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PDBsum entry 2dps
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References listed in PDB file
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Key reference
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Title
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Crystal structures of leucyl/phenylalanyl-Trna-Protein transferase and its complex with an aminoacyl-Trna analog.
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Authors
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K.Suto,
Y.Shimizu,
K.Watanabe,
T.Ueda,
S.Fukai,
O.Nureki,
K.Tomita.
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Ref.
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EMBO J, 2006,
25,
5942-5950.
[DOI no: ]
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PubMed id
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Abstract
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Eubacterial leucyl/phenylalanyl-tRNA protein transferase (L/F-transferase),
encoded by the aat gene, conjugates leucine or phenylalanine to the N-terminal
Arg or Lys residue of proteins, using Leu-tRNA(Leu) or Phe-tRNA(Phe) as a
substrate. The resulting N-terminal Leu or Phe acts as a degradation signal for
the ClpS-ClpAP-mediated N-end rule protein degradation pathway. Here, we present
the crystal structures of Escherichia coli L/F-transferase and its complex with
an aminoacyl-tRNA analog, puromycin. The C-terminal domain of L/F-transferase
consists of the GCN5-related N-acetyltransferase fold, commonly observed in the
acetyltransferase superfamily. The p-methoxybenzyl group of puromycin,
corresponding to the side chain of Leu or Phe of Leu-tRNA(Leu) or Phe-tRNA(Phe),
is accommodated in a highly hydrophobic pocket, with a shape and size suitable
for hydrophobic amino-acid residues lacking a branched beta-carbon, such as
leucine and phenylalanine. Structure-based mutagenesis of L/F-transferase
revealed its substrate specificity. Furthermore, we present a model of the
L/F-transferase complex with tRNA and substrate proteins bearing an N-terminal
Arg or Lys.
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Figure 1.
Figure 1 Overall architecture of E. coli L/F-transferase. (A)
Stereo view of the E. coli L/F-transferase structure. The
NH[2]-terminal domain (residues 2–62) and the COOH-terminal
domain (residues 63–232) are colored blue and green,
respectively. The puromycin bound to the hydrophobic pocket is
colored yellow. (B) Topology diagram of L/F-transferase. The
rimmed elements in the COOH-terminal domain (  3–
5)
and (  5–
12)
are common to the GNAT superfamily fold. The -helices
and -strands
in the COOH-terminal domains are colored red and yellow,
respectively. (C) Comparison of the structures of E. coli
L/F-transferase (left), W. viridescens FemX (wvFemX; middle, PDB
accession number 1P4N; Biarrotte-Sorin et al, 2004) and S.
aureus FemA (saFemA; PDB accession number 1LRZ; Benson et al,
2002). The COOH-terminal domain of L/F-transferase is
topologically similar to the domain 2's of wvFemX and saFemA.
The conserved -helices
and -strands
in L/F-transferase, wvFemX and saFemA, are colored red and
yellow, respectively.
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Figure 3.
Figure 3 Recognition of the puromycin by E. coli
L/F-transferase. (A) Chemical structure of puromycin (left) and
that of the 3'-ends of Leu-tRNA^Leu and Phe-tRNA^Phe (middle and
right, respectively). The amino-acid moiety and the base moiety
are colored pink and blue, respectively. (B) |Fo-Fc| omit map of
puromycin (contour level 3.0  ).
(C) Recognition of the p-methoxybenzyl group and the puromycin
base by the hydrophobic pocket, as shown by a surface model. (D)
Ribbon model of (C). The hydrophobic amino acid involved in the
recognition of the p-methoxybenzyl group and the base moiety of
puromycin are colored green and blue, respectively. (E) The
C-shaped edge of the hydrophobic pocket is composed of
continuous amino-acid residues (Gly155-Glu156-Ser157-Met158;
colored yellow and highlighted). The -,
-
and  -carbons
of puromycin are also shown.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2006,
25,
5942-5950)
copyright 2006.
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