Kinetic isotope effects of nucleoside hydrolase from Escherichia coli

Biochim Biophys Acta. 2005 Aug 10;1751(2):140-9. doi: 10.1016/j.bbapap.2005.06.001.

Abstract

rihC is one of a group of three ribonucleoside hydrolases found in Escherichia coli (E. coli). The enzyme catalyzes the hydrolysis of selected nucleosides to ribose and the corresponding base. A family of Vmax/Km kinetic isotope effects using uridine labeled with stable isotopes, such as 2H, 13C, and 15N, were determined by liquid chromatography/mass spectrometry (LC/MS). The kinetic isotope effects were 1.012+/-0.006, 1.027+/-0.005, 1.134+/-0.007, 1.122+/-0.008, and 1.002+/-0.004 for [1'-13C], [1-15N], [1'-2H], [2'-2H], and [5'-2H2] uridine, respectively. A transition state based upon a bond-energy bond-order vibrational analysis (BEBOVIB) of the observed kinetic isotope effects is proposed. The main features of this transition state are activation of the heterocyclic base by protonation of/or hydrogen bonding to O2, an extensively broken C-N glycosidic bond, formation of an oxocarbenium ion in the ribose ring, C3'-exo ribose ring conformation, and almost no bond formation to the attacking nucleophile. The proposed transition state for the prokaryotic E. coli nucleoside hydrolase is compared to that of a similar enzyme isolated from Crithidia fasciculata (C. fasciculata).

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Carbon Isotopes / chemistry
  • Chromatography, High Pressure Liquid
  • Crithidia fasciculata / enzymology
  • Crithidia fasciculata / genetics
  • Deuterium / chemistry
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Escherichia coli Proteins / biosynthesis
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Isotopes / chemistry
  • Kinetics
  • Mass Spectrometry
  • Models, Molecular
  • Molecular Conformation
  • Molecular Sequence Data
  • N-Glycosyl Hydrolases / biosynthesis
  • N-Glycosyl Hydrolases / chemistry*
  • N-Glycosyl Hydrolases / genetics
  • Nitrogen Isotopes / chemistry
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / isolation & purification
  • Sequence Homology, Amino Acid
  • Uridine / chemistry

Substances

  • Carbon Isotopes
  • Escherichia coli Proteins
  • Isotopes
  • Nitrogen Isotopes
  • Recombinant Proteins
  • Deuterium
  • N-Glycosyl Hydrolases
  • RihC protein, E coli
  • Uridine