Conformational variability of the N-terminal helix in the structure of ribosomal protein S15.
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.
Clemons
W M
WM
Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
Davies
C
C
White
S W
SW
Ramakrishnan
V
V
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D017124:Conserved Sequence / Q000235:genetics; D003460:Crystallization; D018360:Crystallography, X-Ray; D001411:Geobacillus stearothermophilus / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012333:RNA, Messenger / Q000737:chemistry; D012336:RNA, Ribosomal, 16S / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry*; D012269:Ribosomal Proteins / Q000737:chemistry*; D016415:Sequence Alignment
D001426:Bacterial Proteins; D012333:RNA, Messenger; D012336:RNA, Ribosomal, 16S; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; C036004:ribosomal protein S15