Strandwise translocation of a DNA glycosylase on undamaged DNA

Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1086-91. doi: 10.1073/pnas.1111237108. Epub 2012 Jan 4.

Abstract

Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.

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

  • Crystallization
  • DNA / metabolism*
  • DNA Repair / physiology*
  • DNA-Formamidopyrimidine Glycosylase / chemistry
  • DNA-Formamidopyrimidine Glycosylase / genetics
  • DNA-Formamidopyrimidine Glycosylase / metabolism*
  • Escherichia coli
  • Geobacillus stearothermophilus / enzymology*
  • Geobacillus stearothermophilus / genetics
  • Models, Molecular*
  • Molecular Dynamics Simulation
  • Mutagenesis, Site-Directed
  • Nucleic Acid Conformation
  • Protein Conformation
  • Protein Transport / physiology
  • Synchrotrons
  • Translocation, Genetic / physiology*
  • X-Ray Diffraction

Substances

  • DNA
  • DNA-Formamidopyrimidine Glycosylase

Associated data

  • PDB/3SA
  • PDB/3SAR
  • PDB/3SAS
  • PDB/3SAU
  • PDB/3SAV
  • PDB/3SAW
  • PDB/3SBJ