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PDBsum entry 1yeh
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Catalytic antibody
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PDB id
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1yeh
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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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X-Ray structures of a hydrolytic antibody and of complexes elucidate catalytic pathway from substrate binding and transition state stabilization through water attack and product release.
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Authors
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B.Gigant,
J.B.Charbonnier,
Z.Eshhar,
B.S.Green,
M.Knossow.
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Ref.
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Proc Natl Acad Sci U S A, 1997,
94,
7857-7861.
[DOI no: ]
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PubMed id
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Abstract
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The x-ray structures of the unliganded esterase-like catalytic antibody D2.3 and
its complexes with a substrate analogue and with one of the reaction products
are analyzed. Together with the structure of the phosphonate transition state
analogue hapten complex, these crystal structures provide a complete description
of the reaction pathway. At alkaline pH, D2.3 acts by preferential stabilization
of the negatively charged oxyanion intermediate of the reaction that results
from hydroxide attack on the substrate. A tyrosine residue plays a crucial role
in catalysis: it activates the ester substrate and, together with an asparagine,
it stabilizes the oxyanion intermediate. A canal allows facile diffusion of
water molecules to the reaction center that is deeply buried in the structure.
Residues bordering this canal provide targets for mutagenesis to introduce a
general base in the vicinity of the reaction center.
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Figure 1.
Fig. 1. Chemical reaction catalyzed by D2.3 and structures of
the compounds used in this study. Ester 1 is a substrate
hydrolyzed^ by D2.3. Crystal structures examined are those of
complexes of^ D2.3 with p-nitrobenzyl alcohol 2 (one of the
products of the hydrolysis of 1), p-nitrobenzyl phosphonate 3^
(the TSA hapten used to elicit D2.3), and p-nitrobenzyl amide^
4, a stable analogue of the substrate ester 1.
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Figure 2.
Fig. 2. Schematic views of D2.3 Fab residues that interact
with the ligands examined. Residue numbering is according to
ref. 24. In A-C, the ligands are in blue, the C[  ]trace
of the Fab is in green, and water molecules are in red. Hydrogen
bonds are shown as dotted lines. (A) Complex of D2.3 with amide
4, a stable^ SA. (B) Complex of D2.3 with TSA 3. (C) Complex of
D2.3^ with the reaction product 2, p-nitrobenzyl alcohol.
Electron density corresponding to an acetate molecule was
located in the^ combing site. The acetate is in yellow; the
oxygens and the methyl of the acetate were distinguished on the
basis of the hydrogen bonds established. A-C were drawn with
MOLSCRIPT (25). (D) View of the canal (D2.3-4 structure) that
allows water diffusion to the carbon atom of the carbonyl of 4
analogous to the^ reaction center in the complex of D2.3 with 1.
The surface^ accessible to the exterior of a water molecule
represented by a 1.4-Å radius sphere is cut to show the
canal; its face toward^ the complexed Fab atoms is in blue, and
the one facing the exterior is in white. Only the residues that
border the canal are represented. Ligand 4 is in green; the
water molecule (magenta) closest to the analogue of the reaction
center is within hydrogen bonding distance and angle to Arg-H50
(hydrogen bond not shown). Nitrogen N  1 of
His-H35 makes a hydrogen bond to Trp-H47 (not shown) that is
conserved in antibodies; therefore, the N  2 nitrogen
of His-H35^ (which is part of the canal's wall) is protonated,
and His-H35^ most likely does not function as a general base in
the hydrolysis catalyzed by D2.3. D was rendered in the AVS
environment (26).
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