Linkage of catalysis and 5' end recognition in ribonuclease RNase J

• Published in: Nucleic acids research 2015-09, Vol.43 (16), p.8066-8076
• Main Authors: Pei, Xue-Yuan, Bralley, Patricia, Jones, George H, Luisi, Ben F
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Biocatalysis; Catalytic Domain; Models, Molecular; Mutation; Protein Binding; Protein Multimerization; Ribonucleases - chemistry; Ribonucleases - genetics; RNA - chemistry; RNA Cleavage; Streptomyces coelicolor; Streptomyces coelicolor - enzymology; Structural Biology
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkv732

In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-β-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 Å and 2.80 Å resolution, respectively. These structures reveal snapshots of the enzyme cleaving substrate directionally and sequentially from the 5' terminus. In the pre-cleavage state, a water molecule is coordinated to a zinc ion pair in the active site but is imperfectly oriented to launch a nucleophilic attack on the phosphate backbone. A conformational switch is envisaged that enables the in-line positioning of the attacking water and may be facilitated by magnesium ions. Adjacent to the scissile bond, four bases are stacked in a tightly sandwiching pocket, and mutagenesis results indicate that this organization helps to drive processive exo-ribonucleolytic cleavage. Like its numerous homologues, S. coelicolor RNase J can also cleave some RNA internally, and the structural data suggest how the preference for exo- versus endo-cleavage mode is linked with recognition of the chemical status of the substrate's 5' end.