title: Transit of tRNA through the Escherichia coli ribosome. Cross-linking of the 3' end of tRNA to specific nucleotides of the 23 S ribosomal RNA at the A, P, and E sites.
abstract: When bound to Escherichia coli ribosomes and irradiated with near-UV light, various derivatives of yeast tRNA(Phe) containing 2-azidoadenosine at the 3' terminus form cross-links to 23 S rRNA and 50 S subunit proteins in a site-dependent manner. A and P site-bound tRNAs, whose 3' termini reside in the peptidyl transferase center, label primarily nucleotides U2506 and U2585 and protein L27. In contrast, E site-bound tRNA labels nucleotide C2422 and protein L33. The cross-linking patterns confirm the topographical separation of the peptidyl transferase center from the E site domain. The relative amounts of label incorporated into the universally conserved residues U2506 and U2585 depend on the occupancy of the A and P sites by different tRNA ligands and indicates that these nucleotides play a pivotal role in peptide transfer. In particular, the 3'-adenosine of the peptidyl-tRNA analogue, AcPhe-tRNA(Phe), remains in close contact with U2506 regardless of whether its anticodon is located in the A site or P site. Our findings, therefore, modify and extend the hybrid state model of tRNA-ribosome interaction. We show that the 3'-end of the deacylated tRNA that is formed after transpeptidation does not immediately progress to the E site but remains temporarily in the peptidyl transferase center. In addition, we demonstrate that the E site, defined by the labeling of nucleotide C2422 and protein L33, represents an intermediate state of binding that precedes the entry of deacylated tRNA into the F (final) site from which it dissociates into the cytoplasm.
authors.affiliation: Department of Animal and Dairy Sciences, Program in Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849-5415, USA.
authors.forename: J
authors.initials: J
authors.lastname: Wower
authors.forename: S V
authors.initials: SV
authors.lastname: Kirillov
authors.forename: I K
authors.initials: IK
authors.lastname: Wower
authors.forename: S
authors.initials: S
authors.lastname: Guven
authors.forename: S S
authors.initials: SS
authors.lastname: Hixson
authors.forename: R A
authors.initials: RA
authors.lastname: Zimmermann
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000378:metabolism*; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism*
chemical_list: D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D012343:RNA, Transfer