Crystal structure of prokaryotic ribosomal protein L9:
a bi-lobed RNA-binding protein
The crystal structure of protein L9 from the Bacillus stearothermophilus ribosome has been determined at 2.8 Å resolution using X-ray diffraction methods. This primary RNA-binding protein has a highly elongated and unusual structure consisting of two separated domains joined by a long exposed α-helix. Conserved, positively charged and aromatic amino acids on the surfaces of both domains probably represent the sites of specific interactions with 23S rRNA. Comparisons with other prokaryotic L9 sequences show that while the length of the connecting α-helix is invariant, the sequence within the exposed central region is not conserved. This suggests that the α-helix has an architectural role and serves to fix the relative separation and orientation of the N- and C-terminal domains within the ribosome. The N-terminal domain has structural homology to the smaller ribosomal proteins L7/L12 and L30, and the eukaryotic RNA recognition motif (RRM).
End view of 1DIV: click to see larger image Side view of 1DIV: click to see larger image
These ribbon diagrams of ribosomal protein L9 color-ramped blue to red, N-terminus to C-terminus. The molecule contains two discrete α/ß domains joined by a long nine-turn α-helix. Two orthogonal views are shown to emphasize that the molecule has an extended, somewhat flattened structure. In the side view above, the smaller N-terminal domain is at the right and the larger C-terminal domain is on the left. Residues 11-17 form a disordered loop connecting strands Nß1 and Nß2 and are not included in the model. In the end view above, the molecule is turned 90º and viewed down the C-terminal domain. Both ribbon diagrams were generated using RasMol.
Other structures exist in the PDB for ribosomal proteins including one solved by the same group as the L9 protein. It is ribosomal protein L11 from Thermotoga maritima bound to RNA. The PDB entry number is 1MMS. Below is an image of the bound L11 protein.
1MMS: click to view larger image
Important to note is the clear separation of the N-and C-terminal domains similar to the L9 ribosomal protein. Again, suggesting that this separation and orientation serves some architectural role in the ribosome.
There are four known L9 orthologues, including one each from bacterium E.coli, and Synechococcus elongatus, and one each from chloroplastids Pisum sativum and Arabidopsis thaliana. All five (including 1DIV protein from Bacillus stearothermophilus contain conserved residues in the N- and C-terminal domains. Those residues are displayed below and are most likely involved in protein-protein interactions with other ribosomal proteins. The α-helical region itself is filled with many basic residues probably fulfilling the role of RNA binding.
Conserved residues in ribosomal protein L9: click to see larger image
