Crystal Structure of the Metallo-Endoribonuclease YbeY from Staphylococcus aureus
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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 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 ionbound 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 singlestranded RNA in bacteria.
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 Staphylococcus aureus 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 ionbound 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 singlestranded RNA in bacteria.
참고문헌 (19)
- Grunberg-Manago M, "Messenger RNA stability and its role in control of gene expression in bacteria and phages", Ann. Rev. Genet, 33, pp.193~227 (1999)
- Raines RT, "Ribonuclease A", Chem. Rev, 98, pp.1045~1066 (1998)
- Itoh T, , Presented at the Cold Spring Harbor Symposia on Quantitative Biology (1979)
- Jacob AI, "Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation", Mol. Cell, 49, pp.427~438 (2013)
- Vercruysse M, "Identification of YbeY-protein interactions involved in 16S rRNA maturation and stress regulation in Escherichia coli", mBio, 7, pp.e01785-16~ (2016)
- Pandey SP, "Central role for RNase YbeY in Hfq-dependent and Hfqindependent small-RNA regulation in bacteria", BMC Genomics, 15, pp.121~ (2014)
- Xia Y, "Endoribonuclease YbeY is essential for RNA processing and virulence in Pseudomonas aeruginosa", mBio, 11, pp.e00659-20~ (2020)
- Xia Y, "Ybey controls the type III and type VI secretion systems and biofilm formation through RetS in Pseudomonas aeruginosa", Appl. Environ. Microbiol, 87, pp.e02171-20~ (2021)
- Zhan C, "The ybeY protein from Escherichia coli is a metalloprotein", Acta Crystallogr. Sec. F Struct. Biol. Cryst. Commun, 61, pp.959~963 (2005)
- Babu VM, "Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing", NucleicAacids Res, 48, pp.332~348 (2020)
- Davies BW, "Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing", Mol. Microbiol, 78, pp.506~518 (2010)
- Cox EH, "Zinc-dependent protein folding", Curr. Opin. Chem. Biol, 4, pp.162~165 (2000)
- Vercruysse M, "The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing", PLoS Pathog, 10, pp.e1004175~ (2014)
- Otwinowski Z, "Processing of X-ray diffraction data collected in oscillation mode", Methods Enzymol, 276, pp.307~326 (1997)
- Adams PD, "PHENIX: a comprehensive Python-based system for macromolecular structure solution", Acta Crystallogr. Sect. D Biol. Crystallogr, 66, pp.213~221 (2010)
- Emsley P, "Coot: model-building tools for molecular graphics", Acta Crystallographica Section D: Biological Crystallography, 60, pp.2126~2132 (2004)
- Afonine PV, "Joint X-ray and neutron refinement with phenix. refine", Acta Crystallogr. Sect. D Biol. Crystallogr, 66, pp.1153~1163 (2010)
- Kang H, "Biochemical and genetic analyses of murine hepatitis virus Nsp15 endoribonuclease", J. Virol, 81, pp.13587~13597 (2007)
- Tu C, "The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3′ end of 16S rRNA", Proc. Natl. Acad. Sci. USA, 108, pp.10156~10161 (2011)