Determination of the solution structure of the consensus DNA binding site for the yeast cell-cycle transcription factor Mbp1

In budding yeast, Saccharomyces cerevisiae, a complex of Swi4 and Mbp1 mediates transcriptional activation of many genes during G1-S transition of the cell-cycle. The three-dimensional structure of the consensus binding sequence d(CTTACGCGTCATTG)·d(CAATGACGCGTAAG) has been determined in solution using NMR and rMDs calculation to investigate conformational changes due to complex formation with DNA-binding domain of the Mbp1 protein. 346 distance, 188 torsion angle and residual dipolar coupling restraints were used with Insight II and Xplor-NIH programs to obtain final structures. The Insight and Xplor-NIH structures refined to a mean RMSD 1.46 +/- .69A and 1.26 +/- 0.26A respectively. Both structures belong to the B family of DNA. The global geometry of the structure was significantly improved by incorporation of residual dipolar couplings. The analysis of helical parameters indicates the purine/pyrimidine alternation of the consensus binding site.; In the model structure of the Mbpl-DNA complex, the interaction surface includes contacts in the major groove between residues of the Mbp1 recognition helix and the DNA consensus sequence, as well as interactions of the wing, C-terminal tail with the minor groove and phosphodiester backbone of the DNA. The extended binding surface of the protein leads to unwinding and bending of the DNA in the complex, rather than conformational changes of protein, with the exception of some ordering of the tail region. The Mbp1-DNA complex model provides insight into the process of recognition and it is consistent with experimental results and previously reported data.