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PDBsum entry 1lls
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Sugar binding protein
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PDB id
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1lls
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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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Detection and characterization of xenon-Binding sites in proteins by 129xe nmr spectroscopy.
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Authors
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S.M.Rubin,
S.Y.Lee,
E.J.Ruiz,
A.Pines,
D.E.Wemmer.
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Ref.
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J Mol Biol, 2002,
322,
425-440.
[DOI no: ]
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PubMed id
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Abstract
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Xenon-binding sites in proteins have led to a number of applications of xenon in
biochemical and structural studies. Here we further develop the utility of 129Xe
NMR in characterizing specific xenon-protein interactions. The sensitivity of
the 129Xe chemical shift to its local environment and the intense signals
attainable by optical pumping make xenon a useful NMR reporter of its own
interactions with proteins. A method for detecting specific xenon-binding
interactions by analysis of 129Xe chemical shift data is illustrated using the
maltose binding protein (MBP) from Escherichia coli as an example. The crystal
structure of MBP in the presence of 8atm of xenon confirms the binding site
determined from NMR data. Changes in the structure of the xenon-binding cavity
upon the binding of maltose by the protein can account for the sensitivity of
the 129Xe chemical shift to MBP conformation. 129Xe NMR data for xenon in
solution with a number of cavity containing phage T4 lysozyme mutants show that
xenon can report on cavity structure. In particular, a correlation exists
between cavity size and the binding-induced 129Xe chemical shift. Further
applications of 129Xe NMR to biochemical assays, including the screening of
proteins for xenon binding for crystallography are considered.
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Figure 2.
Figure 2. Stereo diagram of MBP with bound xenon. The
density shown in magenta marks the difference Fourier map
(contoured at 5s) generated from the previously published native
data set and the data set presented here for MBP crystals
pressurized with 8 atm xenon. The xenon-binding cavity is
located in the N-terminal domain of the protein below the
surface of the sugar binding cleft.
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Figure 3.
Figure 3. Stereo view of the xenon-binding cavity in MBP.
The electron density in cyan corresponds to a 2F[obs] -F[calc]
map contoured at 2s. The xenon is localized in the cavity away
from the lysine and water that mark the end of the cavity at the
protein surface. While the presence of many hydrophobic
side-chains is often observed in xenon-binding cavities, the
proximity of the cavity to the surface is less common.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2002,
322,
425-440)
copyright 2002.
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Secondary reference #1
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Title
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Detection of a conformational change in maltose binding protein by (129)xe nmr spectroscopy.
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Authors
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S.M.Rubin,
M.M.Spence,
I.E.Dimitrov,
E.J.Ruiz,
A.Pines,
D.E.Wemmer.
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Ref.
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J Am Chem Soc, 2001,
123,
8616-8617.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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The 2.3-A resolution structure of the maltose- Or maltodextrin-Binding protein, A primary receptor of bacterial active transport and chemotaxis.
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Authors
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J.C.Spurlino,
G.Y.Lu,
F.A.Quiocho.
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Ref.
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J Biol Chem, 1991,
266,
5202-5219.
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PubMed id
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Secondary reference #3
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Title
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Crystallographic evidence of a large ligand-Induced hinge-Twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis.
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Authors
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A.J.Sharff,
L.E.Rodseth,
J.C.Spurlino,
F.A.Quiocho.
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Ref.
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Biochemistry, 1992,
31,
10657-10663.
[DOI no: ]
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PubMed id
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Secondary reference #4
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Title
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Size versus polarizability in protein-Ligand interactions: binding of noble gases within engineered cavities in phage t4 lysozyme.
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Authors
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M.L.Quillin,
W.A.Breyer,
I.J.Griswold,
B.W.Matthews.
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Ref.
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J Mol Biol, 2000,
302,
955-977.
[DOI no: ]
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PubMed id
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Figure 4.
This Figure is intended to show how the shape of each cavity restricts the
motion of the noble gas and defines the preferred binding sites. The color at each
point indicates the distance from the closest point on the cavity wall. As can be seen
by comparing with Figure 1, the noble gases bind at sites that are as far as
possible from the walls of the cavity.
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The above figure is
reproduced from the cited reference
with permission from Elsevier
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