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PDBsum entry 1gx0
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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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Structural basis of ordered binding of donor and acceptor substrates to the retaining glycosyltransferase, Alpha-1,3-Galactosyltransferase.
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Authors
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E.Boix,
Y.Zhang,
G.J.Swaminathan,
K.Brew,
K.R.Acharya.
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Ref.
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J Biol Chem, 2002,
277,
28310-28318.
[DOI no: ]
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PubMed id
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Abstract
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Bovine alpha-1,3-galactosyltransferase (alpha3GT) catalyzes the synthesis of the
alpha-galactose (alpha-Gal) epitope, the target of natural human antibodies. It
represents a family of enzymes, including the histo blood group A and B
transferases, that catalyze retaining glycosyltransfer reactions of unknown
mechanism. An initial study of alpha3GT in a crystal form with limited
resolution and considerable disorder suggested the possible formation of a
beta-galactosyl-enzyme covalent intermediate (Gastinel, L. N., Bignon, C.,
Misra, A. K., Hindsgaul, O., Shaper, J. H., and Joziasse, D. H. (2001) EMBO J.
20, 638-649). Highly ordered structures are described for complexes of alpha3GT
with donor substrate, UDP-galactose, UDP- glucose, and two acceptor substrates,
lactose and N-acetyllactosamine, at resolutions up to 1.46 A. Structural and
calorimetric binding studies suggest an obligatory ordered binding of donor and
acceptor substrates, linked to a donor substrate-induced conformational change,
and the direct participation of UDP in acceptor binding. The monosaccharide-UDP
bond is cleaved in the structures containing UDP-galactose and UDP-glucose,
producing non-covalent complexes containing buried beta-galactose and
alpha-glucose. The location of these monosaccharides and molecular modeling
suggest that binding of a distorted conformation of UDP-galactose may be
important in the catalytic mechanism of alpha3GT.
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Figure 2.
Fig. 2. A, C, E, and G: diagrams of the |F[o]|  |F[c]|
electron density omit map, contoured at 3.0-  level, of
LacNAc (1.46 Å), Lac (2.5 Å),  -Gal (1.8
Å), and  -Glc (1.8
Å), respectively. B, D, F, and H: diagrams showing the
interactions of 3GT with
LacNAc, lactose, -Gal, and
-Glc,
respectively. The protein residues are drawn as ball-and-stick
models, water molecules appear as blue spheres, and the ligands
are shown in orange. The Mn2+ ion is shown as a magenta sphere.
H-bonds are indicated by dashed lines. The figures were created
with BOBSCRIPT (34).
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Figure 4.
Fig. 4. Schematic showing the 3GT
residues at the active site and the bound ligands. The Mn2+ ion
is shown in magenta, UDP in orange, -Gal in
green, and LacNAc in pink. The protein residues are drawn as
light gray ball-and-stick models. H-bonds are shown in dashed
lines. The figure was created with MOLSCRIPT (33) and rendered
using Raster3D (35).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
28310-28318)
copyright 2002.
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Secondary reference #1
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Title
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Structure of udp complex of udp-Galactose:beta-Galactoside-Alpha -1,3-Galactosyltransferase at 1.53-A resolution reveals a conformational change in the catalytically important c terminus.
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Authors
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E.Boix,
G.J.Swaminathan,
Y.Zhang,
R.Natesh,
K.Brew,
K.R.Acharya.
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Ref.
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J Biol Chem, 2001,
276,
48608-48614.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. a, structure of 3GT with
bound UDP and Mn2+ ion. The bound ligand and ion identify the
location of the active site. The Mn2+ ion is shown as a magenta
sphere, UDP is brown, and helices are pink, while the strands
are green. This image was created using the program MOLSCRIPT
(38). b, the amino acid sequence of the catalytic domain of 3GT with
all secondary structure elements highlighted. UDP binding
residues are marked in yellow, while the Mn2+ binding residues
are shown by closed magenta spheres. This image was created
using the program ALSCRIPT (39). c, stereoview comparison of the
C^  atoms
of form-II 3GT
(present structure, in red) with the previously determined form
I 3GT
structure (Ref. 18; in black). The C-terminal residues 358-368
in form II show a large difference in conformation and form a
lid for the active site tunnel. This image was created using the
program BOBSCRIPT (40).
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Figure 2.
Fig. 2. a, schematic figure showing the main hydrogen
bond interactions between UDP and 3GT
residues at the catalytic site of the enzyme. The Mn2+ ion and
water molecules are also shown. This image was created using the
program MOLSCRIPT (38) and rendered using Raster3D (41). b, the
location of UDP molecule in the active site tunnel. This image
was created using the program DINO (A. Philippsen; available on
the World Wide Web at www.dino3d.org).
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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