title: Crystal structure of human selenocysteine tRNA.
abstract: Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNA(Sec)) has an anticodon complementary to the UGA codon. We solved the crystal structure of human tRNA(Sec). tRNA(Sec) 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. tRNA(Sec) 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 tRNA(Sec). Instead, tRNA(Sec) 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 tRNA(Sec) to be the target of the Sec synthesis/incorporation machineries.
authors.affiliation: Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Yuzuru
authors.initials: Y
authors.lastname: Itoh
authors.forename: Shiho
authors.initials: S
authors.lastname: Chiba
authors.forename: Shun-Ichi
authors.initials: S
authors.lastname: Sekine
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000926:Anticodon / Q000737:chemistry; D018360:Crystallography, X-Ray; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012345:RNA, Transfer, Amino Acid-Specific / Q000737:chemistry*
chemical_list: D000926:Anticodon; D012345:RNA, Transfer, Amino Acid-Specific; C036928:tRNA, selenocysteine-
references.citation: EMBO J. 1994 Jan 1;13(1):241-8
references.pmid: 8306966
references.citation: Nucleic Acids Res. 1993 Mar 11;21(5):1073-9
references.pmid: 8464694
references.citation: Proc Natl Acad Sci U S A. 1993 May 1;90(9):4181-5
references.pmid: 8483932
references.citation: J Mol Biol. 1978 Aug 25;123(4):607-30
references.pmid: 357742
references.citation: EMBO J. 1993 Aug;12(8):3315-22
references.pmid: 8344267
references.citation: Proc Natl Acad Sci U S A. 1997 May 13;94(10):5018-23
references.pmid: 9144182
references.citation: Nucleic Acids Res. 1994 Apr 25;22(8):1354-8
references.pmid: 8031393
references.citation: RNA. 1999 Dec;5(12):1561-9
references.pmid: 10606267
references.citation: Eur J Biochem. 1992 Jun 15;206(3):767-73
references.pmid: 1606960
references.citation: EMBO J. 1986 Jun;5(6):1221-7
references.pmid: 3015592
references.citation: Structure. 1999 Feb 15;7(2):143-56
references.pmid: 10368282
references.citation: Nature. 1974 Aug 16;250(467):546-51
references.pmid: 4602655
references.citation: EMBO J. 2002 Aug 1;21(15):4145-53
references.pmid: 12145214
references.citation: J Mol Biol. 1993 May 20;231(2):274-92
references.pmid: 8510147
references.citation: J Biol Chem. 1991 Apr 5;266(10):6324-8
references.pmid: 2007585
references.citation: Proc Natl Acad Sci U S A. 1987 May;84(10):3156-60
references.pmid: 3033637
references.citation: Nature. 1989 Nov 23;342(6248):453-6
references.pmid: 2531290
references.citation: Proc Natl Acad Sci U S A. 2006 Dec 12;103(50):18923-7
references.pmid: 17142313
references.citation: Nucleic Acids Res. 2008 Apr;36(6):1871-80
references.pmid: 18267971
references.citation: Science. 1994 Mar 11;263(5152):1404-10
references.pmid: 8128220
references.citation: EMBO J. 2000 Sep 1;19(17):4796-805
references.pmid: 10970870
references.citation: Nucleic Acids Res. 1990 Feb 11;18(3):487-91
references.pmid: 2408012
references.citation: J Mol Biol. 1978 Sep 25;124(3):523-34
references.pmid: 361973
references.citation: Methods Enzymol. 1997;276:307-26
references.pmid: 27754618
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D159-62
references.pmid: 18957446
references.citation: Mol Cell Biol. 1997 Apr;17(4):1977-85
references.pmid: 9121445
references.citation: J Biol Chem. 1995 Sep 15;270(37):21659-64
references.pmid: 7665581
references.citation: Nat Struct Mol Biol. 2005 Feb;12(2):198-203
references.pmid: 15665870
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12848-53
references.pmid: 15317934
references.citation: EMBO J. 2005 Jan 12;24(1):11-22
references.pmid: 15616587
references.citation: Proc Natl Acad Sci U S A. 1986 Jul;83(13):4650-4
references.pmid: 2941757
references.citation: J Biol Chem. 1993 Jul 5;268(19):14215-23
references.pmid: 8314785
references.citation: J Mol Biol. 1996 Oct 18;263(1):8-19
references.pmid: 8890909
references.citation: PLoS Biol. 2007 Jan;5(1):e4
references.pmid: 17194211
references.citation: Nature. 1988 Feb 25;331(6158):723-5
references.pmid: 2963963
references.citation: Proc Natl Acad Sci U S A. 1976 Aug;73(8):2659-63
references.pmid: 1066676
references.citation: RNA Biol. 2008 Jul-Sep;5(3):169-77
references.pmid: 18818520
references.citation: EMBO J. 2000 Jan 17;19(2):306-14
references.pmid: 10637234
references.citation: Nature. 1980 Dec 25;288(5792):669-74
references.pmid: 7005687
references.citation: J Biol Chem. 1995 Aug 4;270(31):18570-4
references.pmid: 7629188
references.citation: Science. 1974 Aug 2;185(4149):435-40
references.pmid: 4601792
references.citation: Nucleic Acids Res. 1993 Dec 11;21(24):5589-94
references.pmid: 8284203
references.citation: EMBO J. 1992 Oct;11(10):3759-66
references.pmid: 1396569
references.citation: Acta Crystallogr A. 1988 Mar 1;44 ( Pt 2):112-23
references.pmid: 3272146
references.citation: J Mol Biol. 2000 Jun 2;299(2):351-8
references.pmid: 10860743
references.citation: Science. 2003 May 30;300(5624):1439-43
references.pmid: 12775843
references.citation: Arch Biochem Biophys. 1967 Oct;122(1):164-73
references.pmid: 6076213
references.citation: FEBS Lett. 1994 Jun 27;347(2-3):137-42
references.pmid: 8033991
references.citation: Acta Crystallogr D Biol Crystallogr. 2001 Oct;57(Pt 10):1373-82
references.pmid: 11567148
references.citation: J Biol Chem. 1991 Oct 25;266(30):20375-9
references.pmid: 1939093
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references.pmid: 15572765
references.citation: J Biol Chem. 2005 Dec 16;280(50):41568-75
references.pmid: 16230358
references.citation: Science. 1995 Dec 1;270(5241):1464-72
references.pmid: 7491491
references.citation: Mol Microbiol. 1991 Mar;5(3):515-20
references.pmid: 1828528
references.citation: J Mol Biol. 1996 Mar 8;256(4):685-700
references.pmid: 8642591