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PDBsum entry 1ulv
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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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Structural insights into substrate specificity and function of glucodextranase.
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Authors
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M.Mizuno,
T.Tonozuka,
S.Suzuki,
R.Uotsu-Tomita,
S.Kamitori,
A.Nishikawa,
Y.Sakano.
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Ref.
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J Biol Chem, 2004,
279,
10575-10583.
[DOI no: ]
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PubMed id
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Abstract
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A glucodextranase (iGDase) from Arthrobacter globiformis I42 hydrolyzes
alpha-1,6-glucosidic linkages of dextran from the non-reducing end to produce
beta-D-glucose via an inverting reaction mechanism and classified into the
glycoside hydrolase family 15 (GH15). Here we cloned the iGDase gene and
determined the crystal structures of iGDase of the unliganded form and the
complex with acarbose at 2.42-A resolution. The structure of iGDase is composed
of four domains N, A, B, and C. Domain A forms an (alpha/alpha)(6)-barrel
structure and domain N consists of 17 antiparallel beta-strands, and both
domains are conserved in bacterial glucoamylases (GAs) and appear to be mainly
concerned with catalytic activity. The structure of iGDase complexed with
acarbose revealed that the positions and orientations of the residues at
subsites -1 and +1 are nearly identical between iGDase and GA; however, the
residues corresponding to subsite 3, which form the entrance of the substrate
binding pocket, and the position of the open space and constriction of iGDase
are different from those of GAs. On the other hand, domains B and C are not
found in the bacterial GAs. The primary structure of domain C is homologous with
a surface layer homology domain of pullulanases, and the three-dimensional
structure of domain C resembles the carbohydrate-binding domain of some
glycohydrolases.
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Figure 4.
FIG. 4. Structural model of acarbose bound to the active
site of iGDase. a, schematic topology of acarbose. The
saccharide units are labeled as A, B, C, and D from the
non-reducing end. The numbers -1 to +3 are subsite numbers
corresponding to each unit of acarbose. b, stereo view of 2F[o]
- F[c] electron density map of acarbose bound in the active site
of iGDase. The map of the acarbose and a water molecule is
contoured at the 1.0  . c, schematic drawing
of the interactions of acarbose bound to the active site.
Hydrogen bonds of less than 3.5 Å are shown as dashed
lines. Water molecules are shown as spheres. Two catalytic
residues are boxed.
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Figure 6.
FIG. 6. The solvent-accessible surface model of iGDase and
GAs around the substrate binding pocket. a, iGDase (PDB ID: 1ULV
[PDB]
). Gln-380 does not directly interact with acarbose, and
constriction of Trp-582 is observed. b, T. thermosaccharolyticum
GA (1LF9 [PDB]
). Trp-390 is stacked with acarbose, and the constriction of
Tyr-590 is not seen. c, A. awamori var. X-100 (1AGM [PDB]
). An extended loop consisting of five amino acid residues
(TGSWG), which are not conserved in iGDase and T.
thermosaccharolyticum GA, interacts with acarbose.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
10575-10583)
copyright 2004.
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