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PDBsum entry 1vq8
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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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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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70 a.a.
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 _SR
×114
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 _MG
×94
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 _NA
×75
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_CL
×22
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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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Structural insights into the roles of water and the 2' Hydroxyl of the p site tRNA in the peptidyl transferase reaction.
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Authors
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T.M.Schmeing,
K.S.Huang,
D.E.Kitchen,
S.A.Strobel,
T.A.Steitz.
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Ref.
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Mol Cell, 2005,
20,
437-448.
[DOI no: ]
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PubMed id
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Abstract
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Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of
the large ribosomal subunit. Crystal structures of the large ribosomal subunit
of Haloarcula marismortui (Hma) complexed with several analogs that represent
either the substrates or the transition state intermediate of the peptidyl
transferase reaction show that this reaction proceeds through a tetrahedral
intermediate with S chirality. The oxyanion of the tetrahedral intermediate
interacts with a water molecule that is positioned by nucleotides A2637 (E. coli
numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent
metal ions observed in the PTC that could directly promote catalysis. The A76 2'
hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and
could facilitate peptide bond formation by substrate positioning and by acting
as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the
peptidyl-tRNA.
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Figure 1.
Figure 1. Unbiased F[o] − F[c] Electron Density Maps for
Some of the Complexes of the 50S Subunit Bound with Peptidyl
Transferase Ligands, All Contoured at 3 σ
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Figure 6.
Figure 6. The Reaction Pathway for Peptide Bond Formation
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The above figures are
reprinted
by permission from Cell Press:
Mol Cell
(2005,
20,
437-448)
copyright 2005.
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