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PDBsum entry 1abf
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Binding protein
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PDB id
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1abf
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References listed in PDB file
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Key reference
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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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Abstract
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Water molecules influence molecular interactions in all biological systems, yet
it is extremely difficult to understand their effects in precise atomic detail.
Here we present evidence, based on highly refined atomic structures of the
complexes of the L-arabinose-binding protein with L-arabinose, D-fucose and
D-galactose, that bound water molecules, coupled with localized conformational
changes, can govern substrate specificity and affinity. The atoms common to the
three sugars are identically positioned in the binding site and the same nine
strong hydrogen bonds are formed in all three complexes. Two hydrogen-bonded
water molecules in the site contribute further to tight binding of L-arabinose
but create an unfavourable interaction with the methyl group of D-fucose.
Equally tight binding of D-galactose is attained by the replacement of one of
the hydrogen-bonded water molecules by its--CH2OH group, coordinated with
localized structural changes which include a shift and redirection of the
hydrogen-bonding interactions of the other water molecule. These observations
illustrate how ordered water molecules can contribute directly to the properties
of proteins by influencing their interaction with ligands.
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Secondary reference #1
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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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