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PDBsum entry 3cme
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Contents |
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237 a.a.
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337 a.a.
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246 a.a.
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140 a.a.
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172 a.a.
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119 a.a.
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29 a.a.
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160 a.a.
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70 a.a.
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142 a.a.
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132 a.a.
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145 a.a.
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194 a.a.
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186 a.a.
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115 a.a.
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143 a.a.
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95 a.a.
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150 a.a.
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81 a.a.
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119 a.a.
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53 a.a.
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65 a.a.
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154 a.a.
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82 a.a.
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142 a.a.
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73 a.a.
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56 a.a.
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46 a.a.
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92 a.a.
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 _SR
×108
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 _NA
×75
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 _CL
×22
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_MG
×93
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 _CD
×5
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 __K
×2
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References listed in PDB file
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Key reference
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Title
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Peptidyl-Cca deacylation on the ribosome promoted by induced fit and the o3'-Hydroxyl group of a76 of the unacylated a-Site tRNA.
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Authors
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M.Simonović,
T.A.Steitz.
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Ref.
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Rna, 2008,
14,
2372-2378.
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PubMed id
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Abstract
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The last step in ribosome-catalyzed protein synthesis is the hydrolytic release
of the newly formed polypeptide from the P-site bound tRNA. Hydrolysis of the
ester link of the peptidyl-tRNA is stimulated normally by the binding of release
factors (RFs). However, an unacylated tRNA or just CCA binding to the ribosomal
A site can also stimulate deacylation under some nonphysiological conditions.
Although the sequence of events is well described by biochemical studies, the
structural basis of the mechanism underlying this process is not well
understood. Two new structures of the large ribosomal subunit of Haloarcula
marismortui complexed with a peptidyl-tRNA analog in the P site and two
oligonucleotide mimics of unacylated tRNA, CCA and CA, in the A site show that
the binding of either CA or CCA induces a very similar conformational change in
the peptidyl-transferase center as induced by aminoacyl-CCA. However, only CCA
positions a water molecule appropriately to attack the carbonyl carbon of the
peptidyl-tRNA and stabilizes the proper orientation of the ester link for
hydrolysis. We, thus, conclude that both the ability of the O3'-hydroxyl group
of the A-site A76 to position the water and the A-site CCA induced
conformational change of the PTC are critical for the catalysis of the
deacylation of the peptidyl-tRNA by CCA, and perhaps, an analogous mechanism is
used by RFs.
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