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1vq6, resolution 2.70Å ()
Ligands: , , , ,
Non-Standard Residues: , , , , , , , ,
Related: 1s72, 1jj2, 1kqs, 1m90, 1q7y, 1q81, 1q82, 1q86, 1qvf, 1qvg, 1ffk, 1ffz, 1fgo, 1vq4, 1vq5, 1vq7, 1vq8, 1vq9, 1vqk, 1vql, 1vqm, 1vqn, 1vqo, 1vqp
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


The structure of c-hpmn and CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortui

Publication Abstract from PubMed

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.

An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA., Schmeing TM, Huang KS, Strobel SA, Steitz TA, Nature. 2005 Nov 24;438(7067):520-4. PMID:16306996

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1vq6 is a 32 chain structure with sequence from Haloarcula marismortui. Full crystallographic information is available from OCA.

See Also


  • Schmeing TM, Huang KS, Strobel SA, Steitz TA. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature. 2005 Nov 24;438(7067):520-4. PMID:16306996 doi:10.1038/nature04152
  • Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA. Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol Cell. 2005 Nov 11;20(3):437-48. PMID:16285925 doi:http://dx.doi.org/10.1016/j.molcel.2005.09.006

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