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PDBsum entry 1ipk
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Sugar binding protein
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PDB id
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1ipk
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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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Crystal structures of recombinant and native soybean beta-Conglycinin beta homotrimers.
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Authors
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N.Maruyama,
M.Adachi,
K.Takahashi,
K.Yagasaki,
M.Kohno,
Y.Takenaka,
E.Okuda,
S.Nakagawa,
B.Mikami,
S.Utsumi.
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Ref.
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Eur J Biochem, 2001,
268,
3595-3604.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structures of recombinant and native beta homotrimers of soybean
beta-conglycinin were determined by X-ray crystallography at 2.7 and 2.8 A
resolutions, respectively. The crystals of the recombinant and native beta
homotrimers belong to space group P21 with cell parameters a = 80.51 A, b =
63.48 A, c = 131.43 A, and beta = 90.01 degrees and with cell parameters a =
82.78 A, b = 69.47 A, c = 125.33 A and beta = 97.22 degrees, respectively. The
beta monomers consist of amino-terminal and carboxyl-terminal modules that are
very similar to each other and are related by a pseudo-dyad axis. Each module of
the beta monomer is subdivided into a core and a loop domain. These structural
features of both beta homotrimers are consistent with those of canavalin and
phaseolin, which are similar vicilin class proteins. The superposition of the
models of the native and recombinant beta monomers shows a root mean square
deviation of 0.43-0.51 A for 343 common Calpha atoms within 2.0 A. This result
indicates that the N-linked glycans do not influence the final structure of the
beta homotrimer. Comparison of the models of beta-conglycinin, phaseolin and
canavalin indicates that beta-conglycinin resembles canavalin rather than
phaseolin, and that canavalin and phaseolin differ the most among them. The
evolutional relationships are discussed.
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Figure 1.
Fig. 1. The ribbon diagrams of the recombinant (A and B)
and native (C and D)  homotrimers.
The three monomers in the recombinant and native homotrimers
are shown in light blue, light green and pink, and blue, green
and magenta, respectively. The carbohydrate moieties of the
native homotrimer
are shown in yellow as a ball and stick model. The views in (A)
and (C) are depicted as threefold symmetry axis runs
perpendicular to the paper and the depictions in (B) and (D) are
related to the view depicted in (A) and (C) by rotation of
90°. This figure was prepared using MOLSCRIPT and RASTER3D
[30,31].
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Figure 4.
Fig. 4. The interactions between modules and between
monomers in the recombinant , canavalin
and phaseolin. Helices and strands are
underlined in red and black, respectively. The residues
contributing to the hydrophobic interactions and the hydrogen
bonds between the modules (A) and between monomers (B) are
indicated by magenta letters and yellow shading, respectively.
The asterisk shows the conserved salt bridge among the three
proteins. The residues which are disordered in at least two
monomers are indicated by blue letters. Sequences are aligned
with reference to the least-squares fitting by the program
TURBOFRODO.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
Eur J Biochem
(2001,
268,
3595-3604)
copyright 2001.
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