1vq7
From Proteopedia
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|PDB= 1vq7 |SIZE=350|CAPTION= <scene name='initialview01'>1vq7</scene>, resolution 2.5Å | |PDB= 1vq7 |SIZE=350|CAPTION= <scene name='initialview01'>1vq7</scene>, resolution 2.5Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2OP:(2S)-2-HYDROXYPROPANOIC+ACID'>2OP</scene>, <scene name='pdbligand=5AA:N6-DIMETHYL-3'-AMINO-ADENOSINE-5'-MONOPHOSPHATE'>5AA</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OMG:O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2'-METHYLURIDINE+5'-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5'-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5'-MONOPHOSHATE'>UR3</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1s72|1S72]], [[1jj2|1JJ2]], [[1kqs|1KQS]], [[1m90|1M90]], [[1q7y|1Q7Y]], [[1q81|1Q81]], [[1q82|1Q82]], [[1q86|1Q86]], [[1qvf|1QVF]], [[1qvg|1QVG]], [[1ffk|1FFK]], [[1ffz|1FFZ]], [[1fgo|1FGO]], [[1vq4|1VQ4]], [[1vq5|1VQ5]], [[1vq6|1VQ6]], [[1vq8|1VQ8]], [[1vq9|1VQ9]], [[1vqk|1VQK]], [[1vql|1VQL]], [[1vqm|1VQM]], [[1vqn|1VQN]], [[1vqo|1VQO]], [[1vqp|1VQP]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vq7 OCA], [http://www.ebi.ac.uk/pdbsum/1vq7 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1vq7 RCSB]</span> | ||
}} | }} | ||
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[[Category: Schmeing, T M.]] | [[Category: Schmeing, T M.]] | ||
[[Category: Steitz, T A.]] | [[Category: Steitz, T A.]] | ||
| - | [[Category: CD]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: K]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: NA]] | ||
[[Category: peptidyl transferase reaction]] | [[Category: peptidyl transferase reaction]] | ||
[[Category: protein-protein complex]] | [[Category: protein-protein complex]] | ||
| Line 35: | Line 33: | ||
[[Category: rna-rna complex]] | [[Category: rna-rna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:27:11 2008'' |
Revision as of 21:27, 30 March 2008
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| , resolution 2.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , , , , , , , , , , | ||||||
| Related: | 1S72, 1JJ2, 1KQS, 1M90, 1Q7Y, 1Q81, 1Q82, 1Q86, 1QVF, 1QVG, 1FFK, 1FFZ, 1FGO, 1VQ4, 1VQ5, 1VQ6, 1VQ8, 1VQ9, 1VQK, 1VQL, 1VQM, 1VQN, 1VQO, 1VQP
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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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