SNAP output for PDB entry 3t3o [SNAP web server]

PDB-id

3t3o; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase-RNA

Method

X-ray (2.5 Å)

Summary

Molecular basis for the recognition and cleavage of RNA (cugg) by the bifunctional 5'-3' exo-endoribonuclease rnase j

Reference

Dorleans A, Li de la Sierra-Gallay I, Piton J, Zig L, Gilet L, Putzer H, Condon C (2011): "Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5'-3' Exo/Endoribonuclease RNase J." Structure, 19, 1252-1261. doi: 10.1016/j.str.2011.06.018.

Abstract

RNase J is a key member of the β-CASP family of metallo-β-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 β-CASP domain to explain the enzyme's processive action.