrower 600-fold range of enzyme-catalyzed reactions.
  • Orotidine 5 omino-phosphate decarboxylase accelerates the reaction by 10(17)-fold, binding the transition state with Kd < 5 x 10(-24) M.

Conclusions:

  • Spontaneous biochemical reactions exhibit extremely long half-lives, highlighting the necessity of enzymatic catalysis for life.
  • Enzymes provide a vastly more efficient catalytic range compared to uncatalyzed reactions.
  • Orotidine 5 omino-phosphate decarboxylase represents a pinnacle of enzyme efficiency, drastically lowering activation energy and stabilizing the transition state.

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