Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB
Selenocysteine (Sec), the 21st amino acid in translation, uses its specific tRNA (tRNASec) to recognize the UGA codon. The Sec-specific elongation factor SelB brings the selenocysteinyl-tRNASec (Sec-tRNASec) to the ribosome, dependent on both an in-frame UGA and a Sec-insertion sequence (SECIS) in t...
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| Format: | Online |
| Language: | English |
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Oxford University Press
2015
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605307/ |
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pubmed-46053072015-10-19 Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB Itoh, Yuzuru Sekine, Shun-ichi Yokoyama, Shigeyuki Structural Biology Selenocysteine (Sec), the 21st amino acid in translation, uses its specific tRNA (tRNASec) to recognize the UGA codon. The Sec-specific elongation factor SelB brings the selenocysteinyl-tRNASec (Sec-tRNASec) 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-tRNASec 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-tRNASec, SECIS RNA, and the 70S ribosome suggest that the unique secondary structure of tRNASec allows SelB to specifically recognize tRNASec and characteristically place it at the ribosomal A-site. Oxford University Press 2015-10-15 2015-10-10 /pmc/articles/PMC4605307/ /pubmed/26304550 http://dx.doi.org/10.1093/nar/gkv833 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Itoh, Yuzuru Sekine, Shun-ichi Yokoyama, Shigeyuki |
| spellingShingle |
Itoh, Yuzuru Sekine, Shun-ichi Yokoyama, Shigeyuki Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB |
| author_facet |
Itoh, Yuzuru Sekine, Shun-ichi Yokoyama, Shigeyuki |
| author_sort |
Itoh, Yuzuru |
| title |
Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB |
| title_short |
Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB |
| title_full |
Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB |
| title_fullStr |
Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB |
| title_full_unstemmed |
Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB |
| title_sort |
crystal structure of the full-length bacterial selenocysteine-specific elongation factor selb |
| description |
Selenocysteine (Sec), the 21st amino acid in translation, uses its specific tRNA (tRNASec) to recognize the UGA codon. The Sec-specific elongation factor SelB brings the selenocysteinyl-tRNASec (Sec-tRNASec) 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-tRNASec 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-tRNASec, SECIS RNA, and the 70S ribosome suggest that the unique secondary structure of tRNASec allows SelB to specifically recognize tRNASec and characteristically place it at the ribosomal A-site. |
| publisher |
Oxford University Press |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605307/ |
| _version_ |
1613488017152933888 |