7Y7O

Crystal structure of metallo-endoribonuclease YbeY from Staphylococcus aureus

Summary for 7Y7O

• Entry DOI: 10.2210/pdb7y7o/pdb
• Descriptor: Endoribonuclease YbeY, ZINC ION, CITRIC ACID, ... (4 entities in total)
• Functional Keywords: rna, endoribonuclease, metalloprotein, zinc, hydrolase
• Biological source: Staphylococcus aureus subsp. aureus Mu50
• Total number of polymer chains: 1
• Total formula weight: 19321.46

Authors

Lee, J.,Ha, N.-C. (deposition date: 2022-06-22, release date: 2023-03-08, Last modification date: 2024-05-29)

Primary citation

Lee, J.,Jo, I.,Kwon, A.R.,Ha, N.C.
Crystal Structure of the Metallo-Endoribonuclease YbeY from Staphylococcus aureus.
J Microbiol Biotechnol., 33:28-34, 2023

PubMed Abstract: 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 at a resolution of 1.9 Å 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.

PubMed: 36457189
DOI: 10.4014/jmb.2209.09019

Experimental method

X-RAY DIFFRACTION (1.9 Å)