title: Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP.
abstract: N(6)-Threonylcarbamoyladenosine (t(6)A) is a modified tRNA base required for accuracy in translation. Qri7 is localized in yeast mitochondria and is involved in t(6)A biosynthesis. In t(6)A biosynthesis, threonylcarbamoyl-adenylate (TCA) is synthesized from threonine, bicarbonate and ATP, and the threonyl-carbamoyl group is transferred to adenine 37 of tRNA by Qri7. Qri7 alone is sufficient to catalyze the second step of the reaction, whereas the Qri7 homologues YgjD (in bacteria) and Kae1 (in archaea and eukaryotes) function as parts of multi-protein complexes. In this study, the crystal structure of Qri7 complexed with AMP (a part of TCA) has been determined at 2.94 Å resolution in a new crystal form. The manner of AMP recognition is similar, with some minor variations, among the Qri7/Kae1/YgjD family proteins. The previously reported dimer formation was also observed in this new crystal form. Furthermore, a comparison with the structure of TobZ, which catalyzes a similar reaction to t(6)A biosynthesis, revealed the presence of a flexible loop that may be involved in tRNA binding.
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
authors.forename: Takumi
authors.initials: T
authors.lastname: Tominaga
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
authors.forename: Kan
authors.initials: K
authors.lastname: Kobayashi
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
authors.forename: Ryohei
authors.initials: R
authors.lastname: Ishii
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
authors.forename: Ryuichiro
authors.initials: R
authors.lastname: Ishitani
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Nureki
mesh_terms: D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D024101:Mitochondrial Proteins / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D011487:Protein Conformation; D012441:Saccharomyces cerevisiae / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: D024101:Mitochondrial Proteins; C544825:Qri7 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins
keywords: AMP; Kae1; Qri7; TobZ; YgjD; tRNA modification
references.citation: EMBO J. 2011 Mar 2;30(5):873-81
references.pmid: 21183954
references.citation: Eur J Biochem. 1981 May;116(1):207-13
references.pmid: 6788546
references.citation: Methods Enzymol. 1997;276:307-26
references.pmid: 27754618
references.citation: EMBO Rep. 2008 Jul;9(7):629-35
references.pmid: 18552770
references.citation: Biochimie. 1995;77(1-2):139-41
references.pmid: 7541252
references.citation: Biochemistry. 2012 Nov 6;51(44):8950-63
references.pmid: 23072323
references.citation: Nucleic Acids Res. 2013 Nov;41(20):9484-99
references.pmid: 23945934
references.citation: Nat Struct Mol Biol. 2004 Dec;11(12):1186-91
references.pmid: 15558052
references.citation: EMBO J. 2011 Mar 2;30(5):882-93
references.pmid: 21285948
references.citation: J Biol Chem. 1972 Oct 25;247(20):6394-401
references.pmid: 4561935
references.citation: J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
references.pmid: 19461840
references.citation: Cell. 2006 Mar 24;124(6):1155-68
references.pmid: 16564010
references.citation: Nat Chem Biol. 2013 Feb;9(2):105-11
references.pmid: 23242255
references.citation: Nucleic Acids Res. 2009 May;37(9):2894-909
references.pmid: 19287007
references.citation: FEMS Microbiol Lett. 2004 Jan 30;230(2):185-90
references.pmid: 14757238
references.citation: Protein Sci. 2013 May;22(5):628-40
references.pmid: 23471679
references.citation: Biochemistry. 2000 Nov 7;39(44):13396-404
references.pmid: 11063577
references.citation: Mol Cell. 2008 Oct 24;32(2):259-75
references.pmid: 18951093
references.citation: Methods Enzymol. 2009;459:459-91
references.pmid: 19362651
references.citation: J Biol Chem. 2012 Apr 20;287(17):13666-73
references.pmid: 22378793
references.citation: EMBO J. 2006 Aug 9;25(15):3576-85
references.pmid: 16874308
references.citation: Nucleic Acids Res. 2013 Feb 1;41(3):1953-64
references.pmid: 23258706
references.citation: Biochem Biophys Res Commun. 1969 Dec 4;37(6):990-5
references.pmid: 4902784
references.citation: Nucleic Acids Res. 2013 Jul;41(12):6332-46
references.pmid: 23620299
references.citation: Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67
references.pmid: 22505256
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references.pmid: 15572765
references.citation: Angew Chem Int Ed Engl. 2012 Apr 23;51(17):4046-52
references.pmid: 22383337
references.citation: Nucleic Acids Res. 2007;35(18):6042-51
references.pmid: 17766251