Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis

Background: During the cell cycle, cells progress through four distinct phases, G1, S, G2 and M; transcriptional controls play an important role at the transition between these phases. MCB-binding factor (MBF), a transcription factor from budding yeast, binds to the so-called MCB (Mlul cell-cycle box) elements found in the promoters of many DNA synthesis genes, and activates the transcription of those at the G1 --> S phase transition, MBF is comprised of two proteins, Mbp1 and Swi6. Results: The three-dimensional structure of the N-terminal DNA-binding domain of Mbp1 has been determined by multiwavelength anomalous diffraction from crystals of the selenomethionyl variant of the protein. The structure is composed of a six-stranded beta sheet interspersed with two pairs of alpha helices. The most conserved core region among Mbp1-related transcription factors folds into a central helix-turn-helix motif with a short N-terminal beta strand and a C-terminal beta hairpin. Conclusions: Despite little sequence similarity, the structure within the core region of the Mbp1 N-terminal domain exhibits a similar fold to that of the DNA-binding domains of other proteins, such as hepatocyte nuclear factor-3 gamma and histone H5 from eukaryotes, and the prokaryotic catabolite gene activator. However, the structure outside the core region defines Mbp1 as a larger entity with substructures that stabilize and display the helix-turn-helix motif.