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


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Authors

Pei, Xue-Yuan 
Bralley, Patricia 
Jones, George H 
Luisi, Ben F 

Abstract

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.

Description

Keywords

Bacterial Proteins, Biocatalysis, Catalytic Domain, Models, Molecular, Mutation, Protein Binding, Protein Multimerization, RNA, RNA Cleavage, Ribonucleases, Streptomyces coelicolor

Journal Title

Nucleic Acids Res

Conference Name

Journal ISSN

0305-1048
1362-4962

Volume Title

43

Publisher

Oxford University Press (OUP)
Sponsorship
Wellcome Trust (076846/Z/05/A)
Wellcome Trust (076846/Z/05/B)
B.F.L. and X.Y.P. are supported by the Wellcome Trust.