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PDBsum entry 1lo2
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Immune system
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PDB id
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1lo2
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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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A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue.
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Authors
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M.Hugot,
N.Bensel,
M.Vogel,
M.T.Reymond,
B.Stadler,
J.L.Reymond,
U.Baumann.
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Ref.
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Proc Natl Acad Sci U S A, 2002,
99,
9674-9678.
[DOI no: ]
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PubMed id
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Abstract
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The nitroxyl synthase catalytic antibodies 10F11, 9D9, and 27C5 catalyze the
release of nitroxyl from a bicyclic pro-drug by accelerating a retro-Diels-Alder
reaction. The Fabs (antigen-binding fragments) of these three catalytic
antibodies were cloned and sequenced. Fab 9D9 was crystallized in the apo-form
and in complex with one transition state analogue of the reaction. Crystal
structures of Fab 10F11 in complex with ligands mimicking substrate, transition
state, and product have been determined at resolutions ranging from 1.8 to 2.3
A. Antibodies 9D9 and 10F11 show increased shape complementarity (as quantified
by the program sc) to the hapten and to a modeled transition state as compared
with substrate and product. The shape complementarity is mediated to a large
extent by an aromatic residue (tyrosine or tryptophan) at the bottom of the
hydrophobic active pocket, which undergoes pi-stacking interactions with the
aromatic rings of the ligands. Another factor contributing to the different
reactivity of the regioisomers probably arises because of hydrogen-bonding
interactions between the nitroxyl bridge and the backbone amide of PheH101 and
possibly a conserved water molecule.
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Figure 1.
Fig. 1. Reaction scheme and haptens used in this study.
The retro-Diels-Alder reaction of pro-drug 1a (k[un] = 9.8 10^
 6 s
1
conditions: 31°C in PBS pH 7.4, 10% vol/vol
dimethylformamide) releases nitroxyl and anthracene 2a. The
reaction is catalyzed by antibodies 9D9 (anti-3), 10F11
(anti-5), and 27C5 (anti-3,4). The reaction with the
regioisomeric substrate 1b (k[un] = 7.1 10^ 6 s
1) is
also catalyzed weakly by the antibodies. The unreactive
substrate analog 6 and product analogue 2b were used for
crystallization. Substrate analogue 1c and product analog 2c and
transition state model 7 were used for docking studies.
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Figure 3.
Fig. 3. Active site of the abzyme. (Left) 10F11 in
complex with OXY (compound 6). The hydrogen bonding network is
shown as dotted lines. (Right) Surface representation of the
binding pocket of Fab 10F11 with the transition state analogue
BCN (compound 4) of the retro-Diels-Alder reaction. View is from
the top of the binding site showing the fit of the ligand BCN.
The light pink transparent surface represents V[L] and the light
blue transparent surface represents V[H]. Note the presence of
water molecules inside the pocket. Figure prepared with DINO
(http://www.dino3d.org).
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