Structural basis for mRNA recognition by elongation factor SelB

Abstract

In bacteria, incorporation of selenocysteine, the 21(st) 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 A. 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.

Roquin binding to target mRNAs involves a winged helix-turn-helix motif

“…Notably, no matches to other proteins with classical wHTH motifs and reported RNA-binding properties were found among the top hits in the structural similarity search 7 . However, to date only few such proteins have been described, displaying diverse RNA recognition modes [11][12][13][14][15][16] . Among these, the selenocysteine tRNA-specific elongation factor SelB is the single example of a wHTH-containing protein recognizing stem-loop mRNA.…”

“…Its C-terminal domain encompasses four wHTH domains. The two terminal tandem wHTH motifs synergize to establish specific interactions with the selenocysteine incorporation site hairpin, and the last motif specifically recognizes the mRNA-specific hairpin tip structure of the mRNA 12,16 . The C-terminal SelB wHTH domain superimposes with an r.m.s.d.…”

Towards deciphering the principles underlying an mRNA recognition code

“…The factor binds selenocysteine insertion sequence (SECIS) in mRNA with extremely high selectivity, and this binding serves as a signal for delivery of selenocysteyl-tRNA at a UGA stop codon upstream of SECIS hairpin. The high binding specificity is achieved through base-specific interactions of a DNA-and RNA-binding winged-helix (WH) motif with consecutive bulged out guanine and unpaired uridine of the 5′-GGUC-U loop, and interactions with the RNA backbone, which are determined by shape complementarity and electrostatic properties of the protein surface [39,40].…”

Thermodynamic and Kinetic Framework of Selenocysteyl-tRNASec Recognition by Elongation Factor SelB

“…SelB domains I (the GTP binding domain), II, and III have the same secondary structure elements as the respective domains of EF-Tu, provide most of the contact surface for Sec-tRNA Sec , and are conserved among bacteria, archaea, and eukarya. The structure of domain IV of SelB, which has no analog in EF-Tu or other translational GTPases, is not conserved between pro-and eukaryotes (7)(8)(9). In bacterial SelB, winged helix motifs of domain IV recognize the hairpin backbone and nucleotides extruded from the SECIS helix (8).…”