scholarly journals A new group of glycoside hydrolase family 13 α-amylases with an aberrant catalytic triad

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Fean D. Sarian ◽  
Štefan Janeček ◽  
Tjaard Pijning ◽  
Ihsanawati ◽  
Zeily Nurachman ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Catalytic Triad ◽  
Glycoside Hydrolase Family ◽  
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 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.

scholarly journals Evolutionary variance analysis of the Glycoside Hydrolase Family 13: Structural evidence in classification and evolution

2017 ◽  
Author(s):  
Jose Sergio Hleap ◽  
Christian Blouin
Keyword(s):  
Glycoside Hydrolase ◽  
Structural Information ◽  
Industrial Applications ◽  
Glycoside Hydrolase Family ◽  
Sequence Information ◽  
Novel Method ◽  
Hydrolysis Of ◽  
Hydrolase Family ◽  
Glycoside Hydrolase Family 13 ◽  
Structural Shifts

AbstractGlycoside Hydrolase Family 13 (GH13) structures are responsible for the hydrolysis of starch into smaller carbohydrates. They important in industrial applications and evolutionary studies. This family has been thoroughly documented in the the Carbohydrate-Active enZYmes Database (CAZY), and divided into subfamilies based mainly in sequence information. Here we give structural evidence into GH13 classification and evolution using structural information. Here we proposed a novel method that is sensitive enough to identify miss-classifications, or to provide evidence for further partition that can be of interests to bio-engineers and evolutionary biologists. We also introduced a method to explore the relative importance of residues with respect to the overall deformation that it causes to the overall structure in an evolutionary time scale. We found that the GH13 family can be classified into three main structural groups. There is a hierarchical structure within these clusters that can be use to inform other classification schemes. We also found that by using structural information, subtle structural shifts can be identified and that can be missed in sequence/phylogeny-only based classifications. When each structural group is explored, we found that identifying the most structurally variable sites can lead to identification of functionally (both catalytically and structurally) important residues.

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