title: An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.
abstract: The large ribosomal subunit catalyses the reaction between the alpha-amino group of the aminoacyl-tRNA bound to the A site and the ester carbon of the peptidyl-tRNA bound to the P site, while preventing the nucleophilic attack of water on the ester, which would lead to unprogrammed deacylation of the peptidyl-tRNA. Here we describe three new structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with peptidyl transferase substrate analogues that reveal an induced-fit mechanism in which substrates and active-site residues reposition to allow the peptidyl transferase reaction. Proper binding of an aminoacyl-tRNA analogue to the A site induces specific movements of 23S rRNA nucleotides 2618-2620 (Escherichia coli numbering 2583-2585) and 2541(2506), thereby reorienting the ester group of the peptidyl-tRNA and making it accessible for attack. In the absence of the appropriate A-site substrate, the peptidyl transferase centre positions the ester link of the peptidyl-tRNA in a conformation that precludes the catalysed nucleophilic attack by water. Protein release factors may also function, in part, by inducing an active-site rearrangement similar to that produced by the A-site aminoacyl-tRNA, allowing the carbonyl group and water to be positioned for hydrolysis.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: T Martin
authors.initials: TM
authors.lastname: Schmeing
authors.forename: Kevin S
authors.initials: KS
authors.lastname: Huang
authors.forename: Scott A
authors.initials: SA
authors.lastname: Strobel
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Steitz
mesh_terms: D000215:Acylation; D019843:Archaeal Proteins / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D019614:Haloarcula marismortui / Q000737:chemistry / Q000235:genetics; D006868:Hydrolysis; D008958:Models, Molecular; D010455:Peptides / Q000378:metabolism*; D014176:Protein Biosynthesis; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism*; D012270:Ribosomes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013033:Sparsomycin / Q000378:metabolism; D014867:Water / Q000737:chemistry / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; D010455:Peptides; D021122:Protein Subunits; D012338:RNA, Ribosomal, 23S; D014867:Water; D013033:Sparsomycin; D012343:RNA, Transfer