The evolutionarily conserved Runt homology domain is characteristic of the RUNX family of heterodimeric eukaryotic
transcription factors, including RUNX1, RUNX2 and RUNX3. The genes for RUNX1, also termed
acute myeloid leukemia protein 1, AML1, and its dimerization partner
core-binding factor beta, CBFbeta, are essential for hematopoietic development and are together the most common targets for gene rearrangements in acute human
leukemias. Here, we describe the crystal structure of the uncomplexed RUNX1 Runt domain at 1.25A resolution and compare its conformation to previously published structures in complex with
DNA, CBFbeta 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 CBFbeta-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 CBFbeta alone; suggesting that one role of CBFbeta 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
chloride ions. One
chloride ion is coordinated by
amino acid residues that make direct
DNA contact. In a series of electrophoretic mobility-shift analyses, we demonstrate a
chloride 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
amino acid residues. This suggests a regulatory mechanism of
RUNX proteins through
acidic amino acid residues provided by activation domains during cooperative interaction with other
transcription factors.