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PDBsum entry 1il2
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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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The structure of an asprs-Trna(asp) complex reveals a tRNA-Dependent control mechanism.
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Authors
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L.Moulinier,
S.Eiler,
G.Eriani,
J.Gangloff,
J.C.Thierry,
K.Gabriel,
W.H.Mcclain,
D.Moras.
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Ref.
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EMBO J, 2001,
20,
5290-5301.
[DOI no: ]
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PubMed id
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Abstract
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The 2.6 A resolution crystal structure of an inactive complex between yeast
tRNA(Asp) and Escherichia coli aspartyl-tRNA synthetase reveals the molecular
details of a tRNA-induced mechanism that controls the specificity of the
reaction. The dimer is asymmetric, with only one of the two bound tRNAs entering
the active site cleft of its subunit. However, the flipping loop, which controls
the proper positioning of the amino acid substrate, acts as a lid and prevents
the correct positioning of the terminal adenosine. The structure suggests that
the acceptor stem regulates the loop movement through sugar phosphate backbone-
protein interactions. Solution and cellular studies on mutant tRNAs confirm the
crucial role of the tRNA three-dimensional structure versus a specific
recognition of bases in the control mechanism.
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Figure 3.
Figure 3 (A) General view of the dimeric aspartyl-tRNA
synthetase from E.coli complexed with yeast tRNA^Asp and
aspartyl-adenylate. The tRNA^Asp molecules, colored in red and
yellow, are bound to one protein subunit shown in brown and
white, respectively. (B) AspRS surface buried by the tRNA in
monomer 1 (left) and monomer 2 (right) calculated and displayed
using GRASP (Nicholls and Honig, 1991). The surface is colored
according to a distance array between the two molecular
surfaces: distances <2.5 Å between the tRNA and the enzyme are
drawn in green, and distances between 2.5 and 3.5 Å are in
yellow. The interaction surfaces are highly similar for the
protein N-terminal domain in both monomers but vary through the
rest of the complex. (C) Ribbon representation of one AspRS
subunit in gray (monomer 1) of the heterologous complex with the
bound yeast tRNA^Asp in yellow. The E.coli tRNA^Asp as seen in
the cognate complex is drawn in blue after superposition of the
enzymes on their active sites. (D) Relative position of the two
tRNAs of the heterologous complex. Superposition was optimized
on the two subunit active sites. The tRNA^Asp from monomer 1 is
drawn in yellow, the tRNA from monomer 2 in red. (E) Comparison
of the tRNA molecule from monomer 2 of the heterologous complex
(red) and the free (uncomplexed) yeast tRNA^Asp (green) (Moras
et al., 1980). Figures 3, Figures 4, 5 were generated using the
Program SETOR (Evans, 1998).
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Figure 4.
Figure 4 Yeast tRNA^Asp acceptor stem in monomer 1 (A) and
monomer 2 (B) showing the U -G mismatches. The tRNA acceptor
stem in monomer 1 is bound to the enzymes and shows a regular
RNA conformation for the backbone dihedral angles  and
 (gauche-/gauche+);
the distance between the phosphorus atoms of G68 and C69 is 5.6
Å. The tRNA molecule in monomer 2 shows no contact between the
acceptor stem and the protein. As a consequence, the dihedral
angles and
are
trans/trans for G68, and the distance between the phosphorus
atoms of G68 and C69 is 6.6 Å. 'Accommodation' of U -G
mismatches has already been observed for the yeast AspRS
-tRNA^Asp complex (equivalent to tRNA 1) and for the free tRNA
(equivalent to tRNA 2). (C) Recognition of the discriminator
base G73 of yeast tRNA^Asp by the E.coli AspRS. The hydrogen
bonds between the protein and the nucleic acid are shown as
yellow dotted lines. They are similar to those observed in the
homologous E.coli AspRS -tRNA^Asp complex.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2001,
20,
5290-5301)
copyright 2001.
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