Molecular Determinants of Substrate Recognition in Thermostable  -glucosidases Belonging to Glycoside Hydrolase Family 13

2007 ◽  
Vol 142 (1) ◽  
pp. 87-93 ◽  
Author(s):  
Y. Tsujimoto ◽  
H. Tanaka ◽  
R. Takemura ◽  
T. Yokogawa ◽  
A. Shimonaka ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Substrate Recognition ◽  
Glycoside Hydrolase Family ◽  
Molecular Determinants ◽  
Hydrolase Family ◽  
Glycoside Hydrolase Family 13

scholarly journals The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach

2017 ◽  
Author(s):  
Jose Sergio Hleap ◽  
Christian Blouin
Keyword(s):  
Glycoside Hydrolase ◽  
Fitness Landscape ◽  
Protein Structures ◽  
Purifying Selection ◽  
Industrial Applications ◽  
Glycoside Hydrolase Family ◽  
Response To Selection ◽  
Effect Change ◽  
Hydrolase Family ◽  
Glycoside Hydrolase Family 13

AbstractThe Glycoside Hydrolase Family 13 (GH13) is both evolutionary diverse and relevant to many industrial applications. Its members perform the hydrolysis of starch into smaller carbohydrates. Members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of GH13 protein structures given some phylogenetic and simulated dynamic information. We found that the TIM-barrel is not selectable since it is under purifying selection. We also show a method to rank important residues with higher inferred response to selection. These residues can be altered to effect change in properties. In this work, we define fitness as inferred thermodynamic stability. We show that under the developed framework, residues 112Y, 122K, 124D, 125W, and 126P are good candidates to increase the stability of the truncated protein 4E2O. Overall, this paper demonstrate the feasibility of a framework for the analysis of protein structures for any other fitness landscape.

scholarly journals Structural basis of catalysis and substrate recognition by the NAD(H)-dependent α-d-glucuronidase from the glycoside hydrolase family 4

2021 ◽  
Vol 478 (4) ◽  
pp. 943-959
Author(s):  
Samar Ballabha Mohapatra ◽  
Narayanan Manoj
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Glycoside Hydrolase ◽  
Metal Ion ◽  
Substrate Recognition ◽  
Structural Basis ◽  
Glycoside Hydrolase Family ◽  
Diverse Range ◽  
Molecular Features ◽  
Hydrolase Family

Members of the glycoside hydrolase family 4 (GH4) employ an unusual glycosidic bond cleavage mechanism utilizing NAD(H) and a divalent metal ion, under reducing conditions. These enzymes act upon a diverse range of glycosides, and unlike most other GH families, homologs here are known to accommodate both α- and β-anomeric specificities within the same active site. Here, we report the catalytic properties and the crystal structures of TmAgu4B, an α-d-glucuronidase from the hyperthermophile Thermotoga maritima. The structures in three different states include the apo form, the NADH bound holo form, and the ternary complex with NADH and the reaction product d-glucuronic acid, at 2.15, 1.97 and 1.85 Å resolutions, respectively. These structures reveal the step-wise route of conformational changes required in the active site to achieve the catalytically competent state, and illustrate the direct role of residues that determine the reaction mechanism. Furthermore, a structural transition of a helical region in the active site to a turn geometry resulting in the rearrangement of a unique arginine residue governs the exclusive glucopyranosiduronic acid recognition in TmAgu4B. Mutational studies show that modifications of the glycone binding site geometry lead to catalytic failure and indicate overlapping roles of specific residues in catalysis and substrate recognition. The data highlight hitherto unreported molecular features and associated active site dynamics that determine the structure–function relationships within the unique GH4 family.

scholarly journals Novel Members of Glycoside Hydrolase Family 13 Derived from Environmental DNA

2008 ◽  
Vol 74 (6) ◽  
pp. 1914-1921 ◽  
Author(s):  
Antje Labes ◽  
Eva Nordberg Karlsson ◽  
Olafur H. Fridjonsson ◽  
Pernilla Turner ◽  
Gudmundur O. Hreggvidson ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Environmental Dna ◽  
Industrial Applications ◽  
Glycoside Hydrolase Family ◽  
Biotechnological Applications ◽  
Consensus Primer ◽  
Thermophilic Conditions ◽  
Maltogenic Amylase ◽  
Hydrolase Family ◽  
Glycoside Hydrolase Family 13

ABSTRACT Starch and pullulan-modifying enzymes of the α-amylase family (glycoside hydrolase family 13) have several industrial applications. To date, most of these enzymes have been derived from isolated organisms. To increase the number of members of this enzyme family, in particular of the thermophilic representatives, we have applied a consensus primer-based approach using DNA from enrichments from geothermal habitats. With this approach, we succeeded in isolating three new enzymes: a neopullulanase and two cyclodextrinases. Both cyclodextrinases displayed significant maltogenic amylase side activity, while one showed significant neopullulanase side activity. Specific motifs and domains that correlated with enzymatic activities were identified; e.g., the presence of the N domain was correlated with cyclodextrinase activity. The enzymes exhibited stability under thermophilic conditions and showed features appropriate for biotechnological applications.

Bacillus licheniformistrehalose-6-phosphate hydrolase structures suggest keys to substrate specificity

2016 ◽  
Vol 72 (1) ◽  
pp. 59-70 ◽  
Author(s):  
Min-Guan Lin ◽  
Meng-Chun Chi ◽  
Vankadari Naveen ◽  
Yi-Ching Li ◽  
Long-Liu Lin ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Bacillus Licheniformis ◽  
Active Site ◽  
Glycoside Hydrolase ◽  
Positive Charge ◽  
Glycoside Hydrolase Family ◽  
Erwinia Rhapontici ◽  
Hydrolysis Of ◽  
Hydrolase Family ◽  
Glycoside Hydrolase Family 13

Trehalose-6-phosphate hydrolase (TreA) belongs to glycoside hydrolase family 13 (GH13) and catalyzes the hydrolysis of trehalose 6-phosphate (T6P) to yield glucose and glucose 6-phosphate. The products of this reaction can be further metabolized by the energy-generating glycolytic pathway. Here, crystal structures ofBacillus licheniformisTreA (BlTreA) and its R201Q mutant complexed withp-nitrophenyl-α-D-glucopyranoside (R201Q–pPNG) are presented at 2.0 and 2.05 Å resolution, respectively. The overall structure ofBlTreA is similar to those of other GH13 family enzymes. However, detailed structural comparisons revealed that the catalytic site ofBlTreA contains a long loop that adopts a different conformation from those of other GH13 family members. Unlike the homologous regions ofBacillus cereusoligo-1,6-glucosidase (BcOgl) andErwinia rhaponticiisomaltulose synthase (NX-5), the surface potential of theBlTreA active site exhibits a largely positive charge contributed by the four basic residues His281, His282, Lys284 and Lys292. Mutation of these residues resulted in significant decreases in the enzymatic activity ofBlTreA. Strikingly, the281HHLK284motif and Lys292 play critical roles in substrate discrimination byBlTreA.

Substrate recognition by glycoside hydrolase family 74 xyloglucanase from the basidiomycetePhanerochaete chrysosporium

FEBS Journal ◽  
2007 ◽  
Vol 274 (21) ◽  
pp. 5727-5736 ◽  
Author(s):  
Takuya Ishida ◽  
Katsuro Yaoi ◽  
Ayako Hiyoshi ◽  
Kiyohiko Igarashi ◽  
Masahiro Samejima
Keyword(s):  
Glycoside Hydrolase ◽  
Substrate Recognition ◽  
Glycoside Hydrolase Family ◽  
Hydrolase Family
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