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PDBsum entry 1ruk
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Immune system
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PDB id
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1ruk
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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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Probing the antibody-Catalyzed water-Oxidation pathway at atomic resolution.
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Authors
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X.Zhu,
P.Wentworth,
A.D.Wentworth,
A.Eschenmoser,
R.A.Lerner,
I.A.Wilson.
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Ref.
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Proc Natl Acad Sci U S A, 2004,
101,
2247-2252.
[DOI no: ]
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PubMed id
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Abstract
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Antibodies can catalyze the generation of hydrogen peroxide (H2O2) from singlet
dioxygen (1O2*) and water via the postulated intermediacy of dihydrogen trioxide
(H2O3) and other trioxygen species. Nine different crystal structures were
determined to elucidate the chemical consequences to the antibody molecule
itself of exposure to such reactive intermediates and to provide insights into
the location on the antibody where these species could be generated. Herein, we
report structural evidence for modifications of two specific antibody residues
within the interfacial region of the variable and constant domains of different
murine antibody antigen-binding fragments (Fabs) by reactive species generated
during the antibody-catalyzed water oxidation process. Crystal structure
analyses of murine Fabs 4C6 and 13G5 after UV-irradiation revealed complex
oxidative modifications to tryptophan L163 and, in 4C6, hydroxylation of the
Cgamma of glutamine H6. These discrete modifications of specific residues add
further support for the "active site" of the water-oxidation pathway
being located within the interfacial region of the constant and variable domains
and highlight the general resistance of the antibody molecule to oxidation by
reactive oxygen species generated during the water-oxidation process.
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Figure 1.
Fig. 1. Stereoview of the crystal structure of 4C6 Fab,
with the C^  trace of the light (L)
and heavy (H) chains colored in light and dark gray,
respectively. The modified tryptophan TrpL163 is highlighted in
red, and other tryptophan residues (such as TrpH97) are colored
green. The modified glutamine residue GlnH6 is also colored red.
All of the figures were generated in BOBSCRIPT (12) and rendered
in RASTER3D (13).
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Figure 4.
Fig. 4. Fourier electron density maps showing TrpL163 in
13G5 Fab for UV-irradiated data set H and native control data
set I. For a and b, the tryptophan residue was refined as
tryptophan, whereas for control (c and d), the tryptophan
residue was refined as alanine to avoid model bias. (a) 2F[o] -
F[c] maps (blue), contoured at 1.0  .(b) F[o] - F[c] maps,
contoured at 3.0 (green) and -3.0 (red).
(c)2F[o] - F[c] maps (blue), contoured at 0.8 .(d)
F[o] - F[c] maps, contoured at 3.0 (green).
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Secondary reference #1
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Title
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Structural basis for antibody catalysis of a cationic cyclization reaction.
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Authors
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X.Zhu,
A.Heine,
F.Monnat,
K.N.Houk,
K.D.Janda,
I.A.Wilson.
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Ref.
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J Mol Biol, 2003,
329,
69-83.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Shape complementarity of benzoic acid (a) and
hapten (b) in the antibody 4C6 combining site. The Fab
4C6-binding pockets are shown with the molecular surfaces (1.4
Å probe radius). The shape of active sites differs
dramatically between two structures primarily due to the
side-chain of TrpL89, which flips downward to form the base of
the hapten-binding pocket by the rotation of the x[2] angle
about 65° on hapten binding. For further information, see
the text and Figure 4. The Figure was generated in GRASP. [59.]
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Figure 9.
Figure 9. Docking of reactants (13, 15, 17) and TS
structures (14, 16, 18) into the hapten-binding site of the 4C6
Fab structure. (a) Pathway yielding of (1S),(2S)-product,
E[docked] (13)= -14.1 kcal/mol, E[docked] (14)= -10.6 kcal/mol.
(b) Pathway yielding of the (1R),(2R)-enantiomeric product with
E[docked] (15)= -14.7 kcal/mol and E[docked] (16)= -10.9
kcal/mol. (c) Pathway yielding cyclohexene, E[docked] (17)=
-14.6 kcal/mol and E[docked] (18)= -9.2 kcal/mol. The first two
TS, 14 and 16, correspond to both enantiomers of the chair-like
TS, whereas the last one (18) is the boat-like TS.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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