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PDBsum entry 1o4z
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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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The three-Dimensional structures of two beta-Agarases.
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Authors
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J.Allouch,
M.Jam,
W.Helbert,
T.Barbeyron,
B.Kloareg,
B.Henrissat,
M.Czjzek.
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Ref.
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J Biol Chem, 2003,
278,
47171-47180.
[DOI no: ]
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PubMed id
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Abstract
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Agars are important gelifying agents for biochemical use and the food industry.
To cleave the beta-1,4-linkages between beta-d-galactose and
alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as
agars, marine bacteria produce polysaccharide hydrolases called beta-agarases.
Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been
biochemically characterized. Here we report the first crystal structure of these
two beta-agarases. The two proteins were overproduced in Escherichia coli and
crystallized, and the crystal structures were determined at 1.48 and 2.3 A for
beta-agarases A and B, respectively. The structure of beta-agarase A was solved
by the multiple anomalous diffraction method, whereas beta-agarase B was solved
with molecular replacement using beta-agarase A as model. Their structures adopt
a jelly roll fold with a deep active site channel harboring the catalytic
machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the
acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively.
The structures of the agarases were compared with those of two lichenases and of
a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases
in order to pinpoint the residues responsible for their widely differing
substrate specificity. The relationship between structure and enzymatic activity
of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of
the degradation products starting with different oligosaccharides. The
combination of the structural and biochemical results allowed the determination
of the number of subsites present in the catalytic cleft of the beta-agarases.
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Figure 1.
FIG. 1. a, schematic diagram showing a disaccharide unit of
agarose. The  (1, 4) bond cleaved
during catalysis is labeled. b, organization of the modules of
-agarases A and B,
respectively.
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Figure 3.
FIG. 3. a, stereo view of -AgaA_CM (top) and -AgaB
(bottom) ribbon models. The calcium ion is displayed in purple,
located on the convex side of the protein. The figure was
produced with Molscript (44). b, electrostatic surface potential
of -AgaA_CM (left) and -AgaB
(right). Blue patches represent positive potential, red
represent negative potential, and white surface is neutral. The
number of subsites and their location within the molecule are
represented by numbers (-4 to +4). The aromatic residues
supposed to interact with the substrate are labeled at their
location on the protein. The figure was produced with GRASP (45).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
47171-47180)
copyright 2003.
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