1VQN

The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortui

Summary for 1VQN

• Entry DOI: 10.2210/pdb1vqn/pdb
• Related: 1FFK 1FFZ 1FGO 1JJ2 1KQS 1M90 1Q7Y 1Q81 1Q82 1Q86 1QVF 1QVG 1S72 1VQ4 1VQ5 1VQ6 1VQ7 1VQ8 1VQ9 1VQK 1VQL 1VQM 1VQO 1VQP
• Descriptor: 23S ribosomal rna, 50S ribosomal protein L7AE, ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG, ... (40 entities in total)
• Functional Keywords: ribosome 50s, protein-protein complex, rna-rna complex, protein-rna complex, peptidyl transferase reaction, ribosome
• Biological source: Haloarcula marismortui; More
• Total number of polymer chains: 33
• Total formula weight: 1491346.43

Authors

Schmeing, T.M.,Steitz, T.A. (deposition date: 2004-12-16, release date: 2005-11-29, Last modification date: 2023-11-15)

Primary citation

Schmeing, T.M.,Huang, K.S.,Strobel, S.A.,Steitz, T.A.
An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.
Nature, 438:520-524, 2005

PubMed 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.

PubMed: 16306996
DOI: 10.1038/nature04152

Experimental method

X-RAY DIFFRACTION (2.4 Å)