Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region

Nucleic Acids Res. 2009 Aug;37(14):4642-56. doi: 10.1093/nar/gkp460. Epub 2009 Jun 5.

Abstract

Terminal deoxynucleotidyltransferase (Tdt) and DNA polymerase mu (pol mu) are two eukaryotic highly similar proteins involved in DNA processing and repair. Despite their high sequence identity, they differ widely in their activity: pol mu has a templated polymerase activity, whereas Tdt has a non-templated one. Loop1, first described when the Tdt structure was solved, has been invoked as the major structural determinant of this difference. Here we describe attempts to transform Tdt into pol mu with the minimal number of mutations in and around Loop1. First we describe the effect of mutations on six different positions chosen to destabilize Tdt Loop1 structure, either by alanine substitution or by deletion; they result at most in a reduction of Tdt activity, but adding Co(++) restores most of this Tdt activity. However, a deletion of the entire Loop1 as in pol lambda does confer a limited template-dependent polymerase behavior to Tdt while a chimera bearing an extended pol mu Loop1 reproduces pol mu behavior. Finally, 16 additional substitutions are reported, targeted at the two so-called 'sequence determinant' regions located just after Loop1 or underneath. Among them, the single-point mutant F401A displays a sequence-specific replicative polymerase phenotype that is stable upon Co(++) addition. These results are discussed in light of the available crystal structures.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Cobalt / chemistry
  • Crystallography
  • DNA Nucleotidylexotransferase / chemistry*
  • DNA Nucleotidylexotransferase / genetics*
  • DNA Nucleotidylexotransferase / metabolism
  • DNA Polymerase beta / chemistry
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism
  • Molecular Sequence Data
  • Mutation*
  • Nucleotides / metabolism
  • Point Mutation
  • Protein Conformation
  • Sequence Deletion
  • Templates, Genetic

Substances

  • Nucleotides
  • Cobalt
  • DNA Polymerase beta
  • DNA polymerase beta2
  • DNA polymerase mu
  • DNA Nucleotidylexotransferase
  • DNA-Directed DNA Polymerase
  • cobaltous chloride