Limits...
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.

Show MeSH

Related in: MedlinePlus

The Alu domain resembles tRNA. (A) Superposition of bacterial Alu RNA (split into 5′ and 3′ parts and helix 1) with the tRNA/EF-Tu complex (PDB entry 2WRN). The 5′ domain and helix 1 match the tRNA structure, whereas parts of the 3′ domain superpose with EF-Tu. (B) Structure of threonine tRNA (PDB entry 2WRN) with domains structurally similar to Alu RNA colored as in Figure 2B. The first two nucleotides of the variable loop and nucleotide 26 would correspond to Alu RNA helix 2 (light blue). The UGU sequence (red) shortcuts the tRNA acceptor stem. (C) Two-dimensional representation of tRNA highlighting the structural similarity to Alu RNA (color code as in Figure 2B and D). (D) The Alu domain-specific MSM between helices 3 and 5. (E) The similar interaction of the tRNA TΨC-stem with EF-Tu domain III. (F) Detail of the tRNA/EF-Tu interaction highlighting the corresponding read-out of a G-U wobble base pair.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4231752&req=5

Figure 5: The Alu domain resembles tRNA. (A) Superposition of bacterial Alu RNA (split into 5′ and 3′ parts and helix 1) with the tRNA/EF-Tu complex (PDB entry 2WRN). The 5′ domain and helix 1 match the tRNA structure, whereas parts of the 3′ domain superpose with EF-Tu. (B) Structure of threonine tRNA (PDB entry 2WRN) with domains structurally similar to Alu RNA colored as in Figure 2B. The first two nucleotides of the variable loop and nucleotide 26 would correspond to Alu RNA helix 2 (light blue). The UGU sequence (red) shortcuts the tRNA acceptor stem. (C) Two-dimensional representation of tRNA highlighting the structural similarity to Alu RNA (color code as in Figure 2B and D). (D) The Alu domain-specific MSM between helices 3 and 5. (E) The similar interaction of the tRNA TΨC-stem with EF-Tu domain III. (F) Detail of the tRNA/EF-Tu interaction highlighting the corresponding read-out of a G-U wobble base pair.

Mentions: The Alu domain has been shown to impose elongation arrest by blocking the elongation factor entry site at the ribosome (12). Superposition of the complete B. subtilis Alu domain with the tRNA/EF-Tu complex (57) based on the loop–loop pseudoknot interaction shows that the 5′ domain including helix 1 resembles a tRNA structure (Figure 5A–C). Transfer RNA resemblance is of broad biological and evolutionary importance as highlighted for disease-related viral tRNA-like RNAs (58,59). Specifically, helix 4 corresponds to the D-stem, helix 3 to the TΨC-stem and helices 1 and 2 to the anticodon stem, although helix 1 is longer with respect to the canonical anticodon stem in mature tRNA (nine compared to five base pairs). In contrast, the acceptor stem is absent in the Alu RNA and shortcut by the ‘UGU-loop’ connecting helices 3 and 4. In addition to the structural similarity, the MSM coincides with the minor groove interaction of the tRNA TΨC-stem with EF-Tu domain III, and although the chemistry is different, hydrogen-bonding patterns are strikingly similar (Figure 5D–F).


Structure of the complete bacterial SRP Alu domain.

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

The Alu domain resembles tRNA. (A) Superposition of bacterial Alu RNA (split into 5′ and 3′ parts and helix 1) with the tRNA/EF-Tu complex (PDB entry 2WRN). The 5′ domain and helix 1 match the tRNA structure, whereas parts of the 3′ domain superpose with EF-Tu. (B) Structure of threonine tRNA (PDB entry 2WRN) with domains structurally similar to Alu RNA colored as in Figure 2B. The first two nucleotides of the variable loop and nucleotide 26 would correspond to Alu RNA helix 2 (light blue). The UGU sequence (red) shortcuts the tRNA acceptor stem. (C) Two-dimensional representation of tRNA highlighting the structural similarity to Alu RNA (color code as in Figure 2B and D). (D) The Alu domain-specific MSM between helices 3 and 5. (E) The similar interaction of the tRNA TΨC-stem with EF-Tu domain III. (F) Detail of the tRNA/EF-Tu interaction highlighting the corresponding read-out of a G-U wobble base pair.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231752&req=5

Figure 5: The Alu domain resembles tRNA. (A) Superposition of bacterial Alu RNA (split into 5′ and 3′ parts and helix 1) with the tRNA/EF-Tu complex (PDB entry 2WRN). The 5′ domain and helix 1 match the tRNA structure, whereas parts of the 3′ domain superpose with EF-Tu. (B) Structure of threonine tRNA (PDB entry 2WRN) with domains structurally similar to Alu RNA colored as in Figure 2B. The first two nucleotides of the variable loop and nucleotide 26 would correspond to Alu RNA helix 2 (light blue). The UGU sequence (red) shortcuts the tRNA acceptor stem. (C) Two-dimensional representation of tRNA highlighting the structural similarity to Alu RNA (color code as in Figure 2B and D). (D) The Alu domain-specific MSM between helices 3 and 5. (E) The similar interaction of the tRNA TΨC-stem with EF-Tu domain III. (F) Detail of the tRNA/EF-Tu interaction highlighting the corresponding read-out of a G-U wobble base pair.
Mentions: The Alu domain has been shown to impose elongation arrest by blocking the elongation factor entry site at the ribosome (12). Superposition of the complete B. subtilis Alu domain with the tRNA/EF-Tu complex (57) based on the loop–loop pseudoknot interaction shows that the 5′ domain including helix 1 resembles a tRNA structure (Figure 5A–C). Transfer RNA resemblance is of broad biological and evolutionary importance as highlighted for disease-related viral tRNA-like RNAs (58,59). Specifically, helix 4 corresponds to the D-stem, helix 3 to the TΨC-stem and helices 1 and 2 to the anticodon stem, although helix 1 is longer with respect to the canonical anticodon stem in mature tRNA (nine compared to five base pairs). In contrast, the acceptor stem is absent in the Alu RNA and shortcut by the ‘UGU-loop’ connecting helices 3 and 4. In addition to the structural similarity, the MSM coincides with the minor groove interaction of the tRNA TΨC-stem with EF-Tu domain III, and although the chemistry is different, hydrogen-bonding patterns are strikingly similar (Figure 5D–F).

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