How the multifunctional yeast Rap1p discriminates between DNA target sites: a crystallographic analysis

Rap1p from Saccharomyces cerevisiae is a multifunctional, sequence-specific, DNA-binding protein involved in diverse cellular processes such as transcriptional activation and silencing, and is an essential factor for telomere length regulation and maintenance. In order to understand how Rap1p discriminates between its different DNA-binding sites, we have determined the crystal structure of the DNA-binding domain of the Rap1p (Rap1pDBD) in complex with two different DNA-binding sites. The first DNA sequence is the HMRE binding site found at silencers, which contains four base-pair substitutions in comparison to the telomeric binding site present in our earlier crystal structure of the Rap1pDBD-TeloA complex. The second complex contains an alternative telomeric binding site, TeloS, in which two half-sites are spaced closer together than in the TeloA complex. The determination of these structures was complicated by the presence of merohedral twinning in the crystals. Through identification of the twinning operator and determination of the twin fraction of the crystals, we were able to deconvolute the twinned intensities into their untwinned components, and to calculate electron density maps for both complexes. The structural information shows that the two domains present in the Rap1pDBD bind to these two biologically relevant binding sites through subtle side-chain movements at the protein-DNA interface, rather than through global domain rearrangements.