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 5' 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 3' mRNA entrance cleft ready to interact with the downstream secondary structure element.
Leibundgut
Marc
M
Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.
Frick
Christian
C
Thanbichler
Martin
M
Böck
August
A
Ban
Nenad
N
D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004252:DNA Mutational Analysis; D039642:Eukaryotic Initiation Factors / Q000737:chemistry; D006153:Guanosine Diphosphate / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000031:analogs & derivatives / Q000378:metabolism; D017017:Methanococcus / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010445:Peptide Elongation Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D039662:Prokaryotic Initiation Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D012343:RNA, Transfer / Q000378:metabolism; D016415:Sequence Alignment
D019843:Archaeal Proteins; D039642:Eukaryotic Initiation Factors; D010445:Peptide Elongation Factors; D039662:Prokaryotic Initiation Factors; C451459:eukaryotic initiation factor-5B; D006153:Guanosine Diphosphate; D006160:Guanosine Triphosphate; D012343:RNA, Transfer