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PDBsum entry 2cda
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Oxidoreductase
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PDB id
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2cda
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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 basis of substrate promiscuity in glucose dehydrogenase from the hyperthermophilic archaeon sulfolobus solfataricus.
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Authors
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C.C.Milburn,
H.J.Lamble,
A.Theodossis,
S.D.Bull,
D.W.Hough,
M.J.Danson,
G.L.Taylor.
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Ref.
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J Biol Chem, 2006,
281,
14796-14804.
[DOI no: ]
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PubMed id
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Abstract
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The hyperthermophilic archaeon Sulfolobus solfataricus grows optimally above 80
degrees C and utilizes an unusual, promiscuous, non-phosphorylative
Entner-Doudoroff pathway to metabolize both glucose and galactose. The first
enzyme in this pathway, glucose dehydrogenase, catalyzes the oxidation of
glucose to gluconate, but has been shown to have activity with a broad range of
sugar substrates, including glucose, galactose, xylose, and L-arabinose, with a
requirement for the glucose stereo configuration at the C2 and C3 positions.
Here we report the crystal structure of the apo form of glucose dehydrogenase to
a resolution of 1.8 A and a complex with its required cofactor, NADP+, to a
resolution of 2.3 A. A T41A mutation was engineered to enable the trapping of
substrate in the crystal. Complexes of the enzyme with D-glucose and D-xylose
are presented to resolutions of 1.6 and 1.5 A, respectively, that provide
evidence of selectivity for the beta-anomeric, pyranose form of the substrate,
and indicate that this is the productive substrate form. The nature of the
promiscuity of glucose dehydrogenase is also elucidated, and a physiological
role for this enzyme in xylose metabolism is suggested. Finally, the structure
suggests that the mechanism of sugar oxidation by this enzyme may be similar to
that described for human sorbitol dehydrogenase.
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Figure 1.
FIGURE 1. Stereo images of the apo SsGDH tetramer (A) and
monomer (B). The A-monomer is shown with the nucleotide-binding
domain in red and the catalytic domain in blue. The position of
the GXGXXG motif is highlighted in yellow. Zinc ions are shown
as magenta spheres, and the catalytic zinc-coordinated water is
shown as a green sphere.In B, the N and C termini of the monomer
are indicated by green and red spheres, respectively.
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Figure 3.
FIGURE 3. A, glucose bound to the SsGDH active site in the
A-monomer. Coloring is as in Fig. 2B with the mutation T41A
highlighted by orange carbons and the glucose molecule shown
with purple carbons and red oxygens, with both C6-hydroxyl
conformations. Unbiased F[c] -F[c] electron density for the
substrate is shown as green mesh (contoured at 2.25  ).
Hydrogen bonds between the protein and glucose are shown as
broken black lines, and gray broken lines indicate interactions
of 3.5-3.7 Å that are possible hydrogen bonds at the
moment of catalysis. Asp^154 sits below the sugar ring
interacting with the C2- and C3-hydroxyls. B, xylose bound to
the SsGDH active site of monomer A. Coloring is as in A, but the
glucose molecule is shown in the equatorial  -form with purple
carbons and red oxygens, and in the axial (  -form) with
wheat-colored carbons. Unbiased F[c] - F[c] electron density for
the substrate is shown as green mesh (contoured at 2.25 ).
Hydrogen bonds between the protein and -xylose are shown as
broken black lines, and gray broken lines indicate interactions
of <3.5-3.7 Å that are possible hydrogen bonds at the
moment of catalysis. Hydrogen bonds to the -form are not shown,
because most, with the exception of the C1-OH interactions, are
maintained and no new hydrogen bonds are formed in the -form.
C, superposition of glucose (green) and xylose (blue) in the
active site of the A-monomer. The two positions for O6 of
glucose are displayed, as are the two positions of O1 of xylose.
Glu^114 undergoes a conformational change between the glucose
and xylose complex structures; the alternative position for this
residue in the xylose structure is depicted in wheat-colored
carbons.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
14796-14804)
copyright 2006.
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