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PDBsum entry 1b23
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Gene regulation/RNA
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PDB id
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1b23
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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 crystal structure of cys-Trnacys-Ef-Tu-Gdpnp reveals general and specific features in the ternary complex and in tRNA.
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Authors
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P.Nissen,
S.Thirup,
M.Kjeldgaard,
J.Nyborg.
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Ref.
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Structure, 1999,
7,
143-156.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND:. The translation elongation factor EF-Tu in its GTP-bound state
forms a ternary complex with any aminoacylated tRNA (aa-tRNA), except initiator
tRNA and selenocysteinyl-tRNA. This complex delivers aa-tRNA to the ribosomal A
site during the elongation cycle of translation. The crystal structure of the
yeast Phe-tRNAPhe ternary complex with Thermus aquaticus EF-Tu-GDPNP (Phe-TC)
has previously been determined as one representative of this general yet highly
discriminating complex formation. RESULTS: The ternary complex of Escherichia
coli Cys-tRNACys and T. aquaticus EF-Tu-GDPNP (Cys-TC) has been solved and
refined at 2.6 degrees resolution. Conserved and variable features of the
aa-tRNA recognition and binding by EF-Tu-GTP have been revealed by comparison
with the Phe-TC structure. New tertiary interactions are observed in the tRNACys
structure. A 'kissing complex' is observed in the very close crystal packing
arrangement. CONCLUSIONS: The recognition of Cys-tRNACys by EF-Tu-GDPNP is
restricted to the aa-tRNA motif previously identified in Phe-TC and consists of
the aminoacylated 3' end, the phosphorylated 5' end and one side of the acceptor
stem and T stem. The aminoacyl bond is recognized somewhat differently, yet by
the same primary motif in EF-Tu, which suggests that EF-Tu adapts to subtle
variations in this moiety among all aa-tRNAs. New tertiary interactions revealed
by the Cys-tRNACys structure, such as a protonated C16:C59 pyrimidine pair, a
G15:G48 'Levitt pair' and an s4U8:A14:A46 base triple add to the generic
understanding of tRNA structure from sequence. The structure of the 'kissing
complex' shows a quasicontinuous helix with a distinct shape determined by the
number of base pairs.
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Figure 7.
Figure 7. Focus on the tertiary interactions in the E. coli
Cys-tRNA^Cys molecule by (a) a stereographic representation and
(b) a schematic clover leaf diagram. Residue numbers refer to
the yeast tRNA^Phe standard, thus residues 17 and 47 are missing
(see Figure 1b ). The acceptor stem has been omitted from (a)
for clarity and the schematic diagram in (b) includes only the
base–base interactions. Further, the variable loop in (b) has
been wrapped into the clover leaf center to indicate the unique
role of A46 in the tertiary interactions. Colour codes are as in
Figure 2 . Part (b) was produced using ‘The Gimp’
(http://www.gimp.org).
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1999,
7,
143-156)
copyright 1999.
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Secondary reference #1
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Title
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Crystal structure of the ternary complex of phe-Trnaphe, Ef-Tu, And a gtp analog.
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Authors
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P.Nissen,
M.Kjeldgaard,
S.Thirup,
G.Polekhina,
L.Reshetnikova,
B.F.Clark,
J.Nyborg.
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Ref.
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Science, 1995,
270,
1464-1472.
[DOI no: ]
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PubMed id
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