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¤1¤ Structural evidence for a programmed general base in the active site of
a catalytic antibody ¤1¤
1. [16]Batrice Golinelli-Pimpaneau [17]* , [18] ,
2. [19]Olivier Gonalves [20]à,
3. [21]Thierry Dintinger [22]à,
4. [23]Dominique Blanchard [24]¤,
5. [25]Marcel Knossow [26]*, and
6. [27]Charles Tellier [28]*
1.
^*Laboratoire d'Enzymologie et Biochimie Structurales, Centre
National de la Recherche Scientifique, Btiment 34, 1 Avenue de la
Terrasse, 91198 Gif-sur-Yvette Cedex, France; ^àCentre National de la
Recherche Scientifique-Formation de Recherche en Evolution 2230
Biocatalyse, Facult des Sciences et des Techniques, 2 Rue de la
Houssinire, B.P. 92208, 44322 Nantes Cedex 03, France; and
^¤Laboratoire de Biotechnologie, Etablissement de Transfusion
Sanguine, 34 Boulevard Jean Monnet, 44011 Nantes Cedex 01, France
1. Edited by Richard A. Lerner, The Scripps Research Institute, La
Jolla, CA, and approved June 27, 2000 (received for review April
24, 2000)
[29]Next Section
¤2¤ Abstract ¤2¤
The crystal structure of the complex of a catalytic antibody with its
cationic hapten at 1.9- resolution demonstrates that the hapten
amidinium group is stabilized through an ionic pair interaction with
the carboxylate of a combining-site residue. The location of this
carboxylate allows it to act as a general base in an allylic
rearrangement. When compared with structures of other antibody
complexes in which the positive moiety of the hapten is stabilized
mostly by cationй interactions, this structure shows that the
amidinium moiety is a useful candidate to elicit a carboxylate in an
antibody combining site at a predetermined location with respect to the
hapten. More generally, this structure highlights the advantage of a
bidentate hapten for the programmed positioning of a chemically
reactive residue in an antibody through charge complementarity to the
hapten.
Allylic rearrangements play a fundamental role in the biosynthesis of
terpenes and steroid hormones and in the biodegradation of fatty acids
([30]1). The enzymatic rearrangement of β-γ unsaturated ketones
requires a general base, usually a carboxylate, to abstract the
α-proton of the ketone (Fig. [31]1; refs. [32]1 and [33]2). This
reaction leads to a dienol or dienolate high-energy intermediate 3 that
does not possess a charge complementing that of the carboxylate.
Therefore, antibodies elicited against a hapten that mimics the
transition state or the dienol intermediate of allylic rearrangement
would acquire a properly positioned general base carboxylate to
catalyze this reaction only by serendipity. However, the extensive
experience available on catalytic antibodies ([34]3, [35]4) and the
structures of catalytic antibodies elicited by transition state
analogue haptens show that properly positioned chemically reactive
residues are rarely present in the active site ([36]5). An alternative
approach that aims to generate functional residues, also termed Òbait
and switchÓ ([37]6, [38]7), uses a charged hapten to induce the
required complementary charged residue ([39]8, [40]9). Haptens
containing a positive charge have provided antibody catalysts for
important reactions such as acyl transfer ([41]7), elimination ([42]9,
[43]10), and phosphodiester hydrolysis ([44]11). However, in the
absence of structural data, it is not possible to establish
unambiguously the nature and identity of the catalytic residue that has
been induced and the relationship between the location of the haptenic
charge and the position of the catalytic residue in the antibody
combining site.
[45]Figure 1
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Figure 1
Scheme of the reaction catalyzed by antibody 4B2. 4B2 catalyzes allylic
rearrangement of α-cyclopent-1-en-1-yl-p-acetamidophenone 2 to
α-cyclopentylidien-p-acetamidophenone 4 via the enediol intermediate 3,
2-[4-(1-carboxy)propylamidobenzylamino]-3,4,5,6-tetrahydropyridinium.
1a is the hapten used to generate 4B2. The structure that was
determined is that of the complex of 4B2 with
2-(4-aminobenzylamino)-3,4,5,6-tetrahydropyridinium 1b. Antibody 5C8
was generated against hapten 5a, and its x-ray structure was determined
in the presence of inhibitor 5b ([49]12).
Indeed, in the few cases in which the use of a hapten containing a
positively charged moiety successfully induced catalytic antibodies and
in which the structure of the haptenÐantibody complex was determined,
there was no negatively charged residue in the active site directly
facing the positive charge, but stabilization of the haptenic charge
was mediated mostly by cationй interactions ([50]12Ð[51]14). Herein,
we report the structure, at 1.87- resolution, of the complex of an
antibody catalyzing an allylic rearrangement with its cationic hapten.
We provide direct evidence for an ionic pair interaction between the
amidinium function of the hapten and a combining site carboxylate,
which allows the precise positioning of this group, and show that this
carboxylate is the general base responsible for catalysis.
[52]Previous Section[53]Next Section
¤2¤ Materials and Methods ¤2¤
¤3¤ Fab Preparation, Purification, and Crystallization. ¤3¤
The 4B2 antibody was purified from the ascitic fluid as described
([54]15). The Fab was generated by papain digestion of the antibody
under standard conditions (30 mM Tris, pH 7.4/138 mM NaCl/1.25 mM
EDTA/1.5 mM 2-mercaptoethanol) by using a 3% (wt/wt) papain-to-antibody
ratio and a 9-h digestion time. Undigested IgG and Fc fragment were
removed by DEAE anion exchange chromatography and gel filtration on a
Sephacryl S100 HR column, and the Fab was purified further by ion
exchange chromatography on a mono Q FPLC column by a NaCl gradient in
20 mM ethanolamine buffer at pH 9.3.
Crystals were grown at 4¡C by using the hanging-drop procedure in wells
containing 1 ml of 16% (vol/vol) polyethylene glycol 4000, 3% (vol/vol)
dioxan, 20% (vol/vol) glycerol, 0.2 M ammonium sulfate, 5 mM strontium
chloride, and 20 mM sodium acetate (final pH 5). Drops consisting of a
2-μl aliquot of a protein solution with hapten (0.25 mM hapten and 11.6
mg of Fab per ml in 0.15 M NaCl/0.05% NaN[3]) were mixed with 2 μl of
the well solution. Despite the simultaneous growth of thin needles and
polyhedral-shaped crystals, this procedure yielded, in some drops,
monocrystals of dimensions up to 0.7 × 0.45 × 0.35 mm^3.
¤3¤ X-Ray Data Collection and Structure Determination. ¤3¤
Diffraction data were recorded by using one crystal kept at 4¡C on the
W32 station of the Laboratoire pour l'Utilisation du Rayonnement
Electromagntique (Orsay, France) synchrotron with a MAR Image Plate
system. Data were processed with denzo and scalepack ([55]16), and
statistics are shown in Table [56]1. The structure of the 4B2 Fab
(IgG1, κ) was solved by molecular replacement with the program amore
([57]17); the models used were the Fv domain of Fab D23 (PDB code
[58]1yec) and the CL-CH1 dimer of Fab 36-71 (PDB code [59]6fab). The
atomic model was refined by alternating cycles of model reconstruction
with the program o ([60]18) and of refinement with cns ([61]19). The
final refinement statistics are given in Table [62]1. Fig. [63]2 AÐC
was drawn with the program o ([64]18).
View this table:
* [65]In this window
* [66]In a new window
Table 1
Data collection and refinement statistics for Fab 4B2 complexed with 1b
[67]Figure 2
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Figure 2
(A) Schematic view of the active site of the 4B2-1b complex. The ligand
is in red; water molecules are indicated as red crosses; Glu L34 is
indicated in green; the other polar residues are represented in blue.
The Cαs of residues L32ÐL36, L89ÐL97, H35ÐH37, and H94ÐH99 in
hypervariable loops L1, L3, H1, and H3 are shown in yellow. The
aromatic residues (Trp H47, Phe L89, Tyr L96, Tyr L32, Trp H103, and
Phe L98) that have hydrophobic interactions with the hapten have been
represented, except Phe L98 and Trp H103 for reasons of clarity.
Nitrogen Nδ1 of His H35 is involved in a conserved H bond with Nɛ1 of
Trp H47. His H35 is therefore neutral but cannot play the role of a
general base, because its protonated nitrogen Nɛ2 points toward the
inside of the cavity. (B) Hydrogen bonding network established with
catalytic residue Glu L34. Hydrogen bonds are shown as dashed lines. A
Fobs-Fcalc electron density map calculated without the amidinium ligand
is superimposed on the structure. The map is contoured at the level of
two standard deviations. One of the oxygens of Glu L34 is hydrogen
bonded to the protonated nitrogen Nɛ2 of His L36. This tautomeric form
of His L36 is stabilized by an additional hydrogen bond between its Nδ1
and the NHɛ1 of Trp H103. Residue His L36 is therefore neutral but
cannot play the role of a general base, because its unprotonated
nitrogen Nɛ1 points away from the substrate. (C) Comparison of the
environment of the charge of the hapten in antibodies 5C8 (in blue) and
4B2 (in yellow). 5C8 catalyzes the disfavored cyclization of an
epoxyalcohol ([71]12). The α-carbons of residues of the combining site
(L32ÐL38, L43ÐL50, L86ÐL93, L96, L98, H32ÐH39, H91ÐH95, and H102ÐH104)
of 5C8 have been superimposed on those of 4B2 (the rms deviation is
0.645 ). The bottom of the active sites is formed by identical
residues in both antibodies (Phe L98, Trp H47, His H35, Trp H103, and
Val H37). The distance between the nitrogen of 5b of 5C8 (light green)
and the carbon between the two nitrogens of 1b of 4B2 (red) is 1.05 .
In addition to the ionic interaction with glutamate L34, the hapten
amidinium charge of 4B2 is stabilized through a cationй interaction
with Phe L89, which is also involved in a stacking interaction with the
amidine cycle. Residues of 5C8 involved in cationй interaction with
the quaternary amine of 5b are (distance to the nitrogen) Tyr L91 (4.97
), Trp H103 (5.59 ), His H35 (4.55 ), His L89 (4.96 ), and Tyr L36
(5.39 ). In addition, in 5C8, Asp H101 (for which there is no
equivalent in 4B2 because of the short H3 loop of this antibody) and
Asp H95, which are, respectively, 4 and 3.7 away from the positive
charge, provide a second sphere polar environment to the quaternary
amine ([72]12). Trp H47, Val H37, and Tyr L96 are not represented for
reasons of clarity.
[73]Previous Section[74]Next Section
¤2¤ Results ¤2¤
¤3¤ Catalytic Activity and Mechanism. ¤3¤
Antibody 4B2 was generated against a cyclic amidinium hapten 1a (Fig.
[75]1). This antibody catalyzes with significant rate enhancement (k
[cat]/k [non] = 1,500) the allylic rearrangement of β-γ unsaturated
ketone 2, which is structurally related to the hapten ([76]15), and the
ring opening of 5-nitro-benzisoxazole in the Kemp elimination (k
[cat]/k [non] = 18,000; ref. [77]20). Both reactions would be catalyzed
by a residue acting as a general base to abstract the α-proton of β-γ
unsaturated ketone in allylic isomerization or the proton of the
isoxazole ring in the Kemp elimination. Three lines of evidence
strongly suggest that a carboxylate residue acts as a base in the
catalytic mechanism of allylic isomerization: the stereoselectivity of
the α-proton exchange showed by deuterium NMR, the pH dependence of the
reaction rate, and the effect of specific chemical modification of
carboxylates ([78]15).
¤3¤ Interaction of the Hapten with the Active Site. ¤3¤
The structure of 4B2 complexed to 1b, an analogue of hapten 1a lacking
the linker arm to the carrier protein (Fig. [79]1), shows that the
hapten is buried in a funnel-shaped deep cleft. The amidine is
accommodated at the bottom of the pocket, which constitutes a highly
hydrophobic environment where no water molecule was detected (Fig.
[80]2 A). Such a cavity at the interface of the heavy- and light-chain
variable domains has been described in antibodies catalyzing various
reactions such as ester hydrolysis ([81]21), pericyclic reactions
([82]22, [83]23), epoxyalcohol cyclization ([84]12), or polyene
cyclization ([85]14).
The hapten establishes three hydrogen bonds with residues of the
antibody. The terminal amine function, which is linked to the carrier
protein for immunization is accessible to solvent and establishes a
hydrogen bond with a main chain carbonyl oxygen and with a water
molecule. The two NH groups of the amidinium are hydrogen bonded to the
two oxygens of the Glu L34 carboxylate (Fig. [86]2 B). At the
crystallization pH (pH = 5), which is close to the pH for optimal
catalysis of allylic isomerization (pH 4.6), the L34 carboxylate
deprotonated form is stabilized by a hydrogen bond network with His L36
and Trp H103, which also likely positions the carboxylate side chain at
the proper location to abstract a proton from the substrate
stereoselectively. There are three other polar residues in the
combining site (Fig. [87]2 A). They cannot play the role of a general
base either, because they point toward the external medium (Asp H95) or
because their protonated nitrogen points toward the hapten (His H35 and
His L36) (Fig. [88]2 A and B). Taken together with the biochemical
data, the structure identifies Glu L34 as the general base that
abstracts the α-proton in the first step of allylic isomerization of 2
to yield the dienol intermediate 3 (Fig. [89]1).
Glutamate occurs at position L34 of only 5% of antibody sequences
([90]24). It is therefore tempting to suggest that the significant
stabilization of the antibodyÐhapten complex provided by the
glutamateÐamidinium interaction because of the bidentate nature of both
groups has favored the selection of a glutamate at this position during
antibody maturation. As a consequence of its bidentate character, the
interactions that the amidinium group establishes are anisotropic. This
property confers on the amidinium the potential to generate a precisely
positioned complementary charged residue.
¤3¤ The Environment of the Charge of the Hapten. ¤3¤
The directional property of the amidinium group is highlighted by a
comparison of the 4B2 combining site to that of another catalytic
antibody, 5C8, elicited against hapten 5a (Fig. [91]1) where the
amidine group of 1a is replaced by a quaternary amine ([92]12). The
piperidinium ring of inhibitor 5b and the amidinium ring of 1b occupy
very similar positions at the bottom of the combining sites (Fig. [93]2
C). Both haptens carry positively charged nitrogens that are positioned
close to aromatic rings, as often observed in proteins ([94]25). In
4B2, the charge of the amidinium group of the hapten is stabilized
mainly by the ion pair with glutamate L34. By contrast, in antibody
5C8, no carboxylate is available to stabilize the quaternary ammonium
of 5b through a direct ionic interaction. In the 5C8Ð5b complex, the
isotropic distribution of the charge of the quaternary ammonium group
induces an environment consisting of distant polar and
¹-electron-containing residues that stabilize the charge in a diffuse
fashion (Fig. [95]2 C). Such charged nitrogenÐaromatic interactions
have also been observed in the structures of small molecules ([96]26),
of antibody McPC603 bound to phosphorylcholine ([97]27), of antibody
catalysts complexed with their aminophosphonic acid ([98]13) or N-oxide
hapten ([99]14), and of acetylcholinesterase complexed with various
quaternary amine ligands ([100]28).
[101]Previous Section[102]Next Section
¤2¤ Discussion ¤2¤
The induction of a precisely positioned carboxylate residue in an
antibody combining site is of general use to generate catalysts for
reactions requiring either a nucleophile ([103]29, [104]30) or a
general base or acid as in enzyme-catalyzed proton transfer reactions
([105]2, [106]31, [107]32). The haptenÐ4B2 complex defines amidinium as
a useful candidate for that purpose and provides a starting point for
the design of haptens capable of eliciting more sophisticated
constellations of catalytic residues in antibody combining sites. The
induction of a second, planned, catalytic residue in the combining site
of an antibody, which would enhance its catalytic efficiency, would be
favored by incorporation in the same hapten structure of two bidentate
charged groups. Such molecules that have been developed as specific
protein binders ([108]33) would be logical hapten candidates to achieve
this goal.
Methods capable of eliciting chemically reactive groups in antibody
combining sites such as those using haptenic charge ([109]6Ð[110]9),
for which an unambiguous demonstration is presented here, or reactive
immunization ([111]34) are particularly useful to produce efficient
catalytic antibodies, especially when transition state analogues are
difficult to synthesize or when reactions proceed via multiple
transition states ([112]35). Indeed, these methods allow the use of a
hapten that does not need to match precisely the transition state of
the reaction but rather elicits a strategically positioned functional
residue. Therefore, antibodies resulting from these strategies have
been found to catalyze different reactions that use the same mechanism,
provided that the various substrates possess the common chemical
function with which the induced residue can react ([113]10, [114]36,
[115]37). This finding is also illustrated by antibody 4B2, which
catalyzes both the Kemp elimination ([116]20) and the allylic
rearrangement of a β-γ unsaturated ketone.
[117]Previous Section[118]Next Section
¤2¤ Acknowledgments ¤2¤
We thank L. Tchertanova (Institut des Substances Naturelles, Centre
National de la Recherche Scientifique, Gif-sur-Yvette) for surveying
the Cambridge Database, J. Perez for helping us to use facilities at
Laboratoire pour l'Utilisation du Rayonnement Electromagntique, Orsay,
France, and J. Janin for reading the manuscript. Partial financial
support was provided by the European Union Training and Mobility
Research Grant ERBFMXCT 98-0193 (to M.K.), and the cost of this article
was covered by the Centre National de la Recherche Scientifique,
Groupement de Recherche 897.
[119]Previous Section[120]Next Section
¤2¤ Footnotes ¤2¤
* [121]↵ To whom reprint requests should be addressed. E-mail:
beatrice.golinelli{at}lebs.cnrs-gif.fr.
* This paper was submitted directly (Track II) to the PNAS office.
* Data deposition: The atomic coordinates have been deposited in the
Protein Data Bank, [122]www.rcsb.org (PDB ID code [123]1F3D).
* Copyright © 2000, The National Academy of Sciences
[124]Previous Section
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