Abstract

The maturation and stability of RNA transcripts is controlled by a combination of endo- and exoRNases. RNase J is unique, as it combines an RNase E–like endoribonucleolytic and a 5|[prime]|-to-3|[prime]| exoribonucleolytic activity in a single polypeptide. The structural basis for this dual activity is unknown. Here we report the crystal structures of Thermus thermophilus RNase J and its complex with uridine 5|[prime]|-monophosphate. A binding pocket coordinating the phosphate and base moieties of the nucleotide in the vicinity of the catalytic center provide a rationale for the 5|[prime]|-monophosphate–dependent 5|[prime]|-to-3|[prime]| exoribonucleolytic activity. We show that this dependence is strict; an initial 5|[prime]|-PPP transcript cannot be degraded exonucleolytically from the 5|[prime]|-end. Our results suggest that RNase J might switch promptly from endo- to exonucleolytic mode on the same RNA, a property that has important implications for RNA metabolism in numerous prokaryotic organisms and plant organelles containing RNase J orthologs.