Crystal structure of a compact α-amylase from Geobacillus thermoleovorans

Mok, Sook-Chen; Teh, Aik-Hong; Saito, Jennifer A.; Najimudin, Nazalan; Alam, Maqsudul

doi:10.1016/j.enzmictec.2013.03.009

Cited by 36 publications

(35 citation statements)

References 61 publications

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“…3). The BmaN1 protein displayed 40% homology (100% confidence, 85% sequence coverage) with the X-ray crystal structure of Geobacillus thermoleovorans α-amylase (GTA, PDB code: 4E2O)25 which was used as a template for the modeling. The comparison between the model and the GTA crystal structure revealed that the global topology is almost the same (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…These α-amylases – BaqA from B. aquimaris 35, ASKA and ADTA from Anoxybacillus sp 3637,. GTA and GTA-II from Geobacillus thermoleovorans 253839 – exhibit a high degree of sequence similarity with BmaN1, but possess the complete GH13 catalytic machinery19. The entire set was finally completed by two selected representatives from well-established GH13 subfamilies with the α-amylase specificity, i.e.…”

Section: Methodsmentioning

confidence: 99%

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

Sarian

Janeček

Pijning

et al. 2017

Sci Rep

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α-Amylases are glycoside hydrolase enzymes that act on the α(1→4) glycosidic linkages in glycogen, starch, and related α-glucans, and are ubiquitously present in Nature. Most α-amylases have been classified in glycoside hydrolase family 13 with a typical (β/α)8-barrel containing two aspartic acid and one glutamic acid residue that play an essential role in catalysis. An atypical α-amylase (BmaN1) with only two of the three invariant catalytic residues present was isolated from Bacillus megaterium strain NL3, a bacterial isolate from a sea anemone of Kakaban landlocked marine lake, Derawan Island, Indonesia. In BmaN1 the third residue, the aspartic acid that acts as the transition state stabilizer, was replaced by a histidine. Three-dimensional structure modeling of the BmaN1 amino acid sequence confirmed the aberrant catalytic triad. Glucose and maltose were found as products of the action of the novel α-amylase on soluble starch, demonstrating that it is active in spite of the peculiar catalytic triad. This novel BmaN1 α-amylase is part of a group of α-amylases that all have this atypical catalytic triad, consisting of aspartic acid, glutamic acid and histidine. Phylogenetic analysis showed that this group of α-amylases comprises a new subfamily of the glycoside hydrolase family 13.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

Sarian

Janeček

Pijning

et al. 2017

Sci Rep

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“…This observation leads to the idea that Trp201 and Trp202 of BaqA might represent a fingerprint of the new GH13 α-amylase subfamily [69]. These two tryptophans are also conserved in Geobacillus thermoleovorans α-amylases GTA [73] and Gt-amyII [61] as W204 and W205 with an important difference that in these two cases W205 is not located on the surface of the protein but hidden within the structure. On the other hand, the role of domain C in raw starch adsorption has been proven by truncation and LangmuirHinshelwood adsorption experiments [61].…”

Section: Industrial Aspects Of Rsda Application In Raw Starch Hydrolysismentioning

confidence: 99%

“…On the other hand, the role of domain C in raw starch adsorption has been proven by truncation and LangmuirHinshelwood adsorption experiments [61]. These findings lead recently to an establishment of a novel subfamily of GH family GH13 for α-amylases from Anoxybacillus species (ASKA and ADTA) [74], G. thermoleovorans (GTA [73], Pizzo [75], Gt-amyII [61]), and B. aquimaris (BaqA) [69]. Members of this new GH13 subfamily act on raw starch and are characterized by a C-terminus composed of five conserved aromatic residues, two tryptophan residues between CSR-V and CSR-II, and an LPDlx motif in CSR-V [76].…”

Section: Industrial Aspects Of Rsda Application In Raw Starch Hydrolysismentioning

confidence: 99%

Raw starch degrading α-amylases: an unsolved riddle

Božić

Lončar

Slavić

et al. 2017

Amylase

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Starch is an important food ingredient and a substrate for the production of many industrial products. Biological and industrial processes involve hydrolysis of raw starch, such as digestion by humans and animals, starch metabolism in plants, and industrial starch conversion for obtaining glucose, fructose and maltose syrup or bioethanol. Raw starch degrading α-amylases (RSDA) can directly degrade raw starch below the gelatinization temperature of starch. Knowledge of the structures and properties of starch and RSDA has increased significantly in recent years. Understanding the relationships between structural peculiarities and properties of RSDA is a prerequisite for efficient application in different aspects of human benefit from health to the industry. This review summarizes recent advances on RSDA research with emphasizes on representatives of glycoside hydrolase family GH13. Definite understanding of raw starch digesting ability is yet to come with accumulating structural and functional studies of RSDA.

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“…The SBSs usually contain aromatic residues. Recently, the bacterial α-amylases from Anoxybacillus species (ASKA and ADTA)20, Geobacillus thermoleovorans (GTA21, Pizzo α-amylase22, and GtamyII23), and Bacillus aquimaris (BaqA24) have been proposed to constitute a novel GH13 subfamily25 of raw-starch-digesting α-amylases, that lack SBDs but exhibit the ability to degrade raw starch. However, enzymes in this subfamily possess an extended C-terminal region that is rich in aromatic residues, and the actual role of this region remains to be investigated.…”

mentioning

confidence: 99%

Crystal structure of a raw-starch-degrading bacterial α-amylase belonging to subfamily 37 of the glycoside hydrolase family GH13

Liu

et al. 2017

Sci Rep

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Subfamily 37 of the glycoside hydrolase family GH13 was recently established on the basis of the discovery of a novel α-amylase, designated AmyP, from a marine metagenomic library. AmyP exhibits raw-starch-degrading activity and consists of an N-terminal catalytic domain and a C-terminal starch-binding domain. To understand this newest subfamily, we determined the crystal structure of the catalytic domain of AmyP, named AmyPΔSBD, complexed with maltose, and the crystal structure of the E221Q mutant AmyPΔSBD complexed with maltotriose. Glu221 is one of the three conserved catalytic residues, and AmyP is inactivated by the E221Q mutation. Domain B of AmyPΔSBD forms a loop that protrudes from domain A, stabilizes the conformation of the active site and increases the thermostability of the enzyme. A new calcium ion is situated adjacent to the -3 subsite binding loop and may be responsible for the increased thermostability of the enzyme after the addition of calcium. Moreover, Tyr36 participates in both stacking and hydrogen bonding interactions with the sugar motif at subsite -3. This work provides the first insights into the structure of α-amylases belonging to subfamily 37 of GH13 and may contribute to the rational design of α-amylase mutants with enhanced performance in biotechnological applications.

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Crystal structure of a compact α-amylase from Geobacillus thermoleovorans

Cited by 36 publications

References 61 publications

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

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

Raw starch degrading α-amylases: an unsolved riddle

Crystal structure of a raw-starch-degrading bacterial α-amylase belonging to subfamily 37 of the glycoside hydrolase family GH13

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