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Nucleic Acids Research Advance Access originally published online on December 23, 2007
Nucleic Acids Research 2008 36(4):1187-1199; doi:10.1093/nar/gkm1122
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Nucleic Acids Research, 2008, Vol. 36, No. 4 1187-1199
© 2007 The Author(s)
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

Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation

Yuhei Araiso1, Sotiria Palioura2, Ryuichiro Ishitani1, R. Lynn Sherrer2, Patrick O’Donoghue2, Jing Yuan2, Hiroyuki Oshikane1, Naoshi Domae3, Julian DeFranco2, Dieter Söll2,* and Osamu Nureki1,4,*

1Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA, 3Biomolecular Characterization, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198 and 4SORST, JST, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan

*To whom correspondence should be addressed. Tel: +1 203 432 6200; Fax: +1 203 432 6202; Email: dieter.soll{at}yale.edu Correspondence may also be addressed to Osamu Nureki. Tel: +81 45 924 5711; Fax: +81 45 924 5831; Email: nureki{at}bio.titech.ac.jp

Received October 25, 2007. Revised November 29, 2007. Accepted November 30, 2007.

The micronutrient selenium is present in proteins as selenocysteine (Sec). In eukaryotes and archaea, Sec is formed in a tRNA-dependent conversion of O-phosphoserine (Sep) by O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS). Here, we present the crystal structure of Methanococcus maripaludis SepSecS complexed with PLP at 2.5 Å resolution. SepSecS, a member of the Fold Type I PLP enzyme family, forms an ({alpha}2)2 homotetramer through its N-terminal extension. The active site lies on the dimer interface with each monomer contributing essential residues. In contrast to other Fold Type I PLP enzymes, Asn247 in SepSecS replaces the conserved Asp in binding the pyridinium nitrogen of PLP. A structural comparison with Escherichia coli selenocysteine lyase allowed construction of a model of Sep binding to the SepSecS catalytic site. Mutations of three conserved active site arginines (Arg72, Arg94, Arg307), protruding from the neighboring subunit, led to loss of in vivo and in vitro activity. The lack of active site cysteines demonstrates that a perselenide is not involved in SepSecS-catalyzed Sec formation; instead, the conserved arginines may facilitate the selenation reaction. Structural phylogeny shows that SepSecS evolved early in the history of PLP enzymes, and indicates that tRNA-dependent Sec formation is a primordial process.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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