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PDBsum entry 2z3l
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References listed in PDB file
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Key reference
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Title
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Protein-Based peptide-Bond formation by aminoacyl-Trna protein transferase.
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Authors
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K.Watanabe,
Y.Toh,
K.Suto,
Y.Shimizu,
N.Oka,
T.Wada,
K.Tomita.
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Ref.
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Nature, 2007,
449,
867-871.
[DOI no: ]
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PubMed id
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Abstract
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Eubacterial leucyl/phenylalanyl-tRNA protein transferase (LF-transferase)
catalyses peptide-bond formation by using Leu-tRNA(Leu) (or Phe-tRNA(Phe)) and
an amino-terminal Arg (or Lys) of a protein, as donor and acceptor substrates,
respectively. However, the catalytic mechanism of peptide-bond formation by
LF-transferase remained obscure. Here we determine the structures of complexes
of LF-transferase and phenylalanyl adenosine, with and without a short peptide
bearing an N-terminal Arg. Combining the two separate structures into one
structure as well as mutation studies reveal the mechanism for peptide-bond
formation by LF-transferase. The electron relay from Asp 186 to Gln 188 helps
Gln 188 to attract a proton from the alpha-amino group of the N-terminal Arg of
the acceptor peptide. This generates the attacking nucleophile for the carbonyl
carbon of the aminoacyl bond of the aminoacyl-tRNA, thus facilitating
peptide-bond formation. The protein-based mechanism for peptide-bond formation
by LF-transferase is similar to the reverse reaction of the acylation step
observed in the peptide hydrolysis reaction by serine proteases.
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Figure 3.
Figure 3: Superposition of two binary complex structures. a,
Structural difference between the complex with rA-Phe (blue) and
that with the product peptide (green). b, Detailed structural
difference of the Gln 188 side chains between the two
structures. c, Superposition of the two complexes. The complex
with rA-Phe and that with the product peptide are coloured blue
and dark green, respectively. The benzyl group of rA-Phe and the
Arg in the product peptide are coloured cyan and green,
respectively, and are shown in stick models.
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Figure 4.
Figure 4: A model of the catalytic mechanism for peptide-bond
formation by LF-transferase.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2007,
449,
867-871)
copyright 2007.
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