5A0V

Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family

Summary for 5A0V

• Entry DOI: 10.2210/pdb5a0v/pdb
• Related: 5A0T
• Descriptor: RIBONUCLEASE J, 5'-R(*CP*GP*CP*CP*UP*CP)-3', ZINC ION, ... (5 entities in total)
• Functional Keywords: hydrolase-rna complex, endonuclease, exonuclease, hydrolase/rna
• Biological source: STREPTOMYCES COELICOLOR A3(2); More
• Total number of polymer chains: 4
• Total formula weight: 126531.29

Authors

Pei, X.Y.,Bralley, P.,Jones, G.H.,Luisi, B.F. (deposition date: 2015-04-23, release date: 2015-08-19, Last modification date: 2024-01-10)

Primary citation

Pei, X.Y.,Bralley, P.,Jones, G.H.,Luisi, B.F.
Linkage of Catalysis and 5' End Recognition in Ribonuclease Rnase J
Nucleic Acids Res., 43:8066-, 2015

PubMed 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.

PubMed: 26253740
DOI: 10.1093/NAR/GKV732

Experimental method

X-RAY DIFFRACTION (2.8 Å)