Surface binding sites in amylase have distinct roles in recognition of starch structure motifs and degradation

Cockburn, Darrell; Nielsen, Morten; Christiansen, C; Andersen, Joakim Mark; Rannes, Julie Bille; Blennow, Andreas; Svensson, Birte

doi:10.1016/j.ijbiomac.2015.01.054

Cited by 50 publications

(59 citation statements)

References 48 publications

(63 reference statements)

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“…These results indicated that these exposed aromatic residues may together facilitate the attachment of the enzyme to glucan substrates; the resulting absence of saccharide-binding ability at these secondary binding sites in the quadruple mutant resulted in a significant reduction in the enzyme activity. A similar synergistic effect has been observed in other RSDEs such as AMY11533 and human salivary α-amylase19. However, this feature may not be as obvious in AmyP ΔSBD as it is in AMY1, because saccharide binding at SBSs is directly seen in the crystal structures of AMY11617, but not in those of AmyP ΔSBD .…”

Section: Discussionsupporting

confidence: 64%

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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Section: Discussionsupporting

confidence: 64%

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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“…Both CBMs and SBSs provide a proximity effect by localizing the starch polymer near the catalytic site to enhance catalysis [61, 62]. While both sites display the canonical dual aromatic residue platform that recognizes the shape of the α(1,4)-linked glucan, the manner in which maltooligosaccharide is bound at both sites is different.…”

Section: Susg Is a Novel Gh13 Amylase Required For Starch Utilizationmentioning

confidence: 99%

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

Foley

Cockburn

Koropatkin

2016

Cell. Mol. Life Sci.

201

157

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Resident bacteria in the densely populated human intestinal tract must efficiently compete for carbohydrate nutrition. The Bacteroidetes, a dominant bacterial phylum in the mammalian gut, encode a plethora of discrete polysaccharide utilization loci (PULs) that are selectively activated to facilitate glycan capture at the cell surface. The most well-studied PUL-encoded glycan-up-take system is the starch utilization system (Sus) of Bacteroides thetaiotaomicron. The Sus includes the requisite proteins for binding and degrading starch at the surface of the cell preceding oligosaccharide transport across the outer membrane for further depolymerization to glucose in the periplasm. All mammalian gut Bacteroidetes possess analogous Sus-like systems that target numerous diverse glycans. In this review, we discuss what is known about the eight Sus proteins of B. thetaiotaomicron that define the Sus-like paradigm of nutrient acquisition that is exclusive to the Gram-negative Bacteroidetes. We emphasize the well-characterized outer membrane proteins SusDEF and the α-amylase SusG, each of which have unique structural features that allow them to interact with starch on the cell surface. Despite the apparent redundancy in starch-binding sites among these proteins, each has a distinct role during starch catabolism. Additionally, we consider what is known about how these proteins dynamically interact and cooperate in the membrane and propose a model for the formation of the Sus outer membrane complex.

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“…The question of conservation of function between different SBSs requires further investigation [38]. Insightful analyses of surface-binding sites in amylolytic enzymes that are not part of distinct CBMs but interact with carbohydrates has been published [38,43,44].…”

Section: Binding To Starch Granulementioning

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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Surface binding sites in amylase have distinct roles in recognition of starch structure motifs and degradation

Cited by 50 publications

References 48 publications

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

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

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

Raw starch degrading α-amylases: an unsolved riddle

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