Structural Insights into Substrate Specificity and Function of Glucodextranase

A glucodextranase (iGDase) from Arthrobacter globiformis I42 hydrolyzes α-1,6-glucosidic linkages of dextran from the non-reducing end to produce β-d-glucose via an inverting reaction mechanism and classified into the glycoside hydrolase family 15 (GH15). Here we cloned the iGDase gene and determine...

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Bibliographic Details
Published in:The Journal of biological chemistry 2004-03, Vol.279 (11), p.10575-10583
Main Authors: Mizuno, Masahiro, Tonozuka, Takashi, Suzuki, Saori, Uotsu-Tomita, Rie, Kamitori, Shigehiro, Nishikawa, Atsushi, Sakano, Yoshiyuki
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Arthrobacter - enzymology
Arthrobacter globiformis
Binding Sites
Carbohydrates - chemistry
Catalytic Domain
Cloning, Molecular
Crystallography, X-Ray
DNA - chemistry
Glucosidases - chemistry
Glucosidases - physiology
Models, Biological
Models, Molecular
Molecular Sequence Data
Protein Binding
Protein Conformation
Protein Structure, Secondary
Protein Structure, Tertiary
Sequence Homology, Amino Acid
Substrate Specificity
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Summary:A glucodextranase (iGDase) from Arthrobacter globiformis I42 hydrolyzes α-1,6-glucosidic linkages of dextran from the non-reducing end to produce β-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-Å resolution. The structure of iGDase is composed of four domains N, A, B, and C. Domain A forms an (α/α)6-barrel structure and domain N consists of 17 antiparallel β-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.
ISSN:0021-9258
1083-351X
DOI:10.1074/jbc.M310771200