title: Tertiary structure of bacterial selenocysteine tRNA.
abstract: Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNA(Sec)) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 Å crystal structure of the tRNA(Sec) from the bacterium Aquifex aeolicus, in complex with the heterologous SerRS from the archaeon Methanopyrus kandleri. The bacterial tRNA(Sec) assumes the L-shaped structure, from which the long extra arm protrudes. Although the D-arm conformation and the extra-arm orientation are similar to those of eukaryal/archaeal tRNA(Sec)s, A. aeolicus tRNA(Sec) has unique base triples, G14:C21:U8 and C15:G20a:G48, which occupy the positions corresponding to the U8:A14 and R15:Y48 tertiary base pairs of canonical tRNAs. Methanopyrus kandleri SerRS exhibited serine ligation activity toward A. aeolicus tRNA(Sec) in vitro. The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNA(Sec). Similar interactions exist in the reported tRNA(Ser) and SerRS complex structure from the bacterium Thermus thermophilus. Although the catalytic C-terminal domain of M. kandleri SerRS lacks interactions with A. aeolicus tRNA(Sec) in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNA(Sec) to enter the SerRS catalytic site.
authors: Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors: Yuzuru
authors: Y
authors: Itoh
authors: Shun-ichi
authors: S
authors: Sekine
authors: Shiro
authors: S
authors: Suetsugu
authors: Shigeyuki
authors: S
authors: Yokoyama
mesh_terms: D019605:Euryarchaeota / Q000201:enzymology; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry*; D012345:RNA, Transfer, Amino Acid-Specific / Q000737:chemistry*; D012714:Serine-tRNA Ligase / Q000737:chemistry* / Q000378:metabolism; D046249:Transfer RNA Aminoacylation
chemical_list: D012329:RNA, Bacterial; D012345:RNA, Transfer, Amino Acid-Specific; C036928:tRNA, selenocysteine-; D012714:Serine-tRNA Ligase
references: Nature. 1974 Aug 16;250(467):546-51
references: 4602655
references: Science. 2009 Jul 17;325(5938):321-5
references: 19608919
references: J Biol Chem. 1991 Apr 5;266(10):6324-8
references: 2007585
references: Proc Natl Acad Sci U S A. 2006 Dec 12;103(50):18923-7
references: 17142313
references: Science. 1994 Mar 11;263(5152):1432-6
references: 8128224
references: Mol Cell. 2010 Aug 13;39(3):410-20
references: 20705242
references: Nucleic Acids Res. 1993 Mar 11;21(5):1073-9
references: 8464694
references: Science. 1974 Aug 2;185(4149):435-40
references: 4601792
references: Nucleic Acids Res. 2009 Oct;37(18):6259-68
references: 19692584
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D210-3
references: 21071414
references: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
references: 20124702
references: PLoS One. 2011;6(5):e20032
references: 21629646
references: Nature. 1990 Sep 20;347(6290):249-55
references: 2205803
references: Nucleic Acids Res. 2008 Apr;36(6):1871-80
references: 18267971
references: Science. 1994 Mar 11;263(5152):1404-10
references: 8128220
references: Nucleic Acids Res. 2011 Feb;39(3):1034-41
references: 20870747
references: Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Jun 1;68(Pt 6):678-82
references: 22684069
references: J Mol Biol. 1994 Feb 25;236(3):738-48
references: 8114091
references: PLoS Biol. 2007 Jan;5(1):e4
references: 17194211
references: Nature. 1988 Feb 25;331(6158):723-5
references: 2963963
references: RNA Biol. 2008 Jul-Sep;5(3):169-77
references: 18818520
references: Nucleic Acids Res. 1994 Jun 25;22(12):2228-33
references: 8036149
references: Nature. 1990 Sep 13;347(6289):203-6
references: 2203971
references: J Biol Chem. 1991 Oct 25;266(30):20375-9
references: 1939093
references: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references: 15572765
references: Nat Struct Mol Biol. 2007 Apr;14(4):272-9
references: 17351629
references: Proc Natl Acad Sci U S A. 1997 May 13;94(10):5018-23
references: 9144182
references: EMBO J. 2006 Jun 7;25(11):2498-509
references: 16675947
references: Mol Microbiol. 1991 Mar;5(3):515-20
references: 1828528