We do not know the structure of the Dna2 OB domain bound to the Rpa70 DBD-A and DBD-B domains, but the OB structure in intact Dna2 is consistent with a role in protein-protein interactions, and the isolated OB domain polypeptide does not exhibit any DNA-binding in EMSA at concentrations up to 80 μM.
Originally characterized from the co-crystal structure of the glucocorticoid receptor (GR) DBD bound to an inverted-repeat 4 DNA element (GR-DBD-IR4), the D-box loop structure contains a conserved AXRND motif within the second zinc-finger of the DBD [42].
The most recent crystal structure of the DBD bound to a TeloA sequence shows that the ∼30 amino acids in the C-terminal region of the DBD (wrapping loop) fold back onto the N-terminal Myb-like domain to form a closed complex on DNA.
Furthermore, structure determinations of this DBD bound to a telomeric G strand provide a model for the very high affinity and specificity of this association (Mitton-Fry et al. 2002, 2004).
Models of Chd1-DBD bound to a 20-bp double-stranded DNA were generated using the HADDOCK web server (de Vries et al, 2010).
However, nearly half of the fragments we isolated did not contain a canonical DBE or DBE-like sequence, suggesting that the DAF-16 DBD bound to a previously unknown binding element.
The Ac-DAF-16 DBD bound to amplicons containing this element, but not individual oligos, suggesting that the new element requires surrounding sequence for DBD binding.
Two copies of the HOT1 DBD are bound to one duplex DNA that comprises two and a half 5′-TTAGGG-3′ repeats in a regular and undistorted B-form conformation (Supplementary Figure S3).
Crystallographic studies of TALEs bound to their target sequences unraveled that TALE DBD forms a right-handed superhelical assembly wrapped around B-form DNA duplex and explained specific repeat-nucleotide interactions [ 15, 23, 24].
These DNA interactions by the catalytic domain of Hin subunits bound to hix1L and hix2R augment the relatively weak interactions between the DBDs of the same subunits and Fis to stabilize the active invertasome structure.
