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Conformational variability of the N-terminal helix in the structure of ribosomal protein S15
W M Clemons1, C Davies, S W White
1Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
Background:
Ribosomal protein S15 is a primary RNA-binding protein that binds to the central domain of 16S rRNA. S15 also regulates its own synthesis by binding to its own mRNA. The binding sites for S15 on both mRNA and rRNA have been narrowed down to less than a hundred nucleotides each, making the protein an attractive candidate for the study of protein-RNA interactions.
Results:
The crystal structure of S15 from Bacillus stearothermophilus has been solved to 2.1 A resolution. The structure consists of four alpha helices. Three of these helices form the core of the protein, while the N-terminal helix protrudes out from the body of the molecule to make contacts with a neighboring molecule in the crystal lattice. S15 contains a large conserved patch of basic residues which could provide a site for binding 16S rRNA.
Conclusions:
The conformation of the N-terminal alpha helix is quite different from that reported in a recent NMR structure of S15 from Thermus thermophilus. The intermolecular contacts that this alpha helix makes with a neighboring molecule in the crystal, however, closely resemble the intramolecular contacts that occur in the NMR structure. This conformational variability of the N-terminal helix has implications for the range of possible S15-RNA interactions. A large, conserved basic patch at one end of S15 and a cluster of conserved but exposed aromatic residues at the other end provide two possible RNA-binding sites on S15.
Insights
Ribosomal protein S15
Area of Science:
- Structural Biology
- Molecular Biology
- Biochemistry
Background:
- Ribosomal protein S15 (S15) is a key RNA-binding protein involved in rRNA and mRNA interactions.
- S15 regulates its own synthesis by binding to its mRNA.
- Specific binding sites for S15 on rRNA and mRNA are localized to under 100 nucleotides.
Purpose of the Study:
- To determine the crystal structure of ribosomal protein S15.
- To investigate potential RNA-binding sites on S15.
- To compare the structure of S15 with existing NMR data.
Main Methods:
- X-ray crystallography to solve the crystal structure of S15 from Bacillus stearothermophilus to 2.1 A resolution.
Main Results:
- The crystal structure reveals S15 comprises four alpha helices, with three forming the core.
- A conserved patch of basic residues is identified as a potential rRNA binding site.
- The N-terminal alpha helix shows conformational variability and forms intermolecular contacts in the crystal.
Conclusions:
- The N-terminal helix conformation differs from NMR structures, suggesting flexibility.
- Intermolecular contacts in the crystal mimic intramolecular interactions seen in NMR.
- Two potential RNA-binding sites exist: a basic patch and a cluster of aromatic residues.