A Novel Mechanism of Sugar Selection Utilized by a Human X-family DNA Polymerase

J Mol Biol. 2010 Jan 15;395(2):282-90. doi: 10.1016/j.jmb.2009.11.003. Epub 2009 Nov 6.

Abstract

During DNA synthesis, most DNA polymerases and reverse transcriptases select against ribonucleotides via a steric clash between the ribose 2'-hydroxyl group and the bulky side chain of an active-site residue. In this study, we demonstrated that human DNA polymerase lambda used a novel sugar selection mechanism to discriminate against ribonucleotides, whereby the ribose 2'-hydroxyl group was excluded mostly by a backbone segment and slightly by the side chain of Y505. Such steric clash was further demonstrated to be dependent on the size and orientation of the substituent covalently attached at the ribonucleotide C2'-position.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Allosteric Regulation
  • Amino Acid Sequence
  • Amino Acid Substitution
  • Base Sequence
  • Catalytic Domain / genetics
  • Conserved Sequence
  • DNA / genetics
  • DNA / metabolism
  • DNA Polymerase beta / chemistry*
  • DNA Polymerase beta / genetics
  • DNA Polymerase beta / metabolism*
  • Humans
  • In Vitro Techniques
  • Kinetics
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Ribonucleotides / chemistry
  • Ribonucleotides / metabolism
  • Sequence Homology, Amino Acid
  • Substrate Specificity

Substances

  • Recombinant Proteins
  • Ribonucleotides
  • DNA
  • DNA Polymerase beta
  • DNA polymerase beta2