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PDBsum entry 1ba2
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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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Multiple open forms of ribose-Binding protein trace the path of its conformational change.
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Authors
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A.J.Björkman,
S.L.Mowbray.
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Ref.
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J Mol Biol, 1998,
279,
651-664.
[DOI no: ]
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PubMed id
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Abstract
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Conformational changes are necessary for the function of bacterial periplasmic
receptors in chemotaxis and transport. Such changes allow entry and exit of
ligand, and enable the correct interaction of the ligand-bound proteins with the
membrane components of each system. Three open, ligand-free forms of the
Escherichia coli ribose-binding protein were observed here by X-ray
crystallographic studies. They are opened by 43 degrees, 50 degrees and 64
degrees with respect to the ligand-bound protein reported previously. The three
open forms are not distinct, but show a clear relationship to each other. All
are the product of a similar opening motion, and are stabilized by a new, almost
identical packing interface between the domains. The changes are generated by
similar bond rotations, although some differences in the three hinge segments
are needed to accommodate the various structural scenarios. Some local repacking
also occurs as interdomain contacts are lost. The least open (43 degrees) form
is probably the dominant one in solution under normal conditions, although a
mixture of species seems likely. The open and closed forms have distinct
surfaces in the regions known to be important in chemotaxis and transport, which
will differentiate their interactions with the membrane components. It seems
certain that the conformational path that links the forms described here is that
followed during ligand retrieval, and in ligand release into the membrane-bound
permease system.
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Figure 3.
Figure 3. The four molecules form a series of related
conformations. The closed (green) and mutant A (blue)
structures are shown after superposition of domain 1.
A single strand of domain 2 (residues 157 to 162) is also
shown as a ribbon of the same color for each protein,
along with the position of the equivalent strands of the
open wt and mutant B structures. The axes of rotation
used to bring domain 2 of the closed form onto the
same domain of each open molecule are shown, using
the colors appropriate to the different open forms. The
two views are 90° apart around the visual x-axis.
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Figure 5.
Figure 5. The location of sites known to be important in transport (red; residues 11, 12, 45, 52, 67, 72, 165 and 166)
and both chemotaxis and transport (blue; residues 44, 70, 73 and 134) are shown for the wild-type closed (a) and
open (b) conformations. The residues buried on ligand binding are shown in yellow, and those buried near the hinge
in the open forms in cyan. The viewpoint differs from that shown in Figure 4 by approximately 45° around the visual
y-axis, and is such that the domains 1 (at bottom) of the two forms are aligned.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
279,
651-664)
copyright 1998.
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Secondary reference #1
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Title
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Identical mutations at corresponding positions in two homologous proteins with nonidentical effects.
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Authors
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A.J.Björkman,
R.A.Binnie,
L.B.Cole,
H.Zhang,
M.A.Hermodson,
S.L.Mowbray.
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Ref.
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J Biol Chem, 1994,
269,
11196-11200.
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PubMed id
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Secondary reference #2
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Title
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Probing protein-Protein interactions. The ribose-Binding protein in bacterial transport and chemotaxis.
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Authors
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A.J.Björkman,
R.A.Binnie,
H.Zhang,
L.B.Cole,
M.A.Hermodson,
S.L.Mowbray.
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Ref.
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J Biol Chem, 1994,
269,
30206-30211.
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PubMed id
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Secondary reference #3
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Title
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1.7 a X-Ray structure of the periplasmic ribose receptor from escherichia coli.
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Authors
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S.L.Mowbray,
L.B.Cole.
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Ref.
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J Mol Biol, 1992,
225,
155-175.
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PubMed id
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Secondary reference #4
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Title
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Functional mapping of the surface of escherichia coli ribose-Binding protein: mutations that affect chemotaxis and transport.
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Authors
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R.A.Binnie,
H.Zhang,
S.Mowbray,
M.A.Hermodson.
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Ref.
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Protein Sci, 1992,
1,
1642-1651.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Alpha-carbon and space-filling representations ofribose-bindingprotein mutations. Both are oriented identically;
viewis directly into the sugar-binding cleftwith the N-terminus-containingDomain 1 on the bottom and the -terminus-
containingDomain 2 on top. itesofsilent are colored green, those that primarily affect transport are red, and those
that affect both chemotaxis and transport are lavender. A: Stereo alpha-carbon tracing withuntestedresidues drawn in white
and mutations that primarily affect chemotaxisdrawn in blue. B: Space-fiing modelwithuntestedresiduedrawn in lighblue.
The mutations that primarily affect chemotaxis are occluded in this view. Modelswereproducedwith the program 0 (Jones
et al., 1990).
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The above figure is
reproduced from the cited reference
which is an Open Access publication published by the Protein Society
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