In vivo reshaping the catalytic site of nucleoside 2'-deoxyribosyltransferase for dideoxy- and didehydronucleosides via a single amino acid substitution

J Biol Chem. 2008 Jul 18;283(29):20053-9. doi: 10.1074/jbc.M802706200. Epub 2008 May 16.

Abstract

Nucleoside 2'-deoxyribosyltransferases catalyze the transfer of 2-deoxyribose between bases and have been widely used as biocatalysts to synthesize a variety of nucleoside analogs. The genes encoding nucleoside 2'-deoxyribosyltransferase (ndt) from Lactobacillus leichmannii and Lactobacillus fermentum underwent random mutagenesis to select variants specialized for the synthesis of 2',3'-dideoxynucleosides. An Escherichia coli strain, auxotrophic for uracil and unable to use 2',3'-dideoxyuridine, cytosine, and 2',3'-dideoxycytidine as a source of uracil was constructed. Randomly mutated lactobacilli ndt libraries from two species, L. leichmannii and L. fermentum, were screened for the production of uracil with 2',3'-dideoxyuridine as a source of uracil. Several mutants suitable for the synthesis of 2',3'-dideoxynucleosides were isolated. The nucleotide sequence of the corresponding genes revealed a single mutation (G --> A transition) leading to the substitution of a small aliphatic amino acid by a nucleophilic one, A15T (L. fermentum) or G9S (L. leichmannii), respectively. We concluded that the "adaptation" of the nucleoside 2'-deoxyribosyltransferase activity to 2,3-dideoxyribosyl transfer requires an additional hydroxyl group on a key amino acid side chain of the protein to overcome the absence of such a group in the corresponding substrate. The evolved proteins also display significantly improved nucleoside 2',3'-didehydro-2',3'-dideoxyribosyltransferase activity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Substitution
  • Catalytic Domain
  • Hydrogen / chemistry*
  • Kinetics
  • Lactobacillus leichmannii / genetics
  • Lactobacillus leichmannii / metabolism
  • Limosilactobacillus fermentum / genetics
  • Limosilactobacillus fermentum / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation / genetics
  • Nucleosides / chemistry*
  • Nucleosides / metabolism*
  • Oxygen / chemistry*
  • Pentosyltransferases / chemistry
  • Pentosyltransferases / genetics
  • Pentosyltransferases / metabolism*
  • Protein Engineering
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Substrate Specificity

Substances

  • Nucleosides
  • Hydrogen
  • Pentosyltransferases
  • nucleoside deoxyribosyltransferase
  • Oxygen