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* Residue conservation analysis
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Proc Natl Acad Sci U S A
93:5363-5367
(1996)
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PubMed id:
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Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution.
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L.C.Hsieh-Wilson,
P.G.Schultz,
R.C.Stevens.
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ABSTRACT
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The x-ray crystal structures of the sulfide oxidase antibody 28B4 and of
antibody 28B4 complexed with hapten have been solved at 2.2-angstrom and
1.9-angstrom resolution, respectively. To our knowledge, these structures are
the highest resolution catalytic antibody structures to date and provide insight
into the molecular mechanism of this antibody-catalyzed monooxygenation
reaction. Specifically, the data suggest that entropic restriction plays a
fundamental role in catalysis through the precise alignment of the thioether
substrate and oxidant. The antibody active site also stabilizes developing
charge on both sulfur and periodate in the transition state via cation-pi and
electrostatic interactions, respectively. In addition to demonstrating that the
active site of antibody 28B4 does indeed reflect the mechanistic information
programmed in the aminophosphonic acid hapten, these high-resolution structures
provide a basis for enhancing turnover rates through mutagenesis and improved
hapten design.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.E.Wong,
B.D.Sellers,
and
M.P.Jacobson
(2011).
Effects of somatic mutations on CDR loop flexibility during affinity maturation.
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Proteins,
79,
821-829.
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A.Dörr,
and
W.D.Lubell
(2007).
Synthesis of a new pi-deficient phenylalanine derivative from a common 1,4-diketone intermediate and study of the influence of aromatic density on prolyl amide isomer population.
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Biopolymers,
88,
290-299.
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B.Golinelli-Pimpaneau
(2005).
Structure of a pseudomerohedrally twinned monoclinic crystal form of a pyridoxal phosphate-dependent catalytic antibody.
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Acta Crystallogr D Biol Crystallogr,
61,
472-476.
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PDB code:
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M.Hugot,
N.Bensel,
M.Vogel,
M.T.Reymond,
B.Stadler,
J.L.Reymond,
and
U.Baumann
(2002).
A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue.
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Proc Natl Acad Sci U S A,
99,
9674-9678.
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PDB codes:
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T.A.Muranova,
S.N.Ruzheinikov,
S.E.Sedelnikova,
A.Moir,
L.J.Partridge,
H.Kakinuma,
N.Takahashi,
K.Shimazaki,
J.Sun,
Y.Nishi,
and
D.W.Rice
(2001).
The preparation and crystallization of Fab fragments of a family of mouse esterolytic catalytic antibodies and their complexes with a transition-state analogue.
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Acta Crystallogr D Biol Crystallogr,
57,
1192-1195.
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B.Golinelli-Pimpaneau,
O.Goncalves,
T.Dintinger,
D.Blanchard,
M.Knossow,
and
C.Tellier
(2000).
Structural evidence for a programmed general base in the active site of a catalytic antibody.
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Proc Natl Acad Sci U S A,
97,
9892-9895.
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PDB code:
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B.Golinelli-Pimpaneau
(2000).
Novel reactions catalysed by antibodies.
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Curr Opin Struct Biol,
10,
697-708.
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D.B.Smithrud,
P.A.Benkovic,
S.J.Benkovic,
V.Roberts,
J.Liu,
I.Neagu,
S.Iwama,
B.W.Phillips,
A.B.Smith,
and
R.Hirschmann
(2000).
Cyclic peptide formation catalyzed by an antibody ligase.
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Proc Natl Acad Sci U S A,
97,
1953-1958.
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J.L.Pellequer,
S.Chen,
V.A.Roberts,
J.A.Tainer,
and
E.D.Getzoff
(1999).
Unraveling the effect of changes in conformation and compactness at the antibody V(L)-V(H) interface upon antigen binding.
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J Mol Recognit,
12,
267-275.
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K.Gruber,
B.Zhou,
K.N.Houk,
R.A.Lerner,
C.G.Shevlin,
and
I.A.Wilson
(1999).
Structural basis for antibody catalysis of a disfavored ring closure reaction.
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Biochemistry,
38,
7062-7074.
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PDB codes:
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R.D.Stigler,
B.Hoffmann,
R.Abagyan,
and
J.Schneider-Mergener
(1999).
Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics.
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Structure,
7,
663-670.
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S.T.Kim,
H.Shirai,
N.Nakajima,
J.Higo,
and
H.Nakamura
(1999).
Enhanced conformational diversity search of CDR-H3 in antibodies: role of the first CDR-H3 residue.
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Proteins,
37,
683-696.
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M.Nakasako,
T.Motoyama,
Y.Kurahashi,
and
I.Yamaguchi
(1998).
Cryogenic X-ray crystal structure analysis for the complex of scytalone dehydratase of a rice blast fungus and its tight-binding inhibitor, carpropamid: the structural basis of tight-binding inhibition.
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Biochemistry,
37,
9931-9939.
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PDB code:
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D.B.Smithrud,
and
S.J.Benkovic
(1997).
The state of antibody catalysis.
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Curr Opin Biotechnol,
8,
459-466.
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H.Wade,
and
T.S.Scanlan
(1997).
The structural and functional basis of antibody catalysis.
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Annu Rev Biophys Biomol Struct,
26,
461-493.
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J.B.Charbonnier,
B.Golinelli-Pimpaneau,
B.Gigant,
D.S.Tawfik,
R.Chap,
D.G.Schindler,
S.H.Kim,
B.S.Green,
Z.Eshhar,
and
M.Knossow
(1997).
Structural convergence in the active sites of a family of catalytic antibodies.
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Science,
275,
1140-1142.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
