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PDBsum entry 1ktw
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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 structural bases of the processive degradation of iota-Carrageenan, A main cell wall polysaccharide of red algae.
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Authors
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G.Michel,
W.Helbert,
R.Kahn,
O.Dideberg,
B.Kloareg.
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Ref.
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J Mol Biol, 2003,
334,
421-433.
[DOI no: ]
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PubMed id
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Abstract
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iota-Carrageenans are sulfated 1,3-alpha-1,4-beta-galactans from the cell walls
of red algae, which auto-associate into crystalline fibers made of aggregates of
double-stranded helices. iota-Carrageenases, which constitute family 82 of
glycoside hydrolases, fold into a right-handed beta-helix. Here, the structure
of Alteromonas fortis iota-carrageenase bound to iota-carrageenan fragments was
solved at 2.0A resolution (PDB 1KTW). The enzyme holds a iota-carrageenan
tetrasaccharide (subsites +1 to +4) and a disaccharide (subsites -3, -4), thus
providing the first direct determination of a 3D structure of iota-carrageenan.
Electrostatic interactions between basic protein residues and the sulfate
substituents of the polysaccharide chain dominate iota-carrageenan recognition.
Glu245 and Asp247 are the proton donor and the base catalyst, respectively.
C-terminal domain A, which was highly flexible in the native enzyme structure,
adopts a alpha/beta-fold, also found in DNA/RNA-binding domains. In the
substrate-enzyme complex, this polyanion-binding module shifts toward the
beta-helix groove, forming a tunnel. Thus, from an open conformation which
allows for the initial endo-attack of iota-carrageenan chains, the enzyme
switches to a closed-tunnel form, consistent with its highly processive
character, as seen from the electron-microscopy analysis of the degradation of
iota-carrageenan fibers.
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Figure 3.
Figure 3. Movement of domain A results in the formation of
a tunnel-shaped active site. A, Stereo view of the superposition
of molecule 1 complexed to i-carrageenan oligosaccharides with
molecule 2. Molecules 1 and 2 are shown as blue and brown coils,
respectively. Molecular surface of A. fortis i-carrageenase in
the open conformation (B) and in the substrate-induced tunnel
conformation (C). The surface is colored according to
electrostatic potential, ranging from + (deep blue) to - (red).
The i-carrageenan oligosaccharides are shown as balls and
sticks. Oxygen and sulfur atoms are shown in red and green,
respectively. Carbon atoms are shown in yellow (A) or in white
(C). Figure 3 and Figure 6 were prepared using GRASP. [65.]
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Figure 6.
Figure 6. Model of the enzymatic dissociation of
i-carrageenan fibers. A, Molecular surface of A. fortis
i-carrageenase seen from the direction opposite to the active
site groove. The surface is colored according to electrostatic
potential, ranging from + (deep blue) to - (red). The trace of a
i-carrageenan chain engaged in hydrolysis is shown as a black
line, from the reducing (R) to the non-reducing (NR) ends. B,
Model of the enzymatic dissociation of i-carrageenan
double-helix aggregates. Positive signs represent basic residues
at the outer surface of i-carrageenase. The calcium ions
coordinating the i-carrageenan double helices are shown as red
dots. We postulate that the polycationic character of the outer,
non-catalytic face of i-carrageenase is invoved with the
displacement of these calcium ions, resulting in the peeling of
the i-carrageenan fibers.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2003,
334,
421-433)
copyright 2003.
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Secondary reference #1
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Title
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The iota-Carrageenase of alteromonas fortis. A beta-Helix fold-Containing enzyme for the degradation of a highly polyanionic polysaccharide.
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Authors
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G.Michel,
L.Chantalat,
E.Fanchon,
B.Henrissat,
B.Kloareg,
O.Dideberg.
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Ref.
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J Biol Chem, 2001,
276,
40202-40209.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. Solvent-flattened multiple anomalous diffraction
electron density map at 1.6 Å resolution. Map contoured at
2.0  of the
N-terminal calcium-binding hairpin loop. Calcium ion and water
molecules are indicated as yellow and red spheres, respectively.
The oxygen, nitrogen, and carbon atoms in the protein are shown
in red, blue, and yellow, respectively. This figure was created
using O (23).
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Figure 6.
Fig. 6.  -Carrageenan
recognition by -carrageenase.
A, view of the molecular surface of the -carrageenase
groove. The potential catalytic residues and the conserved basic
amino acids are shown in red and blue, respectively. The
distances between clusters of basic residues are shown. Fig. 6
was created using Grasp (51). B, ball and stick representation
of a -neocarrahexaose-sulfate
(7). Oxygen, sulfur, and carbon atoms are shown in red, yellow,
and black, respectively. Distances between the sulfate
substituents are shown.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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