title: The kink-turn: a new RNA secondary structure motif.
abstract: Analysis of the Haloarcula marismortui large ribosomal subunit has revealed a common RNA structure that we call the kink-turn, or K-turn. The six K-turns in H.marismortui 23S rRNA superimpose with an r.m.s.d. of 1.7 A. There are two K-turns in the structure of Thermus thermophilus 16S rRNA, and the structures of U4 snRNA and L30e mRNA fragments form K-turns. The structure has a kink in the phosphodiester backbone that causes a sharp turn in the RNA helix. Its asymmetric internal loop is flanked by C-G base pairs on one side and sheared G-A base pairs on the other, with an A-minor interaction between these two helical stems. A derived consensus secondary structure for the K-turn includes 10 consensus nucleotides out of 15, and predicts its presence in the 5'-UTR of L10 mRNA, helix 78 in Escherichia coli 23S rRNA and human RNase MRP. Five K-turns in 23S rRNA interact with nine proteins. While the observed K-turns interact with proteins of unrelated structures in different ways, they interact with L7Ae and two homologous proteins in the same way.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.
authors.forename: D J
authors.initials: DJ
authors.lastname: Klein
authors.forename: T M
authors.initials: TM
authors.lastname: Schmeing
authors.forename: P B
authors.initials: PB
authors.lastname: Moore
authors.forename: T A
authors.initials: TA
authors.lastname: Steitz
mesh_terms: D000595:Amino Acid Sequence; D004247:DNA; D019614:Haloarcula marismortui / Q000235:genetics*; D018257:Helix-Loop-Helix Motifs; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D019642:RNA, Archaeal / Q000737:chemistry* / Q000378:metabolism; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000378:metabolism; D012269:Ribosomal Proteins / Q000378:metabolism
chemical_list: D019642:RNA, Archaeal; D012335:RNA, Ribosomal; D012269:Ribosomal Proteins; C015314:kinked DNA; D004247:DNA