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PDBsum entry 1k9f
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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 geobacillus stearothermophilus alpha-Glucuronidase complexed with its substrate and products: mechanistic implications.
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Authors
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G.Golan,
D.Shallom,
A.Teplitsky,
G.Zaide,
S.Shulami,
T.Baasov,
V.Stojanoff,
A.Thompson,
Y.Shoham,
G.Shoham.
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Ref.
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J Biol Chem, 2004,
279,
3014-3024.
[DOI no: ]
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PubMed id
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Abstract
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Alpha-glucuronidases cleave the alpha-1,2-glycosidic bond between
4-O-methyl-d-glucuronic acid and short xylooligomers as part of the
hemicellulose degradation system. To date, all of the alpha-glucuronidases are
classified as family 67 glycosidases, which catalyze the hydrolysis via the
investing mechanism. Here we describe several high resolution crystal structures
of the alpha-glucuronidase (AguA) from Geobacillus stearothermophilus, in
complex with its substrate and products. In the complex of AguA with the intact
substrate, the 4-O-methyl-d-glucuronic acid sugar ring is distorted into a
half-chair conformation, which is closer to the planar conformation required for
the oxocarbenium ion-like transition state structure. In the active site, a
water molecule is coordinated between two carboxylic acids, in an appropriate
position to act as a nucleophile. From the structural data it is likely that two
carboxylic acids, Asp(364) and Glu(392), activate together the nucleophilic
water molecule. The loop carrying the catalytic general acid Glu(285) cannot be
resolved in some of the structures but could be visualized in its
"open" and "closed" (catalytic) conformations in other
structures. The protonated state of Glu(285) is presumably stabilized by its
proximity to the negative charge of the substrate, representing a new variation
of substrate-assisted catalysis mechanism.
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Figure 3.
FIG. 3. The dimeric structure of AguA. a, two views of the
suggested AguA dimer, related by a 90° rotation. One of the
monomers is shown in blue/green colors, and the other is shown
in yellow/red colors. The aldotetraouronic substrate is
superimposed here (stick model) to indicate the position of the
active site of each monomer. b, an enlarged view of the
dimerization contact region, showing the specific interactions
between the two monomers (dotted lines).
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Figure 5.
FIG. 5. The active site architecture of AguA. a, stereo
view of the E285N-substrate complex (red) superimposed with the
WT-products complex (green), showing the hydrogen bonds (dotted
lines) and distances between the catalytic residues, the
nucleophilic water and the substrate/products. The inset on the
right shows the two different conformations of the MeGlcA sugar
ring in the two complexes. b, a superposition of the E386Q
mutant active site (purple), the active site of the WT AguA in
complex with the reaction products MeGlcA and xylotriose
(green), and the free WT enzyme (cyan), demonstrating the
conformational flexibility and movement of the 283-287 loop
following substrate binding and catalysis. The relevant parts of
WT AguA confirm that it is practically identical to the E386Q
mutant.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
3014-3024)
copyright 2004.
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