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PDBsum entry 7abp
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Binding proteins
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PDB id
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7abp
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References listed in PDB file
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Key reference
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Title
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Sugar-Binding and crystallographic studies of an arabinose-Binding protein mutant (met108leu) that exhibits enhanced affinity and altered specificity.
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Authors
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P.S.Vermersch,
D.D.Lemon,
J.J.Tesmer,
F.A.Quiocho.
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Ref.
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Biochemistry, 1991,
30,
6861-6866.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
86%.
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Abstract
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In addition to hydrogen bonds, van der Waals forces contribute to the affinity
of protein-carbohydrate interactions. Nonpolar van der Waals contacts in the
complexes of the L-arabinose-binding protein (ABP) with monosaccharides have
been studied by means of site-directed mutagenesis, equilibrium and rapid
kinetic binding techniques, and X-ray crystallography. ABP, a periplasmic
transport receptor of Escherichia coli, binds L-arabinose, D-galactose, and
D-fucose with preferential affinity in the order of Ara greater than Gal much
greater than Fuc. Well-refined, high-resolution structures of ABP complexed with
the three sugars revealed that the structural differences in the ABP-sugar
complexes are localized around C5 of the sugars, where the equatorial H of Ara
has been substituted for CH3 (Fuc) or CH2OH (Gal). The side chain of Met108
undergoes a sterically dictated, ligand-specific, conformational change to
optimize nonpolar interactions between its methyl group and the sugar. We found
that the Met108Leu ABP binds Gal tighter than wild-type ABP binds Ara and
exhibits a preference for ligand in the order of Gal much greater than Fuc
greater than Ara. The differences in affinity can be attributed to differences
in the dissociation rates of the ABP-sugar complexes. We have refined at better
than 1.7-A resolution the crystal structures of the Met108Leu ABP complexed with
each of the sugars and offer a molecular explanation for the altered binding
properties.
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Secondary reference #1
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Title
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Substrate specificity and affinity of a protein modulated by bound water molecules.
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Authors
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F.A.Quiocho,
D.K.Wilson,
N.K.Vyas.
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Ref.
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Nature, 1989,
340,
404-407.
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PubMed id
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Secondary reference #2
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Title
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Novel stereospecificity of the l-Arabinose-Binding protein.
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Authors
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F.A.Quiocho,
N.K.Vyas.
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Ref.
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Nature, 1984,
310,
381-386.
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PubMed id
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Secondary reference #3
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Title
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Hinge-Bending in l-Arabinose-Binding protein. The "venus'S-Flytrap" model.
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Authors
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B.Mao,
M.R.Pear,
J.A.Mccammon,
F.A.Quiocho.
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Ref.
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J Biol Chem, 1982,
257,
1131-1133.
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PubMed id
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Secondary reference #4
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Title
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Structure of the l-Arabinose-Binding protein from escherichia coli at 2.4 a resolution.
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Authors
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G.L.Gilliland,
F.A.Quiocho.
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Ref.
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J Mol Biol, 1981,
146,
341-362.
[DOI no: ]
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PubMed id
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Figure 3.
FVG
G VI H
H VII I
I VIII
J - L/l
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Figure 6.
Fro. 6. A stereo view showing the location of acidic and basic residues. An iarabinose model
representing both anomers is in the cleft. The positively charged residues Lys, Arg and His, and te
negatively charged residues Glu and Asp are highlighted by thicker lines.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #5
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Title
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L-Arabinose-Binding protein-Sugar complex at 2.4 a resolution. Stereochemistry and evidence for a structural change.
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Authors
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M.E.Newcomer,
G.L.Gilliland,
F.A.Quiocho.
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Ref.
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J Biol Chem, 1981,
256,
13213-13217.
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PubMed id
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Secondary reference #6
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Title
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The radius of gyration of l-Arabinose-Binding protein decreases upon binding of ligand.
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Authors
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M.E.Newcomer,
B.A.Lewis,
F.A.Quiocho.
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Ref.
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J Biol Chem, 1981,
256,
13218-13222.
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PubMed id
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Secondary reference #7
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Title
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The thiol group of the l-Arabinose-Binding protein. Chromophoric labeling and chemical identification of the sugar-Binding site.
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Authors
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D.M.Miller,
M.E.Newcomer,
F.A.Quiocho.
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Ref.
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J Biol Chem, 1979,
254,
7521-7528.
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PubMed id
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Secondary reference #8
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Title
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Location of the sugar-Binding site of l-Arabinose-Binding protein. Sugar derivative syntheses, Sugar binding specificity, And difference fourier analyses.
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Authors
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M.E.Newcomer,
D.M.Miller,
F.A.Quiocho.
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Ref.
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J Biol Chem, 1979,
254,
7529-7533.
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PubMed id
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Secondary reference #9
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Title
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The 2.8-A resolution structure of the l-Arabinose-Binding protein from escherichia coli. Polypeptide chain folding, Domain similarity, And probable location of sugar-Binding site.
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Authors
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F.A.Quiocho,
G.L.Gilliland,
G.N.Phillips.
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Ref.
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J Biol Chem, 1977,
252,
5142-5149.
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PubMed id
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Secondary reference #10
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Title
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Structure of l-Arabinose-Binding protein from escherichia coli at 5 a resolution and preliminary results at 3.5 a.
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Authors
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G.N.Phillips,
V.K.Mahajan,
A.K.Siu,
F.A.Quiocho.
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Ref.
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Proc Natl Acad Sci U S A, 1976,
73,
2186-2190.
[DOI no: ]
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PubMed id
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