Structural basis for mRNA recognition by elongation factor SelB

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In bacteria, incorporation of selenocysteine, the 21st amino acid, into proteins requires elongation factor SelB, which has the unusual property of binding to both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity, the molecular basis of which has been unknown. We have determined the crystal structure of the mRNA-binding domain of SelB in complex with SECIS RNA at a resolution of 2.3 Å. This is the first example of a complex between an RNA and a winged-helix (WH) domain, a motif found in many DNA-binding proteins and recently discovered in RNA-binding proteins. Notably, RNA binding does not induce a major conformational change in the WH motif. The structure reveals a new mode of RNA recognition with a geometry that allows the complex to wrap around the small ribosomal subunit.

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Figure 1: Secondary structure of SECIS and domain structure of SelB.
Figure 2: Structure of the SelB mRNA-binding domain–SECIS RNA complex.
Figure 3: Comparison of WH protein–DNA complexes.
Figure 4: Protein-RNA interactions in the SelB-M–SECIS RNA complex.
Figure 5: Functional groups of SECIS RNA required for SelB-M binding.
Figure 6: A model of SelB–tRNASec–mRNA complex bound to the ribosome.

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We thank M. Kawamoto, H. Sakai and K. Miura for assistance in data collection at SPring-8. This work was supported by the joint program JSPS-CNRS to S.Y. and K.M. and the French national program GEOMEX to S.Y. and D.F. K.M. and D.K. were supported in part by the Ministry of Education, Science, Sports, Culture and Technology of Japan, and the Protein 3000 project. L.R. was supported by a Japan Society for the Promotion of Science postdoctoral fellowship for foreign researchers.

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Correspondence to Satoko Yoshizawa or Katsumi Maenaka.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Crystal packing of SelB-M–RNA complexes. (PDF 249 kb)

Supplementary Fig. 2

Structure-based sequence alignment of bacterial SelB mRNA-binding domains. (PDF 464 kb)

Supplementary Fig. 3

Protein-RNA interactions in the SelB-M–SECIS RNA complex. (PDF 343 kb)

Supplementary Fig. 4

Overview of the protein-RNA loop interactions. (PDF 1859 kb)

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