Crystal Structure of the Metallo- Endoribonuclease YbeY from Staphylococcus aureus

Endoribonuclease YbeY is specific to the single-stranded RNA of ribosomal RNAs and small RNAs. This enzyme is essential for the maturation and quality control of ribosomal RNA in a wide range of bacteria and for virulence in some pathogenic bacteria. In this study, we determined the crystal structure of YbeY from Staphylococcus aureus at a resolution of 1.9 angstrom in the presence of zinc chloride. The structure showed a zinc ion at the active site and two molecules of tricarboxylic acid citrate, which were also derived from the crystallization conditions. Our structure showed the zinc ion-bound local environment at the molecular level for the first time. Molecular comparisons were performed between the carboxylic moieties of citrate and the phosphate moiety of the RNA backbone, and a model of YbeY in complex with a single strand of RNA was subsequently constructed. Our findings provide molecular insights into how the YbeY enzyme recognizes single -stranded RNA in bacteria.

Automated summary

Endoribonuclease YbeY specifically targets single-stranded RNA in ribosomal RNAs and small RNAs. It plays crucial roles in the maturation and quality control of ribosomal RNA in a wide range of bacteria and in the virulence of certain pathogenic bacteria. The crystal structure of YbeY from Staphylococcus aureus was determined, revealing a zinc ion at the active site and two molecules of tricarboxylic acid citrate. Molecular comparisons and a model of YbeY in complex with a single strand of RNA were constructed, providing insights into the molecular mechanism of how the YbeY enzyme recognizes single-stranded RNA in bacteria.