Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID)

EMBO J. 1999 Nov 1;18(21):6084-94. doi: 10.1093/emboj/18.21.6084.


The Dead ringer protein from Drosophila melanogaster is a transcriptional regulatory protein required for early embryonic development. It is the founding member of a large family of DNA binding proteins that interact with DNA through a highly conserved domain called the AT-rich interaction domain (ARID). The solution structure of the Dead ringer ARID (residues Gly262-Gly398) was determined using NMR spectroscopy. The ARID forms a unique globular structure consisting of eight alpha-helices and a short two-stranded anti-parallel beta-sheet. Amino acid sequence homology indicates that ARID DNA binding proteins are partitioned into three structural classes: (i) minimal ARID proteins that consist of a core domain formed by six alpha-helices; (ii) ARID proteins that supplement the core domain with an N-terminal alpha-helix; and (iii) extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. Studies of the Dead ringer-DNA complex suggest that the major groove of DNA is recognized by a helix-turn-helix (HTH) motif and the adjacent minor grooves are contacted by a beta-hairpin and C-terminal alpha-helix. Primary homology suggests that all ARID-containing proteins contact DNA through the HTH and hairpin structures, but only extended-ARID proteins supplement this binding surface with a terminal helix.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • DNA-Binding Proteins / chemistry*
  • Drosophila Proteins*
  • Drosophila melanogaster / metabolism*
  • Helix-Turn-Helix Motifs
  • Homeodomain Proteins / chemistry*
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Proteins / chemistry*
  • Nucleic Acid Conformation
  • Protein Structure, Secondary
  • Sequence Alignment


  • DNA-Binding Proteins
  • Drosophila Proteins
  • Homeodomain Proteins
  • Nuclear Proteins
  • Retn protein, Drosophila

Associated data

  • PDB/1C20