The XXXX Runt domain at 1.25A resolution: a structural switch and specifically bound @entity2865 ions modulate DNA binding.

@entity1 @entity8087 @entity535 @entity2865 @entity17793 @entity2800 @entity1778 @entity10429 @entity5316
The evolutionarily conserved Runt homology domain is characteristic of the RUNX family of heterodimeric eukaryotic transcription factors, including @entity5316 , @entity8087 and @entity10429 . The genes for @entity5316 , also termed acute @entity2800 protein 1, @entity5316 , and its dimerization partner core-binding factor beta, @entity17793 , are essential for hematopoietic development and are together the most common targets for gene rearrangements in acute @entity1 @entity1778 . Here, we describe the crystal structure of the uncomplexed @entity5316 Runt domain at 1.25A resolution and compare its conformation to previously published structures in complex with DNA, @entity17793 or both. We find that complex formation induces significant structural rearrangements in this immunoglobulin (Ig)-like DNA-binding domain. Most pronounced is the movement of loop L11, which changes from a closed conformation in the free Runt structure to an open conformation in the @entity17793 -bound and DNA-bound forms. This transition, which we refer to as the S-switch, and accompanying structural movements that affect other parts of the Runt domain are crucial for sustained DNA binding. The closed to open transition can be induced by @entity17793 alone; suggesting that one role of @entity17793 is to trigger the S-switch and to stabilize the Runt domain in a conformation enhanced for DNA binding.A feature of the Runt domain hitherto unobserved in any Ig-like DNA-binding domain is the presence of two specifically bound @entity2865 ions. One @entity2865 ion is coordinated by @entity535 residues that make direct DNA contact. In a series of electrophoretic mobility-shift analyses, we demonstrate a @entity2865 ion concentration-dependent stimulation of the DNA-binding activity of Runt in the physiological range. A comparable DNA-binding stimulation was observed for negatively charged @entity535 residues. This suggests a regulatory mechanism of RUNX proteins through acidic @entity535 residues provided by activation domains during cooperative interaction with other transcription factors.
