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Updated: Mar 14, 2026
DNAzyme-dependent Analysis of rRNA 2’-O-Methylation
Published on: September 16, 2019
Structural Insights into the Methylation of C1402 in 16S rRNA by Methyltransferase RsmI
Mohan Zhao1, Heng Zhang1, Guangfeng Liu2
1Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
Abstract:
RsmI and RsmH are conserved S-Adenosylmethionine (AdoMet)-dependent methyltransferases (MTases) that are responsible for the 2'-O-methylation and N4-methylation of C1402 in bacterial 16S rRNA, respectively. Methylation of m4Cm1402 plays a role in fine-tuning the shape and functions of the P-site to increase the decoding fidelity, and was recently found to contribute to the virulence of Staphylococcus aureus in host animals. Here we report the 2.20-Å crystal structure of homodimeric RsmI from Escherichia coli in complex with the cofactor AdoMet. RsmI consists of an N-terminal putative RNA-binding domain (NTD) and a C-terminal catalytic domain (CTD) with a Rossmann-like fold, and belongs to the class III MTase family. AdoMet is specifically bound into a negatively charged deep pocket formed by both domains by making extensive contacts. Structure-based mutagenesis and isothermal titration calorimetry (ITC) assays revealed Asp100 and Ala124 are vital for AdoMet-binding. Although the overall fold of RsmI shows remarkable similarities to the characterized MTases involved in vitamin B12 biosynthesis, it exhibits a distinct charge distribution especially around the AdoMet-binding pocket because of different substrate specificity. The docking model of RsmI-AdoMet-RNA ternary complex suggested a possible base-flipping mechanism of the substrate RNA that has been observed in several known RNA MTases. Our structural and biochemical studies provide novel insights into the catalytic mechanism of C1402 methylation in 16S rRNA.
Insights
Researchers determined the crystal structure of RsmI, an S-Adenosylmethionine-dependent methyltransferase crucial for bacterial 16S rRNA modification. This structure reveals key interactions for cofactor binding and provides insights into the methylation mechanism.
Area of Science:
- Molecular Biology
- Structural Biology
- Biochemistry
Background:
- RsmI and RsmH are methyltransferases (MTases) responsible for modifying bacterial 16S rRNA.
- C1402 methylation by RsmI influences ribosomal P-site function and bacterial virulence.
Purpose of the Study:
- To elucidate the structure of RsmI and its interaction with the cofactor S-Adenosylmethionine (AdoMet).
- To understand the catalytic mechanism of C1402 methylation in 16S rRNA.
Main Methods:
- X-ray crystallography (2.20-Å resolution)
- Structure-based mutagenesis
- Isothermal titration calorimetry (ITC)
- Molecular docking
Main Results:
- The homodimeric RsmI structure reveals an N-terminal RNA-binding domain and a C-terminal catalytic domain.
- AdoMet binds in a deep, negatively charged pocket, with Asp100 and Ala124 identified as critical for binding.
- RsmI shares structural similarities with other methyltransferases but has distinct charge distributions.
- A docking model suggests a base-flipping mechanism for substrate RNA binding.
Conclusions:
- The study provides novel structural and biochemical insights into the RsmI-AdoMet complex.
- Understanding RsmI's mechanism can inform research on bacterial 16S rRNA modification and virulence.
