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Nucleic Acids Research Advance Access originally published online on August 19, 2009
Nucleic Acids Research 2009 37(18):6259-6268; doi:10.1093/nar/gkp648
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Nucleic Acids Research, 2009, Vol. 37, No. 18 6259-6268
© The Author 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses?by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Crystal structure of human selenocysteine tRNA

Yuzuru Itoh1,2, Shiho Chiba1, Shun-ichi Sekine1,2 and Shigeyuki Yokoyama1,2,*

1Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and 2RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan

*To whom correspondence should be addressed. Tel: +81 3 5841 4392; Fax: +81 3 5841 8057; Email: yokoyama{at}biochem.s.u-tokyo.ac.jp

Received June 23, 2009. Revised July 18, 2009. Accepted July 20, 2009.

Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNASec) has an anticodon complementary to the UGA codon. We solved the crystal structure of human tRNASec. tRNASec has a 9-bp acceptor stem and a 4-bp T stem, in contrast with the 7-bp acceptor stem and the 5-bp T stem in the canonical tRNAs. The acceptor stem is kinked between the U6:U67 and G7:C66 base pairs, leading to a bent acceptor-T stem helix. tRNASec has a 6-bp D stem and a 4-nt D loop. The long D stem includes unique A14:U21 and G15:C20a pairs. The D-loop:T-loop interactions include the base pairs G18:U55 and U16:U59, and a unique base triple, U20:G19:C56. The extra arm comprises of a 6-bp stem and a 4-nt loop. Remarkably, the D stem and the extra arm do not form tertiary interactions in tRNASec. Instead, tRNASec has an open cavity, in place of the tertiary core of a canonical tRNA. The linker residues, A8 and U9, connecting the acceptor and D stems, are not involved in tertiary base pairing. Instead, U9 is stacked on the first base pair of the extra arm. These features might allow tRNASec to be the target of the Sec synthesis/incorporation machineries.


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