title: Three-dimensional folding of the tRNA-like domain of Escherichia coli tmRNA.
abstract: UV irradiation of Escherichia coli tmRNA both on and off the ribosome induced covalent cross-links between its 3'- and its 5'-terminal segments. Cross-linking was unaffected in a molecule that lacked the tag-peptide codon region and pseudoknots 2, 3, and 4. Intact and truncated cross-linked tmRNAs were aminoacylated as efficiently as the respective nonirradiated molecules, suggesting that the added UV-induced bonds did not disturb tmRNA conformation. Using RNase H digestion followed by primer extension with reverse transcriptase, two cross-linked sites were identified within the tRNA-like region of tmRNA. The first was formed between nucleotides U9/U10 near the 5' end and nucleotides C346/U347 in the T loop. The second cross-link involved residues at positions 25-28 and 326-329 within helix 2a. Together with comparative sequence analysis, these findings yielded a three-dimensional model of the tRNA-like domain of E. coli tmRNA. Despite significant reduction of the D domain and the proximity of U9/U10 and C346/U347, the model closely resembles the L-shaped structure of canonical tRNA.
authors.affiliation: Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 75708-3154, USA.
authors.forename: C
authors.initials: C
authors.lastname: Zwieb
authors.forename: S A
authors.initials: SA
authors.lastname: Guven
authors.forename: I K
authors.initials: IK
authors.lastname: Wower
authors.forename: J
authors.initials: J
authors.lastname: Wower
mesh_terms: D001483:Base Sequence; D003432:Cross-Linking Reagents; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D012329:RNA, Bacterial / Q000737:chemistry* / Q000528:radiation effects; D012343:RNA, Transfer / Q000737:chemistry* / Q000528:radiation effects; D014466:Ultraviolet Rays
chemical_list: D003432:Cross-Linking Reagents; D012329:RNA, Bacterial; C096222:tmRNA; D012343:RNA, Transfer