1KQQ

Solution Structure of the Dead ringer ARID-DNA Complex

Summary for 1KQQ

• Entry DOI: 10.2210/pdb1kqq/pdb
• NMR Information: BMRB: 4334
• Descriptor: 5'-D(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3', 5'-D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3', DEAD RINGER PROTEIN (3 entities in total)
• Functional Keywords: arid, protein-dna complex, transcription-dna complex, transcription/dna
• Biological source: Drosophila melanogaster (fruit fly)
• Cellular location: Nucleus: Q24573
• Total number of polymer chains: 3
• Total formula weight: 25323.51

Authors

Iwahara, J.,Iwahara, M.,Daughdrill, G.W.,Ford, J.,Clubb, R.T. (deposition date: 2002-01-07, release date: 2002-03-06, Last modification date: 2024-05-22)

Primary citation

Iwahara, J.,Iwahara, M.,Daughdrill, G.W.,Ford, J.,Clubb, R.T.
The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA.
EMBO J., 21:1197-1209, 2002

PubMed Abstract: The AT-rich interaction domain (ARID) is a DNA-binding module found in many eukaryotic transcription factors. Using NMR spectroscopy, we have determined the first ever three-dimensional structure of an ARID--DNA complex (mol. wt 25.7 kDa) formed by Dead ringer from Drosophila melanogaster. ARIDs recognize DNA through a novel mechanism involving major groove immobilization of a large loop that connects the helices of a non-canonical helix-turn-helix motif, and through a concomitant structural rearrangement that produces stabilizing contacts from a beta-hairpin. Dead ringer's preference for AT-rich DNA originates from three positions within the ARID fold that form energetically significant contacts to an adenine-thymine base step. Amino acids that dictate binding specificity are not highly conserved, suggesting that ARIDs will bind to a range of nucleotide sequences. Extended ARIDs, found in several sequence-specific transcription factors, are distinguished by the presence of a C-terminal helix that may increase their intrinsic affinity for DNA. The prevalence of serine amino acids at all specificity determining positions suggests that ARIDs within SWI/SNF-related complexes will interact with DNA non-sequence specifically.

PubMed: 11867548
DOI: 10.1093/emboj/21.5.1197

Experimental method

SOLUTION NMR