DNA Recognition by the RUNX1 Transcription Factor Is Mediated by an Allosteric Transition in the RUNT Domain and by DNA Bending

• Published in: Structure (London) 2002-10, Vol.10 (10), p.1395-1407
• Main Authors: Bartfeld, Deborah, Shimon, Linda, Couture, Graeme C., Rabinovich, Dov, Frolow, Felix, Levanon, Ditsa, Groner, Yoram, Shakked, Zippora
• Format: Article
• Language: English
• Subjects: Allosteric Regulation; allosteric transition; Amino Acid Sequence; Core Binding Factor Alpha 2 Subunit; crystal structure; Crystallography, X-Ray; DNA - chemistry; DNA - metabolism; DNA conformation; DNA-Binding Proteins - metabolism; gene regulation; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Proto-Oncogene Proteins; RUNX1 Runt domain; Transcription Factors - metabolism
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/S0969-2126(02)00853-5

The Runt domain proteins are transcription regulators of major developmental pathways. Here we present the crystal structures of the Runt domain (RD) of the human protein RUNX1 and its DNA binding site in their free states and compare them with the published crystal structures of RD bound to DNA and to the partner protein CBFβ. We demonstrate that (1) RD undergoes an allosteric transition upon DNA binding, which is further stabilized by CBFβ, and that (2) the free DNA target adopts a bent-helical conformation compatible with that of the complex. These findings elucidate the mechanism by which CBFβ enhances RD binding to DNA as well as the role of the intrinsic conformation of the DNA target in the recognition process.