Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding

Nucleic Acids Res. 2014;42(16):10762-75. doi: 10.1093/nar/gku729. Epub 2014 Aug 12.

Abstract

Rad2/XPG belongs to the flap nuclease family and is responsible for a key step of the eukaryotic nucleotide excision DNA repair (NER) pathway. To elucidate the mechanism of DNA binding by Rad2/XPG, we solved crystal structures of the catalytic core of Rad2 in complex with a substrate. Rad2 utilizes three structural modules for recognition of the double-stranded portion of DNA substrate, particularly a Rad2-specific α-helix for binding the cleaved strand. The protein does not specifically recognize the single-stranded portion of the nucleic acid. Our data suggest that in contrast to related enzymes (FEN1 and EXO1), the Rad2 active site may be more accessible, which would create an exit route for substrates without a free 5' end.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Endodeoxyribonucleases / chemistry*
  • Endodeoxyribonucleases / metabolism
  • Endonucleases / genetics
  • Exodeoxyribonucleases / chemistry
  • Flap Endonucleases / chemistry
  • Models, Molecular
  • Mutation
  • Nuclear Proteins / genetics
  • Protein Binding
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Transcription Factors / genetics

Substances

  • DNA excision repair protein ERCC-5
  • DNA-Binding Proteins
  • Nuclear Proteins
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • RAD2 protein, S cerevisiae
  • DNA
  • Endodeoxyribonucleases
  • Endonucleases
  • Exodeoxyribonucleases
  • Flap Endonucleases
  • exodeoxyribonuclease I

Associated data

  • PDB/4Q0R
  • PDB/4Q0W
  • PDB/4Q0Z
  • PDB/4Q10