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PDBsum entry 1hv6
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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 structure of alginate lyase a1-Iii complexed with trisaccharide product at 2.0 a resolution.
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Authors
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H.J.Yoon,
W.Hashimoto,
O.Miyake,
K.Murata,
B.Mikami.
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Ref.
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J Mol Biol, 2001,
307,
9.
[DOI no: ]
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PubMed id
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Abstract
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The structure of A1-III from a Sphingomonas species A1 complexed with a
trisaccharide product
(4-deoxy-l-erythro-hex-4-enepyranosyluronate-mannuronate-mannuronic acid) was
determined by X-ray crystallography at 2.0 A with an R-factor of 0.16. The final
model of the complex form comprising 351 amino acid residues, 245 water
molecules, one sulfate ion and one trisaccharide product exhibited a C(alpha)
r.m.s.d. value of 0.154 A with the reported apo form of the enzyme. The
trisaccharide was bound in the active cleft at subsites -3 approximately -1 from
the non-reducing end by forming several hydrogen bonds and van der Waals
interactions with protein atoms. The catalytic residue was estimated to be
Tyr246, which existed between subsites -1 and +1 based on a mannuronic acid
model oriented at subsite +1.
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Figure 3.
Figure 3. (a) The bound trisaccharide molecule on the
active site of A1-III. The Figure shows the bound trisaccharide
molecule and the surrounding amino acid residues and water
molecules interacting with the trisaccharide. The trisaccharide
molecule is represented by means of an orange ball-and-stick
model. The side-chains of Tyr and Trp, Asn and Gln, Asp, Arg,
and His residues are colored yellow, green, red, cyan and
purple, respectively. The water molecules are shown as a filled
circle ( o ). The hydrogen bonds between trisaccharide and
protein residues or water molecules less than 3.25 Å are
shown as dotted lines. This Figure was drawn using the program
GRASP.[23] (b) The conformational change of A1-III induced by
the binding of trisaccharide products. A1-III and A1-III with
trisaccharide structures are represented as thin and thick
lines, respectively. The water molecules are shown as a filled
circle ( o ). The hydrogen bonds in trisaccharide, protein
residues or water molecules less than 3.25 Å are shown as
dotted lines. This Figure was prepared using the programs
TURBO-FRODO (Bio-Graphics) on a Silicon Graphics INDY computer
and Adobe Illustrator 5.5.
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Figure 4.
Figure 4. (a) Stereo diagram showing the spatial
orientation of M - 1, reducing end of the bound trisaccharide
product with manually constructed M+1 in the catalytic site of
A1-III. (b) Schematic representation of polymannuronic acid
degradation mechanism. (1) Arg239 interacts with the carboxyl
group of M+1 and with Tyr246 to stabilize the negative charge of
the ionized side-chain. His192 is hydrogen-bonded to O-5 of the
sugar. Tyr246 is positioned close to O-4 and C-5. (2) Tyr246
extracts the proton of C-5, resulting in the formation of a
carboxylate dianion intermediate. (3) Tyr246 donates a proton to
the glycosidic oxygen, resulting in the cleavage of the
glycosidic bond and the formation of a double bond between the
C-4 and C-5 atoms.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
307,
9-0)
copyright 2001.
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Secondary reference #1
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Title
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Crystal structure of alginate lyase a1-Iii from sphingomonas species a1 at 1.78 a resolution.
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Authors
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H.J.Yoon,
B.Mikami,
W.Hashimoto,
K.Murata.
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Ref.
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J Mol Biol, 1999,
290,
505-514.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Overall structure of the
ALYIII ribbon stereo-diagram. The
Figure shows loops (red), 12
a-helices (blue), two sulfate ions
(green), and two S-S bridges, Cys49
- Cys112 and Cys188 - Cys189 (yel-
low). The 12 a-helices are num-
bered from the N-terminal. The
bound sulfate ions and the cystine
residues are represented as ball-
and-sticks. The Figure was pre-
pared using the programs MOL-
SCRIPT (Kraulis, 1991) and
RASTER3D (Merrit & Murphy,
1994).
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Figure 10.
Figure 10. Structural comparison
of a-helices within the a/a-barrel
structure of ALYIII (blue), gluco-
amylase (yellow) and cellulase
(pink). The superimposed result is
shown as a schematic view in
C
a
-traces of a-helices. The co-
ordinates of glucoamylase (1DOG)
and cellulase (1CEM) were taken
from the Brookhaven Protein Data
Bank.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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