Substrate recognition and catalytic mechanism of 5 –3 exoribonucleases

The family of 5 -3 exoribonucleases (XRNs) plays a significant role in RNA processing, RNA turnover and decay, RNA interference, mRNA transcription, and other cellular processes. Cytoplasmic Xrn1 and nuclear Xrn2/Rat1 are observed in most eukaryotes. The structural information for Xrn1 and Rat1 is available, revealing the detailed enzymatic mechanism of these nucleases. Sequence analysis of XRNs shows 2 highly conserved regions, named CR1 and CR2, which form a single domain. An additional C-terminal region containing 510 residues is only found in Xrn1. Structural analysis showed that CR1 has homology with the FEN superfamily of endonucleases, while CR2 blocks substrate penetration to the active site. Therefore, XRNs are exclusive exoribonucleases. This review summarizes our current understanding of these enzymes, focusing on their crystal structures, substrate recognition, selectivity and processivity.