This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1vq7
From Proteopedia
(New page: 200px<br /><applet load="1vq7" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vq7, resolution 2.5Å" /> '''The structure of the ...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1vq7.gif|left|200px]]<br /><applet load="1vq7" size=" | + | [[Image:1vq7.gif|left|200px]]<br /><applet load="1vq7" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1vq7, resolution 2.5Å" /> | caption="1vq7, resolution 2.5Å" /> | ||
'''The structure of the transition state analogue "DCA" bound to the large ribosomal subunit of haloarcula marismortui'''<br /> | '''The structure of the transition state analogue "DCA" bound to the large ribosomal subunit of haloarcula marismortui'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The large ribosomal subunit catalyses the reaction between the alpha-amino | + | 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== | ==About this Structure== | ||
| - | 1VQ7 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] with MG, K, NA, CD and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1VQ7 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=K:'>K</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=CD:'>CD</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VQ7 OCA]. |
==Reference== | ==Reference== | ||
| Line 13: | Line 13: | ||
[[Category: Haloarcula marismortui]] | [[Category: Haloarcula marismortui]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Schmeing, T | + | [[Category: Schmeing, T M.]] |
| - | [[Category: Steitz, T | + | [[Category: Steitz, T A.]] |
[[Category: CD]] | [[Category: CD]] | ||
[[Category: CL]] | [[Category: CL]] | ||
| Line 26: | Line 26: | ||
[[Category: rna-rna complex]] | [[Category: rna-rna complex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:37:29 2008'' |
Revision as of 13:37, 21 February 2008
|
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 , , , and 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
Page seeded by OCA on Thu Feb 21 15:37:29 2008
