A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases

Nat Struct Biol. 1998 Nov;5(11):959-64. doi: 10.1038/2934.


A novel class of DNA-binding domains has been established from at least sixteen recently identified DNA-binding proteins. The three-dimensional structure of one of these domains, Mrf-2, has been solved using NMR methods. This structure is significantly different from known DNA-binding domain structures. The mechanism of DNA recognition by this motif has been suggested based on conserved residues, surface electrostatic potentials and chemical shift changes. This new DNA-binding motif shares structural homology with T4 RNase H, E. coli endonuclease III and Bacillus subtilis DNA polymerase I. The structural homology suggests a mechanism for substrate recognition by these enzymes.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Bacillus subtilis / enzymology
  • Bacteriophage T4 / enzymology
  • Conserved Sequence / genetics
  • Crystallography, X-Ray
  • DNA Polymerase I / chemistry*
  • DNA Repair
  • DNA Replication
  • DNA-Binding Proteins / chemistry*
  • Deoxyribonuclease (Pyrimidine Dimer)
  • Endodeoxyribonucleases / chemistry*
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Structure, Tertiary
  • Recombinant Fusion Proteins
  • Ribonuclease H / chemistry*
  • Sequence Alignment
  • Transcription Factors / chemistry*


  • DNA-Binding Proteins
  • Recombinant Fusion Proteins
  • Transcription Factors
  • DNA Polymerase I
  • Endodeoxyribonucleases
  • Deoxyribonuclease (Pyrimidine Dimer)
  • Ribonuclease H

Associated data

  • PDB/1BMY