Every mature RNA is derived from a primary transcript by one or more essential RNA-processing events. These events, which include cleavage, ligation, and modification, are carried out by a diverse set of processes. In all cases, these processes exhibit exquisite specificity for their RNA substrates, altering only one or a few defined chemical bonds in limited sets of RNA within total cellular RNA molecules. These processing events are intimately related to the structure of RNA–enzyme complexes, as the RNA–protein interactions create the transition states required for chemical reactions.

The pathway of nuclear tRNA splicing is best characterized in Saccharomyces cerevisiae, in which tRNA introns are removed via the stepwise action of three essential enzymes: an endonuclease, a ligase, and a 2’-phosphotransferase (Figure 1). We are interested in the structure and function of these enzymes. The specific questions that we would like to address include (1) how do the enzymes recognize their RNA substrates and (2) how do the enzymes catalyze RNA cleavage and joining reactions.

Figure 2 illustrates that all endonucleases known so far comprise four units, two are catalytic and two are structural. The precise assembly of the four units confers specificity recognition and cleavage of RNA. We are using structural, biochemical, and biophysical techniques to learn how these enzymes are assembled and how they cleave RNA.