Catalysis by orotidine 5'-monophosphate decarboxylase: effect of 5-fluoro and 4'-substituents on the decarboxylation of two-part substrates

Biochemistry. 2013 Jan 22;52(3):537-46. doi: 10.1021/bi301650d. Epub 2013 Jan 11.

Abstract

The syntheses of two novel truncated analogs of the natural substrate orotidine 5'-monophosphate (OMP) for orotidine 5'-monophosphate decarboxylase (OMPDC) with enhanced reactivity toward decarboxylation are reported: 1-(β-d-erythrofuranosyl)-5-fluoroorotic acid (FEO) and 5'-deoxy-5-fluoroorotidine (5'-dFO). A comparison of the second-order rate constants for the OMPDC-catalyzed decarboxylations of FEO (10 M⁻¹ s⁻¹) and 1-(β-d-erythrofuranosyl)orotic acid (EO, 0.026 M⁻¹ s⁻¹) shows that the vinyl carbanion-like transition state is stabilized by 3.5 kcal/mol by interactions with the 5-F substituent of FEO. The OMPDC-catalyzed decarboxylations of FEO and EO are both activated by exogenous phosphite dianion (HPO₃²⁻), but the 5-F substituent results in only a 0.8 kcal stabilization of the transition state for the phosphite-activated reaction of FEO. This provides strong evidence that the phosphite-activated OMPDC-catalyzed reaction of FEO is not limited by the chemical step of decarboxylation of the enzyme-bound substrate. Evidence is presented that there is a change in the rate-limiting step from the chemical step of decarboxylation for the phosphite-activated reaction of EO, to closure of the phosphate gripper loop and an enzyme conformational change at the ternary E•FEO•HPO₃²⁻ complex for the reaction of FEO. The 4'-CH₃ and 4'-CH₂OH groups of 5'-dFO and orotidine, respectively, result in identical destabilizations of the transition state for the unactivated decarboxylation of 2.9 kcal/mol. By contrast, the 4'-CH₃ group of 5'-dFO and the 4'-CH₂OH group of orotidine result in very different 4.7 and 8.3 kcal/mol destabilizations of the transition state for the phosphite-activated decarboxylation. Here, the destabilizing effect of the 4'-CH₃ substituent at 5'-dFO is masked by the rate-limiting conformational change that depresses the third-order rate constant for the phosphite-activated reaction of the parent substrate FEO.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biocatalysis
  • Buffers
  • Decarboxylation
  • Enzyme Activation
  • Enzyme Stability
  • Kinetics
  • Mutant Proteins / metabolism
  • Orotic Acid / analogs & derivatives*
  • Orotic Acid / chemical synthesis
  • Orotic Acid / chemistry
  • Orotic Acid / metabolism
  • Orotidine-5'-Phosphate Decarboxylase / genetics
  • Orotidine-5'-Phosphate Decarboxylase / metabolism*
  • Osmolar Concentration
  • Phosphites / chemistry
  • Protein Conformation
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Substrate Specificity
  • Uridine / analogs & derivatives
  • Uridine / chemistry
  • Uridine / metabolism
  • Uridine Monophosphate / analogs & derivatives
  • Uridine Monophosphate / chemistry
  • Uridine Monophosphate / metabolism

Substances

  • 1-(beta-D-erythrofuranosyl)-5-fluoroorotic acid
  • 1-(beta-D-erythrofuranosyl)orotic acid
  • 5'-deoxy-5-fluoroorotidine
  • Buffers
  • Mutant Proteins
  • Phosphites
  • Saccharomyces cerevisiae Proteins
  • orotidylic acid
  • Orotic Acid
  • orotidine
  • Uridine Monophosphate
  • Orotidine-5'-Phosphate Decarboxylase
  • Uridine