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PDBsum entry 2gfb
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Immunoglobulin
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PDB id
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2gfb
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Contents |
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(+ 2 more)
214 a.a.
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(+ 2 more)
219 a.a.
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a catalytic antibody FAB with esterase-Like activity.
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Authors
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B.Golinelli-Pimpaneau,
B.Gigant,
T.Bizebard,
J.Navaza,
P.Saludjian,
R.Zemel,
D.S.Tawfik,
Z.Eshhar,
B.S.Green,
M.Knossow.
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Ref.
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Structure, 1994,
2,
175-183.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Antibodies with catalytic properties can be prepared by eliciting an
antibody response against 'transition state analog' haptens. The specificity,
rate and number of reaction cycles observed with these antibodies more closely
resemble the properties of enzymes than any of the many other known
enzyme-mimicking systems. RESULTS: We have determined to 3 A resolution the
first X-ray structure of a catalytic antibody Fab. This antibody catalyzes the
hydrolysis of a p-nitrophenyl ester. In conjunction with binding studies in
solution, this structure of the uncomplexed site suggests a model for transition
state fixation where two tyrosines mimic the oxyanion binding hole of serine
proteases. A comparison with the structures of known Fabs specific for low
molecular weight haptens reveals that this catalytic antibody has an unusually
long groove at its combining site. CONCLUSION: Since transition state analogs
contain elements of the desired product, product inhibition is a severe problem
in antibody catalysis. The observation of a long groove at the combining site
may relate to the ability of this catalytic antibody to achieve multiple cycles
of reaction.
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Figure 1.
Figure 1. Diagrams of the hydrolysis reaction catalyzed by
CNJ206 and of the compounds used in this study. 1 is the
substrate (a p- nitrophenyl ester); 2 is the transition state
analog (TSA) hapten used to elicit CNJ206; 3 is a short TSA used
to select catalytic antibodies; 4 and 5 were used in binding
studies with CNJ206. Figure 1. Diagrams of the hydrolysis
reaction catalyzed by CNJ206 and of the compounds used in this
study. 1 is the substrate (a p- nitrophenyl ester); 2 is the
transition state analog (TSA) hapten used to elicit CNJ206; 3 is
a short TSA used to select catalytic antibodies; 4 and 5 were
used in binding studies with CNJ206.
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Figure 5.
Figure 5. Model of the transition-state analog bound to
CNJ206. (a) The same view as in Figure 2, illustrating a model
of p-nitrophenyl methylphosphonate (compound 3 of Figure 1)
bound to CNJ206. The inhibitor 3 was modeled using SYBYL
(Molecular Modeling Software, Tripos Associates, St Louis, MO)
and structural data [43] and adjusted into the binding site of
CNJ206 using FRODO [44]. Atomic positions were then subjected to
energy refinement with X-PLOR [41]. Atoms further than 9
å from the hapten were kept fixed, while soft harmonic
constraints were applied to atoms in a shell between 7 and 9
å from the hapten. For residues within 7 å of the
hapten, softer constraints were applied to main-chain atoms,
while side chains were left unconstrained. Polar or charged
residues lining the cavity are labeled. The intramolecular salt
link between Arg L46 and Asp L55, which stabilizes the
conformation of the arginine is shown. The orientation
presented allows hydrogen bonds (dotted lines) to be made both
to the nitro group and to the methyl phosphonate (atom colours
as described for Figure 4). (b)A space-filling representation
of the same model. The phosphorous atom is shown here in green
with the phenyl ring and methyl group of compound 3 in yellow.
In this orientation, compound 3 buries 242 å ^2of
surface, which is 71 % of its total accessible surface area
(calculated using a 1.4 å radius probe). Figure 5.
Model of the transition-state analog bound to CNJ206. (a) The
same view as in [3]Figure 2, illustrating a model of
p-nitrophenyl methylphosphonate (compound 3 of [4]Figure 1)
bound to CNJ206. The inhibitor 3 was modeled using SYBYL
(Molecular Modeling Software, Tripos Associates, St Louis, MO)
and structural data [[5]43] and adjusted into the binding site
of CNJ206 using FRODO [[6]44]. Atomic positions were then
subjected to energy refinement with X-PLOR [[7]41]. Atoms
further than 9 å from the hapten were kept fixed, while
soft harmonic constraints were applied to atoms in a shell
between 7 and 9 å from the hapten. For residues within 7
å of the hapten, softer constraints were applied to
main-chain atoms, while side chains were left unconstrained.
Polar or charged residues lining the cavity are labeled. The
intramolecular salt link between Arg L46 and Asp L55, which
stabilizes the conformation of the arginine is shown. The
orientation presented allows hydrogen bonds (dotted lines) to be
made both to the nitro group and to the methyl phosphonate (atom
colours as described for [8]Figure 4). (b)A space-filling
representation of the same model. The phosphorous atom is shown
here in green with the phenyl ring and methyl group of compound
3 in yellow. In this orientation, compound 3 buries 242 å
^2of surface, which is 71 % of its total accessible surface area
(calculated using a 1.4 å radius probe).
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The above figures are
reprinted
by permission from Cell Press:
Structure
(1994,
2,
175-183)
copyright 1994.
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Secondary reference #1
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Title
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Differences in the biochemical properties of esterolytic antibodies correlate with structural diversity.
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Authors
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R.Zemel,
D.G.Schindler,
D.S.Tawfik,
Z.Eshhar,
B.S.Green.
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Ref.
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Mol Immunol, 1994,
31,
127-137.
[DOI no: ]
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PubMed id
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