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PDBsum entry 1d5b
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Immune system
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PDB id
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1d5b
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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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Conformational effects in biological catalysis: an antibody-Catalyzed oxy-Cope rearrangement.
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Authors
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E.C.Mundorff,
M.A.Hanson,
A.Varvak,
H.Ulrich,
P.G.Schultz,
R.C.Stevens.
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Ref.
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Biochemistry, 2000,
39,
627-632.
[DOI no: ]
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PubMed id
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Abstract
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Antibody AZ-28 was generated against the chairlike transition-state analogue
(TSA) 1 and catalyzes the oxy-Cope rearrangement of substrate 2 to product 3.
The germline precursor to AZ-28 catalyzes the reaction with a 35-fold higher
rate (k(cat)/k(uncat) = 163 000), despite a 40-fold lower binding affinity for
TSA.1 (K(D) = 670 nM). To determine the structural basis for the differences in
the binding and catalytic properties of the germline and affinity-matured
antibodies, the X-ray crystal structures of the unliganded and TSA.1 complex of
antibody AZ-28 have been determined at 2.8 and 2.6 A resolution, respectively;
the structures of the unliganded and TSA.1 complex of the germline precursor to
AZ-28 were both determined at 2. 0 A resolution. In the affinity-matured
antibody.hapten complex the TSA is fixed in a catalytically unfavorable
conformation by a combination of van der Waals and hydrogen-bonding
interactions. The 2- and 5-phenyl substituents of TSA.1 are almost perpendicular
to the cyclohexyl ring, leading to decreased orbital overlap and decreased
stabilization of the putative transition state. The active site of the germline
antibody appears to have an increased degree of flexibility-CDRH3 moves 4.9 A
outward from the active site upon binding of TSA.1. We suggest that this
conformational flexibility in the germline antibody, which results in a lower
binding affinity for TSA.1, allows dynamic changes in the dihedral angle of the
2-phenyl substituent along the reaction coordinate. These conformational changes
in turn lead to enhanced orbital overlap and increased catalytic rate. These
studies suggest that protein and substrate dynamics play a key role in this
antibody-catalyzed reaction.
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