1vq7
From Proteopedia
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The structure of the transition state analogue "DCA" bound to the large ribosomal subunit of haloarcula marismortui
Overview
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.
About this Structure
1VQ7 is a Protein complex structure of sequences from Haloarcula marismortui with MG, K, NA, CD and CL as ligands. Full crystallographic information is available from OCA.
Reference
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
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