Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors

In all three kingdoms of life, SelB is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop. Here, we present the X- ray structures of SelB from the archaeon Methanococcus maripaludis in the apo-, GDP- and GppNHp- bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl- binding pocket. All three SelB structures reveal an EF- Tu: GTP- like domain arrangement. Upon binding of the GTP analogue GppNHp, a conformational change of the Switch 2 region in the GTPase domain leads to the exposure of SelB residues involved in clamping the 50 phosphate of the tRNA. A conserved extended loop in domain III of SelB may be responsible for specific interactions with tRNA Sec and act as a ruler for measuring the extra long acceptor arm. Domain IV of SelB adopts a beta barrel fold and is flexibly tethered to domain III. The overall domain arrangement of SelB resembles a ' chalice' observed so far only for initiation factor IF2/ eIF5B. In our model of SelB bound to the ribosome, domain IV points towards the 30 mRNA entrance cleft ready to interact with the downstream secondary structure element.