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Structure of the complete bacterial SRP Alu domain.

Kempf G, Wild K, Sinning I - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.

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Structure of the Alu domain. (A) The structure of Bacillus subtilis Alu domain. Helices and the tertiary interaction (t1) in the loop-loop pseudoknot are indicated. (B) Two-dimensional representation of the Alu domain with helix and junction numbering and tertiary interactions. The four-base platform is boxed and the UGU sequence is highlighted in red. Artificial bases at the ends are shown in gray. Base-pairs are classified according to the nomenclature by Leontis and Westhof (46). (C) Superposition of B. subtilis and human Alu domains (combined human model based on PDB entries 1E8O and 1E8S; (10)) based on highly conserved nucleotides within helices 3 and 4 (shown as sticks). The additional helix 1 and L4.1 lobe in bacteria are labeled, and the U-turn including the UGU sequence in human SRP is shown in red. Human helix 5 belongs to a crystallographic neighbor (10). (D) Two-dimensional representation of the human Alu domain in the closed conformation (as in (B)). A dashed red line boxes the conserved Alu domain core. Labels also used in (B) are given in the inset. (E) The 3-way junction IIIB between helices 2, 3 and 4 and the UGU sequence (nucleotides 34 to 36, boxed in red) shown for the B. subtilis Alu domain. An intra-strand trans Hoogsteen/sugar-edge base pair (G35/A37) bends the connecting loop between helices 3 and 4. Color-coding as in Figure 2B. (F) Superposition of the B. subtilis UGU sequence and 3-way junction IIIB (colored in brown) with the corresponding part of the human Alu domain (blue, PDB code 1E8O) including the U-turn motif (U25-G27, red) instead of an intra-strand base pair.
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Figure 2: Structure of the Alu domain. (A) The structure of Bacillus subtilis Alu domain. Helices and the tertiary interaction (t1) in the loop-loop pseudoknot are indicated. (B) Two-dimensional representation of the Alu domain with helix and junction numbering and tertiary interactions. The four-base platform is boxed and the UGU sequence is highlighted in red. Artificial bases at the ends are shown in gray. Base-pairs are classified according to the nomenclature by Leontis and Westhof (46). (C) Superposition of B. subtilis and human Alu domains (combined human model based on PDB entries 1E8O and 1E8S; (10)) based on highly conserved nucleotides within helices 3 and 4 (shown as sticks). The additional helix 1 and L4.1 lobe in bacteria are labeled, and the U-turn including the UGU sequence in human SRP is shown in red. Human helix 5 belongs to a crystallographic neighbor (10). (D) Two-dimensional representation of the human Alu domain in the closed conformation (as in (B)). A dashed red line boxes the conserved Alu domain core. Labels also used in (B) are given in the inset. (E) The 3-way junction IIIB between helices 2, 3 and 4 and the UGU sequence (nucleotides 34 to 36, boxed in red) shown for the B. subtilis Alu domain. An intra-strand trans Hoogsteen/sugar-edge base pair (G35/A37) bends the connecting loop between helices 3 and 4. Color-coding as in Figure 2B. (F) Superposition of the B. subtilis UGU sequence and 3-way junction IIIB (colored in brown) with the corresponding part of the human Alu domain (blue, PDB code 1E8O) including the U-turn motif (U25-G27, red) instead of an intra-strand base pair.

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.


Structure of the complete bacterial SRP Alu domain.

Kempf G, Wild K, Sinning I - Nucleic Acids Res. (2014)

Structure of the Alu domain. (A) The structure of Bacillus subtilis Alu domain. Helices and the tertiary interaction (t1) in the loop-loop pseudoknot are indicated. (B) Two-dimensional representation of the Alu domain with helix and junction numbering and tertiary interactions. The four-base platform is boxed and the UGU sequence is highlighted in red. Artificial bases at the ends are shown in gray. Base-pairs are classified according to the nomenclature by Leontis and Westhof (46). (C) Superposition of B. subtilis and human Alu domains (combined human model based on PDB entries 1E8O and 1E8S; (10)) based on highly conserved nucleotides within helices 3 and 4 (shown as sticks). The additional helix 1 and L4.1 lobe in bacteria are labeled, and the U-turn including the UGU sequence in human SRP is shown in red. Human helix 5 belongs to a crystallographic neighbor (10). (D) Two-dimensional representation of the human Alu domain in the closed conformation (as in (B)). A dashed red line boxes the conserved Alu domain core. Labels also used in (B) are given in the inset. (E) The 3-way junction IIIB between helices 2, 3 and 4 and the UGU sequence (nucleotides 34 to 36, boxed in red) shown for the B. subtilis Alu domain. An intra-strand trans Hoogsteen/sugar-edge base pair (G35/A37) bends the connecting loop between helices 3 and 4. Color-coding as in Figure 2B. (F) Superposition of the B. subtilis UGU sequence and 3-way junction IIIB (colored in brown) with the corresponding part of the human Alu domain (blue, PDB code 1E8O) including the U-turn motif (U25-G27, red) instead of an intra-strand base pair.
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Figure 2: Structure of the Alu domain. (A) The structure of Bacillus subtilis Alu domain. Helices and the tertiary interaction (t1) in the loop-loop pseudoknot are indicated. (B) Two-dimensional representation of the Alu domain with helix and junction numbering and tertiary interactions. The four-base platform is boxed and the UGU sequence is highlighted in red. Artificial bases at the ends are shown in gray. Base-pairs are classified according to the nomenclature by Leontis and Westhof (46). (C) Superposition of B. subtilis and human Alu domains (combined human model based on PDB entries 1E8O and 1E8S; (10)) based on highly conserved nucleotides within helices 3 and 4 (shown as sticks). The additional helix 1 and L4.1 lobe in bacteria are labeled, and the U-turn including the UGU sequence in human SRP is shown in red. Human helix 5 belongs to a crystallographic neighbor (10). (D) Two-dimensional representation of the human Alu domain in the closed conformation (as in (B)). A dashed red line boxes the conserved Alu domain core. Labels also used in (B) are given in the inset. (E) The 3-way junction IIIB between helices 2, 3 and 4 and the UGU sequence (nucleotides 34 to 36, boxed in red) shown for the B. subtilis Alu domain. An intra-strand trans Hoogsteen/sugar-edge base pair (G35/A37) bends the connecting loop between helices 3 and 4. Color-coding as in Figure 2B. (F) Superposition of the B. subtilis UGU sequence and 3-way junction IIIB (colored in brown) with the corresponding part of the human Alu domain (blue, PDB code 1E8O) including the U-turn motif (U25-G27, red) instead of an intra-strand base pair.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.

Show MeSH
Related in: MedlinePlus