Crystal structure and functional analysis of the Rap1 C‐terminus: Insights into transcriptional silencing and telomere length regulation

The Saccharomyces cerevisiae protein Rap1 plays an important role in transcriptional silencing at the mating‐type loci and telomeres and in telomere length regulation. At both the mating‐type loci and the telomeres, Rap1 tethers a complex of silent information regulator (Sir) proteins through interactions with Sir3 and Sir4. At the telomeres, Rap1 also tethers Rif1 and Rif2, proteins which act as negative regulators of telomere length. Yeast two‐hybrid studies indicate that Rap1 mediates all of these protein‐protein interactions through a C‐terminal domain. We have determined a 1.85 Å crystal structure of this C‐terminal Rap1 protein‐interaction domain by single‐wavelength anomalous dispersion (SAD). The structure consists of seven helices connected by well‐ordered loops; comparisons with known structures using Dali found no structures with significant homology. Through in vivo functional studies, we have identified surface mutations that disrupt transcriptional silencing or cause an increase in telomere length. Mapping these mutations onto our structure reveals potential interaction surfaces for the Sir and Rif proteins.