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PDBsum entry 2cv2
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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 bases of transfer RNA-Dependent amino acid recognition and activation by glutamyl-Trna synthetase.
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Authors
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S.Sekine,
M.Shichiri,
S.Bernier,
R.Chênevert,
J.Lapointe,
S.Yokoyama.
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Ref.
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Structure, 2006,
14,
1791-1799.
[DOI no: ]
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PubMed id
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Abstract
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Glutamyl-tRNA synthetase (GluRS) is one of the aminoacyl-tRNA synthetases that
require the cognate tRNA for specific amino acid recognition and activation. We
analyzed the role of tRNA in amino acid recognition by crystallography. In the
GluRS*tRNA(Glu)*Glu structure, GluRS and tRNA(Glu) collaborate to form a highly
complementary L-glutamate-binding site. This collaborative site is functional,
as it is formed in the same manner in pretransition-state mimic,
GluRS*tRNA(Glu)*ATP*Eol (a glutamate analog), and posttransition-state mimic,
GluRS*tRNA(Glu)*ESA (a glutamyl-adenylate analog) structures. In contrast, in
the GluRS*Glu structure, only GluRS forms the amino acid-binding site, which is
defective and accounts for the binding of incorrect amino acids, such as
D-glutamate and L-glutamine. Therefore, tRNA(Glu) is essential for formation of
the completely functional binding site for L-glutamate. These structures,
together with our previously described structures, reveal that tRNA plays a
crucial role in accurate positioning of both L-glutamate and ATP, thus driving
the amino acid activation.
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Figure 3.
Figure 3. Glutamate Interaction Manners in the Absence and
Presence of tRNA^Glu
(A) A stereo view showing the manner
of glutamate recognition by the GluRS•tRNA^Glu complex in the
ERS/tRNA/Glu structure. The bound glutamate, the protein amino
acid residues, and A76 are colored green, white, and salmon,
respectively.
(B) The GluRS-glutamate interaction in the
ERS/Glu structure (stereo view). The glutamate molecule is
colored yellow.
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Figure 6.
Figure 6. Glutamol in ERS/tRNA/ATP/Eol and Glutamyl-Sulfamoyl
Adenosine in ERS/tRNA/ESA
(A) Schematic drawings of
L-glutamate (upper) and L-glutamol (Eol; lower) (Desjardins et
al., 1998).
(B) Schematic drawings of L-glutamyl-adenylate
(upper) and 5′-O-[N-(L-glutamyl)-sulfamoyl] adenosine (ESA;
lower). ESA is a nonhydrolyzable analog of glutamyl-adenylate,
and it is known as a potent competitive inhibitor of E. coli
GluRS with respect to glutamic acid (K[i] = 2.8 nM) (Bernier et
al., 2005).
(C) The annealed |F[o] − F[c]| omit electron
density contoured at 3 σ, showing the L-glutamol molecule in
ERS/tRNA/ATP/Eol. Two alternative conformations of the Eol
molecule (cyan and marine) are superimposed.
(D) The omit
electron density map corresponding to glutamyl-sulfamoyl
adenosine in ERS/tRNA/ESA. The refined ESA model (light green)
is superimposed on the density contoured at 3 σ.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2006,
14,
1791-1799)
copyright 2006.
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