PDBsum entry 1mt4

RNA

PDB id: 1mt4

Contents

DNA/RNA

PDB id:

1mt4

Name:

RNA

Title:

Structure of 23s ribosomal RNA hairpin 35

Structure:

23s ribosomal hairpin 35. Chain: a. Fragment: hairpin 35 from e. Coli. Engineered: yes

Source:

Synthetic: yes. Other_details: synthetic-t7 RNA transcript. Sequence from escherichia coli

NMR struc:

17 models

Authors:

I.Lebars,S.Yoshizawa,A.R.Stenholm,E.Guittet,S.Douthwaite,D.Fourmy

Key ref:

I.Lebars et al. (2003). Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII. EMBO J, 22, 183-192. PubMed id: 12514124 DOI: 10.1093/emboj/cdg022

Date:

20-Sep-02 Release date: 14-Jan-03

DNA/RNA chain

G-G-C-G-U-A-A-C-G-U-U-G-A-A-A-A-G-U-U-A-C-G-C-C 24 bases

DOI no: 10.1093/emboj/cdg022

EMBO J 22:183-192 (2003)

PubMed id: 12514124

Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII.

I.Lebars, S.Yoshizawa, A.R.Stenholm, E.Guittet, S.Douthwaite, D.Fourmy.

ABSTRACT

The bacterial rRNA methyltransferase RlmAII (formerly TlrB) contributes to resistance against tylosin-like 16-membered ring macrolide antibiotics. RlmAII was originally discovered in the tylosin-producer Streptomyces fradiae, and members of this subclass of methyltransferases have subsequently been found in other Gram-positive bacteria, including Streptococcus pneumoniae. In all cases, RlmAII methylates 23S rRNA at nucleotide G748, which is situated in a stem-loop (hairpin 35) at the macrolide binding site of the ribosome. The conformation of hairpin 35 recognized by RlmAII is shown here by NMR spectroscopy to resemble the anticodon loop of tRNA. The loop folds independently of the rest of the 23S rRNA, and is stabilized by a non-canonical G-A pair and a U-turn motif, rendering G748 accessible. Binding of S.pneumoniae RlmAII induces changes in NMR signals at specific nucleotides that are involved in the methyltransferase-RNA interaction. The conformation of hairpin 35 that interacts with RlmAII is radically different from the structure this hairpin adopts within the 50S subunit. This indicates that the hairpin undergoes major structural rearrangement upon interaction with ribosomal proteins during 50S assembly.

Selected figure(s)

Figure 5.
Figure 5 (A) View of hairpin 35 solution structure. (B) View of the crystal structure of tRNA^Phe anticodon stem -loop. All heavy atoms are displayed. Bases are colored in light blue with nitrogen and oxygen atoms in dark blue and red, respectively. Hydrogen bonds that contribute to stabilize the U-turn conformation are represented as dashed lines.

Figure 6.
Figure 6 Two different views of the hairpin 35 loop RNA indicating nucleotides involved in the interaction with RlmA^II methyltransferase. Nucleotides for which NMR signals broaden upon binding to RlmA^II are highlighted in yellow.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 183-192) copyright 2003.

Figures were selected by an automated process.