In Saccharomyces cerevisiae, a large complex, known as the Ccr4-Not complex, 
containing two nucleases, is responsible for mRNA deadenylation. One of these 
nucleases is called Pop2 and has been identified by similarity with PARN, a 
human poly(A) nuclease. Here, we present the crystal structure of the nuclease 
domain of Pop2 at 2.3 A resolution. The domain has the fold of the DnaQ family 
and represents the first structure of an RNase from the DEDD superfamily. 
Despite the presence of two non-canonical residues in the active site, the 
domain displays RNase activity on a broad range of RNA substrates. Site-directed 
mutagenesis of active-site residues demonstrates the intrinsic ability of the 
Pop2 RNase D domain to digest RNA. This first structure of a nuclease involved 
in the 3'-5' deadenylation of mRNA in yeast provides information for the 
understanding of the mechanism by which the Ccr4-Not complex achieves its 
functions.