Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5′-3′ Exo/Endoribonuclease RNase J

RNase J is a key member of the beta-CASP family of metallo-beta-lactamases involved in the maturation and turnover of RNAs in prokaryotes. The B. subtilis enzyme possesses both 5'-3' exoribonucleolytic and endonucleolytic activity, an unusual property for a ribonuclease. Here, we present the crystal structure of T. thermophilus RNase J bound to a 4 nucleotide RNA. The structure reveals an RNA-binding channel that illustrates how the enzyme functions in 5'-3' exoribonucleolytic mode and how it can function as an endonuclease. A second, negatively charged tunnel leads from the active site, and is ideally located to evacuate the cleaved nucleotide in 5'-3' exonucleolytic mode. We show that B. subtilis RNase J1, which shows processive behavior on long RNAs, behaves distributively for substrates less than 5 nucleotides in length. We propose a model involving the binding of the RNA to the surface of the beta-CASP domain to explain the enzyme's processive action.