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PDBsum entry 1h3e
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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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Class I tyrosyl-Trna synthetase has a class ii mode of cognate tRNA recognition.
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Authors
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A.Yaremchuk,
I.Kriklivyi,
M.Tukalo,
S.Cusack.
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Ref.
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EMBO J, 2002,
21,
3829-3840.
[DOI no: ]
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PubMed id
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Abstract
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Bacterial tyrosyl-tRNA synthetases (TyrRS) possess a flexibly linked C-terminal
domain of approximately 80 residues, which has hitherto been disordered in
crystal structures of the enzyme. We have determined the structure of Thermus
thermophilus TyrRS at 2.0 A resolution in a crystal form in which the C-terminal
domain is ordered, and confirm that the fold is similar to part of the
C-terminal domain of ribosomal protein S4. We have also determined the structure
at 2.9 A resolution of the complex of T.thermophilus TyrRS with cognate
tRNA(tyr)(G Psi A). In this structure, the C-terminal domain binds between the
characteristic long variable arm of the tRNA and the anti-codon stem, thus
recognizing the unique shape of the tRNA. The anticodon bases have a novel
conformation with A-36 stacked on G-34, and both G-34 and Psi-35 are
base-specifically recognized. The tRNA binds across the two subunits of the
dimeric enzyme and, remarkably, the mode of recognition of the class I TyrRS for
its cognate tRNA resembles that of a class II synthetase in being from the major
groove side of the acceptor stem.
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Figure 3.
Figure 3 Interactions between tyrosyl-tRNA synthetase and
tRNA^tyr. (A) The C-terminal domain (orange) binds in the elbow
between the long variable arm and the anti-codon stem of the
tRNA (red backbone, green bases). The anti-codon stem loop
interacts with both the C-terminal domain and the  -helical
domain (pink). The tRNA makes no contact with the catalytic
domain of the same subunit (cyan). (B) The unusual conformation
of the anti-codon triplet in which Ade-36 is stacked on Gua-34,
while Psu-35 bulges out. (C) Base-specific interactions of
Asp-259 from the -helical
domain with Gua-34 and Asp-423 from the C-terminal domain with
Psu-35.
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Figure 4.
Figure 4 Structure of tRNAtyr compared with that of tRNA^ser.
(A) Comparison of the secondary structures of T.thermophilus
tRNA^tyr(G  A)
(left) and tRNA^tyr(GGA) (right), highlighting differences,
conserved in other prokaryotic organisms, that determine the
orientation of the long variable arm. tRNA^tyr nucleotides with
only backbone contacts to TyrRSTT are shown in purple, those
with only base contacts are shown in green and those with
backbone and base contacts are shown in orange. (B) Comparison
of the 3D structures of the base of the long variable arm in
T.thermophilus tRNA^tyr and T.thermophilus tRNA^ser (Biou et
al., 1994), based on the structural alignment in (C). In
tRNA^ser, Gua-20B is unpaired and stacks against the first base
pair of the long variable arm, which comprises A45:U48-1 (top).
In tRNA^tyr, U48-1 is unpaired and stacks against the first base
pair of the long variable arm, which comprises A20B:U48−2
(bottom). (C) View looking down the anticodon stem-loop of the
structural alignment of tRNA^tyr (blue) and tRNA^ser (red) based
on superposition of 46 phosphates from the acceptor stem, D- and
T-loops (r.m.s.d. = 1.16 Å). The tRNA cores have a very
similar structure, but the variable arms project at an angle
differing by  50°.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
3829-3840)
copyright 2002.
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