4ZU9

Crystal structure of bacterial selenocysteine-specific elongation factor EF-Sec

Summary for 4ZU9

• Entry DOI: 10.2210/pdb4zu9/pdb
• Descriptor: Elongation factor SelB, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: small gtpase, ef-tu like, translation
• Biological source: Aquifex aeolicus VF5
• Total number of polymer chains: 1
• Total formula weight: 67663.73

Authors

Itoh, Y.,Sekine, S.,Yokoyama, S. (deposition date: 2015-05-15, release date: 2015-09-23, Last modification date: 2020-02-19)

Primary citation

Itoh, Y.,Sekine, S.,Yokoyama, S.
Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB
Nucleic Acids Res., 43:9028-9038, 2015

PubMed Abstract: Selenocysteine (Sec), the 21(st) amino acid in translation, uses its specific tRNA (tRNA(Sec)) to recognize the UGA codon. The Sec-specific elongation factor SelB brings the selenocysteinyl-tRNA(Sec) (Sec-tRNA(Sec)) to the ribosome, dependent on both an in-frame UGA and a Sec-insertion sequence (SECIS) in the mRNA. The bacterial SelB binds mRNA through its C-terminal region, for which crystal structures have been reported. In this study, we determined the crystal structure of the full-length SelB from the bacterium Aquifex aeolicus, in complex with a GTP analog, at 3.2-Å resolution. SelB consists of three EF-Tu-like domains (D1-3), followed by four winged-helix domains (WHD1-4). The spacer region, connecting the N- and C-terminal halves, fixes the position of WHD1 relative to D3. The binding site for the Sec moiety of Sec-tRNA(Sec) is located on the interface between D1 and D2, where a cysteine molecule from the crystallization solution is coordinated by Arg residues, which may mimic Sec binding. The Sec-binding site is smaller and more exposed than the corresponding site of EF-Tu. Complex models of Sec-tRNA(Sec), SECIS RNA, and the 70S ribosome suggest that the unique secondary structure of tRNA(Sec) allows SelB to specifically recognize tRNA(Sec) and characteristically place it at the ribosomal A-site.

PubMed: 26304550
DOI: 10.1093/nar/gkv833

Experimental method

X-RAY DIFFRACTION (3.191 Å)