The Solution Structure of the Escherichia coli Initiator tRNA and Its Interactions with Initiation Factor 2 and the Ribosomal 30 S Subunit

• Published in: The Journal of biological chemistry Vol. 264; no. 34; pp. 20363 - 20371
• Main Authors: Wakao, H, Romby, P, Westhof, E, Laalami, S, Grunberg-Manago, M, Ebel, J.P., Ehresmann, C, Ehresmann, B
• Format: Journal Article
• Language: English
• Published: Bethesda, MD Elsevier Inc 05-12-1989; American Society for Biochemistry and Molecular Biology
• Subjects: Base Sequence; Biological and medical sciences; Escherichia coli - genetics; Escherichia coli - metabolism; Eukaryotic Initiation Factor-2 - metabolism; Fundamental and applied biological sciences. Psychology; Models, Molecular; Molecular biophysics; Molecular Sequence Data; Nucleic Acid Conformation; Protein Binding; Protein Conformation; Ribosomes - metabolism; RNA, Transfer, Amino Acyl - metabolism; RNA, Transfer, Met; Solutions; Structure in molecular biology; Tridimensional structure; Initiation complex; Yeast; Gel electrophoresis; Escherichia coli; Molecular interaction; Modeling; Spatial structure; Chemical modification; Ribosomal RNA; Computerized processing; Bacteria; Molecular probe; Escherichieae; Comparative study; Enterobacteriaceae
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1016/S0021-9258(19)47072-5

The conformation of the Escherichia coli initiator tRNA has been investigated using enzymatic and chemical probes. This study was conducted on the naked tRNA and on the tRNA involved in the various steps leading to the formation of the 30 S • IF-2 • GTP • fMet-tRNA • AUG complex. A three-dimensional model of the initiator tRNA is presented, which displays several differences with yeast tRNAPhe: (i) the anticodon arm is more rigid; (ii) the presence of an additional nucleotide in the D loop results in specific features in both T and D loops; (iii) C1 and A72 might form a noncanonical base pair. Aminoacylation and formylation induce subtle conformational adjustments near the 3′ end, the T arm and the D loop. Initiation factor (IF) 2 interacts with a rather limited portion of the tRNA, covering the T loop and the minor groove of the T stem, and induces an increased flexibility in the anticodon arm. The specific structural features observed in the T loop are probably recognized by IF-2. In the 30 S • IF-2 • GTP • fMet-tRNA • AUG complex, additional protections are observed in the acceptor stem and in the anticodon arm, resulting from a strong steric hindrance and from the codon-anticodon interaction within the subunit decoding site.