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PDBsum entry 1efc
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RNA binding protein
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PDB id
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1efc
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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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Crystal structure of intact elongation factor ef-Tu from escherichia coli in gdp conformation at 2.05 a resolution.
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Authors
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H.Song,
M.R.Parsons,
S.Rowsell,
G.Leonard,
S.E.Phillips.
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Ref.
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J Mol Biol, 1999,
285,
1245-1256.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of intact elongation factor Tu (EF-Tu) from Escherichia
coli in GDP-bound conformation has been determined using a combination of
multiple isomorphous replacement (MIR) and multiwavelength anomalous diffraction
(MAD) methods. The current atomic model has been refined to a crystallographic R
factor of 20.3 % and free R-factor of 26.8 % in the resolution range of 10-2.05
A. The protein consists of three domains: domain 1 has an alpha/beta structure;
while domain 2 and domain 3 are beta-barrel structures. Although the global fold
of the current model is similar to those of published structures, the secondary
structural assignment has been improved due to the high quality of the current
model. The switch I region (residues 40-62) is well ordered in this structure.
Comparison with the structure of EF-Tu in GDP-bound form from Thermus aquaticus
shows that although the individual domain structures are similar in these two
structures, the orientation of domains changes significantly. Interactions
between domains 1 and 3 in our E. coli EF-Tu-GDP complex are quite different
from those of EF-Tu with bound GTP from T. aquaticus, due to the domain
rearrangement upon GTP binding. The binding sites of the Mg2+ and guanine
nucleotide are revealed in detail. Two water molecules that co-ordinate the Mg2+
have been identified to be well conserved in the GDP and GTP-bound forms of
EF-Tu structures, as well as in the structure of Ras p21 with bound GDP.
Comparisons of the Mg2+ binding site with other guanine nucleotide binding
proteins in GDP-bound forms show that the Mg2+ co-ordination patterns are well
preserved among these structures.
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Figure 1.
Figure 1. Ribbon diagrams of EF-Tu molecules.
(a) EC-EF-Tu-GDP; (b) same view of EF-Tu-GTP from
T. aquaticus (TA-EF-Tu-GTP). The switch I region is
shown in yellow and the switch II region in green. The
rest of the polypeptide backbone is shown in purple,
royal blue and dark blue for domain 1 (residues 8-204),
domain 2 (residues 205-298) and domain 3 (299-393),
respectively. GDP or GTP molecules are shown in ball-
and-stick models, and Mg
2+
are shown as cyan spheres.
The Figure was drawn with MOLSCRIPT (Kraulis,
1991), as are Figures 4 and 5.
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Figure 5.
Figure 5. Stereo view of the interface between domain
1 and domain 3. The switch I and II regions are shown
in yellow and green, respectively. The rest of the poly-
peptide chain in domain 1 is shown in purple, and that
of the domain 3 in slate blue. Hydrogen bonds are
shown as broken lines, and water molecules as cyan
spheres. Residues involved in interactions between
domains 1 and 3 are shown as ball-and-stick. (a) EC-EF-
Tu-GDP; (b) TA-EF-Tu-GTP.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
285,
1245-1256)
copyright 1999.
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Secondary reference #1
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Title
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An alpha to beta conformational switch in ef-Tu.
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Authors
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K.Abel,
M.D.Yoder,
R.Hilgenfeld,
F.Jurnak.
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Ref.
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Structure, 1996,
4,
1153-1159.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. A comparison of E. coli EF-Tu-GDP and T.
thermophilus EF-Tu-GTP. The polypeptide backbone is shown in
blue, except as noted: the Switch I region, in yellow; the
Switch II region, in orange; the GDP or GTP molecule, in red;
and Mg2+ ions, in magenta. The standard view of EF-Tu from E.
coli (a) and T. thermophilus (b), comparing the GDP form (a) to
the GTP form (b). The view illustrates the major differences in
the relative rearrangement of the domains between the GDP and
GTP forms as well as the local conformational differences
between the Switch I and II regions. A side view of EF-Tu, from
E. coli (c) and T. thermophilus (d), indicates the regions of
interaction between the Switch I tip of the GDP form, shown in
(c), and Domain 3. The analogous region in the Switch I sequence
of EF-Tu-GTP does not interact with Domain 3. (The figure has
been generated by MOLSCRIPT [29].)
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Helix unwinding in the effector region of elongation factor ef-Tu-Gdp.
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Authors
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G.Polekhina,
S.Thirup,
M.Kjeldgaard,
P.Nissen,
C.Lippmann,
J.Nyborg.
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Ref.
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Structure, 1996,
4,
1141-1151.
[DOI no: ]
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PubMed id
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Figure 6.
Figure 6. Comparison of the Mg2+-binding sites in T.
aquaticus EF-Tu-GDP and EF-Tu-GDPNP. (a) EF-Tu-GDP and (b)
EF-Tu-GDPNP; GDP and GDPNP are shown in ball-and-stick
representation. The atoms are coloured as in Figure 4. (Figure
produced with MOLSCRIPT [37].)
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #3
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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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Secondary reference #4
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Title
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The crystal structure of elongation factor ef-Tu from thermus aquaticus in the gtp conformation.
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Authors
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M.Kjeldgaard,
P.Nissen,
S.Thirup,
J.Nyborg.
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Ref.
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Structure, 1993,
1,
35-50.
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PubMed id
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Secondary reference #5
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Title
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Refined structure of elongation factor ef-Tu from escherichia coli.
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Authors
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M.Kjeldgaard,
J.Nyborg.
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Ref.
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J Mol Biol, 1992,
223,
721-742.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5. ''-trace of omain 3. he nterface to omain s ormed by the antiparallel p-sheet formed
that enters the domain and the strand eading to he C terminus.
by the strand
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Figure 10.
Figure 10. he side-chain of Tvr87 wedged between B-strands a and c, intercepting the ydrogen bod could
therwise form between the pep&es of yg81 ad Thrl6
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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