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PDBsum entry 1j09
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Atp binding by glutamyl-Trna synthetase is switched to the productive mode by tRNA binding.
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Authors
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S.Sekine,
O.Nureki,
D.Y.Dubois,
S.Bernier,
R.Chênevert,
J.Lapointe,
D.G.Vassylyev,
S.Yokoyama.
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Ref.
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EMBO J, 2003,
22,
676-688.
[DOI no: ]
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PubMed id
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Abstract
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Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an
amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of
aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a
regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In
this study, we determined the crystal structure of the 'non-productive' complex
of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the
GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes.
In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite
within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate
alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to
react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically
different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP
moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore,
tRNA binding to GluRS switches the ATP-binding mode. The interactions of the
three tRNA(Glu) regions with GluRS cause conformational changes around the
ATP-binding site, and allow ATP to bind to the 'productive' subsite.
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Figure 1.
Figure 1 Thermus thermophilus GluRS crystal structures. (A)
Ribbon representation of the ERS/ATP/Glu structure. Five
domains, the Rossmann fold (1), connective peptide (or
acceptor-binding) (2), stem-contact fold (3) and two
anticodon-binding (4 and 5) domains, are colored khaki, light
blue, pink, steel blue and deep blue, respectively. The HVGT and
KISKR motifs of GluRS are highlighted in purple. The ATP and
glutamate molecules in the GluRS catalytic pocket are shown in
green. (B) Overall structure of ERS/tRNA/ATP. The ATP and
tRNA^Glu molecules in the complex are shown in orange and
turquoise, respectively. These figures were produced using the
MOLSCRIPT (Kraulis, 1991) and RASTER3D (Merritt and Murphy,
1994) programs.
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Figure 4.
Figure 4 Substrate/ligand(s) binding in the GluRS complexes. (A
-D) The GluRS catalytic site structures in the present complexes
are shown in the same orientation. The HVGT and KISKR motifs are
highlighted in purple. (A) The ERS/ATP/Glu structure. The
ATP-Mg2+ and glutamate molecules are shown in green. (B) The
ERS/ATP structure. The ATP-Mg2+ is colored light blue. (C) The
ERS/tRNA/ATP structure. The ATP molecule is colored salmon, and
the 3'-terminal adenosine (A76) of tRNA^Glu is cyan. (D) The
ERS/tRNA/GoA structure. The GoA (glutamol-AMP) molecule is
colored yellow. (E) A stereo view showing the ATP recognition in
ERS/tRNA/ATP. (F) A stereo view showing the GoA recognition in
ERS/tRNA/GoA.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2003,
22,
676-688)
copyright 2003.
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Secondary reference #1
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Title
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Structural basis for anticodon recognition by discriminating glutamyl-Trna synthetase.
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Authors
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S.Sekine,
O.Nureki,
A.Shimada,
D.G.Vassylyev,
S.Yokoyama.
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Ref.
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Nat Struct Biol, 2001,
8,
203-206.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Crystal structure of the complex. a, Ribbon
representation of the T. thermophilus GluRS  tRNA^Glu
complex structure. The Rossmann-fold (1), connective-peptide
(2), stem-contact (3), and two anticodon-binding (4 and 5)
domains31 are green, deep blue, light blue, red, and purple,
respectively. The tRNA molecule is highlighted in gold, except
that the anticodon region is shown in cyan. b, The anticodon
bases within the tRNA^Glu anticodon loop (the backbone is gold
and the bases are cyan) and the GluRS domains 4 and 5. c, The
anticodon loop of tRNA^Gln (the backbone is gold and the bases
are cyan) in the GlnRS complex15. The figures were produced
using the MOLSCRIPT32 and RASTER3D^33 programs.
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Figure 2.
Figure 2. The anticodon interface in the T. thermophilus GluRS
tRNA^Glu
complex (stereo view). The anticodon-loop nucleotides, C 34,
U 35, C 36, and A 37 are cyan. Amino acid residues of domains 4
and 5 are light green and orange, respectively.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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Secondary reference #2
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Title
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Architectures of class-Defining and specific domains of glutamyl-Trna synthetase.
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Authors
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O.Nureki,
D.G.Vassylyev,
K.Katayanagi,
T.Shimizu,
S.Sekine,
T.Kigawa,
T.Miyazawa,
S.Yokoyama,
K.Morikawa.
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Ref.
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Science, 1995,
267,
1958-1965.
[DOI no: ]
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PubMed id
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