The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode

Nat Struct Biol. 1997 Feb;4(2):122-32. doi: 10.1038/nsb0297-122.


The structure of a complex between the DNA binding domain of the GAGA factor (GAGA-DBD) and an oligonucleotide containing its GAGAG consensus binding site has been determined by nuclear magnetic resonance spectroscopy. The GAGA-DBD comprises a single classical Cys2-His2 zinc finger core, and an N-terminal extension containing two highly basic regions, BR1 and BR2. The zinc finger core binds in the major groove and recognizes the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. Unlike the latter, which require tandem zinc finger repeats with a minimum of two units for high affinity binding, the GAGA-DBD makes use of only a single finger complemented by BR1 and BR2. BR2 forms a helix that interacts in the major groove recognizing the last G of the consensus, while BR1 wraps around the DNA in the minor groove and recognizes the A in the fourth position of the consensus. The implications of the structure of the GAGA-DBD-DNA complex for chromatin remodelling are discussed.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Binding Sites
  • Consensus Sequence
  • DNA / chemistry*
  • DNA / metabolism
  • DNA-Binding Proteins*
  • Drosophila Proteins*
  • Homeodomain Proteins / chemistry*
  • Homeodomain Proteins / metabolism
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Oligodeoxyribonucleotides / chemistry*
  • Oligodeoxyribonucleotides / metabolism
  • Protein Conformation*
  • Protein Structure, Secondary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism


  • DNA-Binding Proteins
  • Drosophila Proteins
  • Homeodomain Proteins
  • Oligodeoxyribonucleotides
  • Recombinant Proteins
  • Transcription Factors
  • Trl protein, Drosophila
  • DNA