Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase

EMBO J. 2002 Feb 1;21(3):427-39. doi: 10.1093/emboj/21.3.427.

Abstract

The crystal structure of the catalytic core of murine terminal deoxynucleotidyltransferase (TdT) at 2.35 A resolution reveals a typical DNA polymerase beta-like fold locked in a closed form. In addition, the structures of two different binary complexes, one with an oligonucleotide primer and the other with an incoming ddATP-Co(2+) complex, show that the substrates and the two divalent ions in the catalytic site are positioned in TdT in a manner similar to that described for the human DNA polymerase beta ternary complex, suggesting a common two metal ions mechanism of nucleotidyl transfer in these two proteins. The inability of TdT to accommodate a template strand can be explained by steric hindrance at the catalytic site caused by a long lariat-like loop, which is absent in DNA polymerase beta. However, displacement of this discriminating loop would be sufficient to unmask a number of evolutionarily conserved residues, which could then interact with a template DNA strand. The present structure can be used to model the recently discovered human polymerase mu, with which it shares 43% sequence identity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Crystallization
  • DNA Nucleotidylexotransferase / chemistry*
  • DNA Nucleotidylexotransferase / genetics
  • Humans
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation

Substances

  • DNA Nucleotidylexotransferase

Associated data

  • PDB/1KDH
  • PDB/1KEJ