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PDBsum entry 2dqf
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Immune system/hydrolase
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PDB id
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2dqf
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Contents |
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107 a.a.
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114 a.a.
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129 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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Structural consequences of mutations in interfacial tyr residues of a protein antigen-Antibody complex. The case of hyhel-10-Hel.
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Authors
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M.Shiroishi,
K.Tsumoto,
Y.Tanaka,
A.Yokota,
T.Nakanishi,
H.Kondo,
I.Kumagai.
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Ref.
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J Biol Chem, 2007,
282,
6783-6791.
[DOI no: ]
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PubMed id
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Abstract
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Tyrosine is an important amino acid in protein-protein interaction hot spots. In
particular, many Tyr residues are located in the antigen-binding sites of
antibodies and endow high affinity and high specificity to these antibodies. To
investigate the role of interfacial Tyr residues in protein-protein
interactions, we performed crystallographic studies and thermodynamic analyses
of the interaction between hen egg lysozyme (HEL) and the anti-HEL antibody
HyHEL-10 Fv fragment. HyHEL-10 has six Tyr residues in its antigen-binding site,
which were systematically mutated to Phe and Ala using site-directed
mutagenesis. The crystal structures revealed several critical roles for these
Tyr residues in the interaction between HEL and HyHEL-10 as follows: 1) the
aromatic ring of Tyr-50 in the light chain (LTyr-50) was important for the
correct ternary structure of variable regions of the immunoglobulin light chain
and heavy chain and of HEL; 2) deletion of the hydroxyl group of Tyr-50 in the
heavy chain (HTyr-50) resulted in structural changes in the antigen-antibody
interface; and 3) the side chains of HTyr-33 and HTyr-53 may help induce fitting
of the antibody to the antigen. Hot spot Tyr residues may contribute to the high
affinity and high specificity of the antigen-antibody interaction through a
diverse set of structural and thermodynamic interactions.
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Figure 1.
FIGURE 1. Tyr residues participating in the interaction of
HyHEL10 and HEL. a, overall structure of the wild-type HyHEL-10
Fv-HEL complex. C-  traces of VL, VH, and
HEL are drawn in green, cyan, and pink, respectively. Tyr
residues contacting HEL are represented by orange sticks.
Interfacial water molecules bridging Fv and HEL are represented
by red balls. b, space-filling model of the wild-type HyHEL-10
Fv fragment from the direction of the antigen-binding site. The
contacting residues in VL and VH are shown in green and cyan,
respectively. Tyr residues are shown in orange. Interfacial
water molecules are shown in red. c, space-filling model of HEL.
The residues contacting the six Tyr residues of HyHEL-10 are
shown in orange, and the other contacting residues are shown in
pink.
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Figure 3.
FIGURE 3. Comparison of local structures (at the mutation
site) between mutant and wild-type Fv-HEL complexes. a,
LY50A-HEL; b, HY33F-HEL; c, HY50F-HEL; d, HY58A-HEL; and e,
HY53A-HEL. C- atoms of all
polypeptide chains of each mutant complex are superimposed on
those of the wild-type complex. Wild-type complex is shown in
gray. Residues of VL, VH, and HEL of the mutant complexes are
shown in green, cyan, and pink, respectively. Water molecules
are shown as red balls. Hydrogen bonds in the mutant complexes
and wild-type complexes are depicted as red dotted lines and
gray dotted lines, respectively. The amino-aromatic (cation-
 )
interaction is represented as a gray thick dashed line.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
6783-6791)
copyright 2007.
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