Enzyme Architecture: Erection of Active Orotidine 5'-Monophosphate Decarboxylase by Substrate-Induced Conformational Changes

J Am Chem Soc. 2017 Nov 15;139(45):16048-16051. doi: 10.1021/jacs.7b08897. Epub 2017 Nov 1.

Abstract

Orotidine 5'-monophosphate decarboxylase (OMPDC) catalyzes the decarboxylation of 5-fluoroorotate (FO) with kcat/Km = 1.4 × 10-7 M-1 s-1. Combining this and related kinetic parameters shows that the 31 kcal/mol stabilization of the transition state for decarboxylation of OMP provided by OMPDC represents the sum of 11.8 and 10.6 kcal/mol stabilization by the substrate phosphodianion and the ribosyl ring, respectively, and an 8.6 kcal/mol stabilization from the orotate ring. The transition state for OMPDC-catalyzed decarboxylation of FO is stabilized by 5.2, 7.2, and 9.0 kcal/mol, respectively, by 1.0 M phosphite dianion, d-glycerol 3-phosphate and d-erythritol 4-phosphate. The stabilization is due to the utilization of binding interactions of the substrate fragments to drive an enzyme conformational change, which locks the orotate ring of the whole substrate, or the substrate pieces in a caged complex. We propose that enzyme-activation is a possible, and perhaps probable, consequence of any substrate-induced enzyme conformational change.

Publication types

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

MeSH terms

  • Biocatalysis
  • Kinetics
  • Models, Molecular
  • Molecular Conformation
  • Orotic Acid / analogs & derivatives*
  • Orotic Acid / chemistry
  • Orotic Acid / metabolism
  • Orotidine-5'-Phosphate Decarboxylase / chemistry
  • Orotidine-5'-Phosphate Decarboxylase / metabolism*
  • Substrate Specificity

Substances

  • Orotic Acid
  • 5-fluoroorotic acid
  • Orotidine-5'-Phosphate Decarboxylase