Structure of the complete bacterial SRP Alu domain.
Bottom Line: The mammalian Alu domain is a protein-RNA complex, while prokaryotic Alu domains are protein-free with significant extensions of the RNA.The 5' region includes an extended loop-loop pseudoknot made of five consecutive Watson-Crick base pairs.Homology modeling with the human Alu domain in context of the ribosome shows that an additional lobe in the pseudoknot approaches the large subunit, while the absence of protein results in the detachment from the small subunit.
Affiliation: Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.Show MeSH
Related in: MedlinePlus
Mentions: The B. subtilis Alu domain consists of five RNA helices with helices 1, 2 and 4 being continuously stacked (Figure 2A and B). Helices 5 and 3 are connected via two 3-way junctions with helices 1 and 2 (junction IIIA) and helices 2 and 4 (IIIB), respectively. Junction IIIA is specific to prokaryotes due to the absence of helix 1 in eukaryotic SRP RNA and can be assigned to the family A of 3-way junctions, so far only described for rRNA (53). As in case of the human Alu domain, junction IIIB belongs to the more widespread family C of 3-way junctions, but does not contain a U-turn motif (see below). The closing loops of helices 3 and 4 interact in an extended loop–loop pseudoknot forming an additional helix (t1) of five consecutive Watson–Crick base pairs. The structure comprises both the 5′ and 3′ regions that adopt a compact ‘closed’ conformation with the 5′ region folded back onto the 3′ region. This closed conformation is established by perpendicular packing of helix 3 on helix 5 via minor groove interactions. In case of the human Alu domain, the complete structure is not available, as this conformation could not be crystallized. It was however predicted based on biochemical data and inferred from crystal packing (10,54,55) (Figure 2C and D). In general, the 5′ region consists of helices 2 to 4 and the 3′ region of helix 5. The additional helix 1 including the 5′ and 3′ termini is specific to bacterial and archaeal Alu domains (Supplementary Figure S3A). In our 3.1 Å structure solved in a different space group, helix 1 is tilted due to different crystal packing at the 5′, 3′ end revealing some plasticity of the fold (Supplementary Figure S1C). Taken together, our structure of B. subtilis Alu RNA is the first complete structure of an Alu domain and provides the basis to understand the function and evolution of Alu domains in general.
Affiliation: Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.