Unusual Role of the 3-OH Group of Oligosaccharide Substrates in the Mechanism of<i>Bacillus</i>1,3-1,4-β-glucanase

Planas, Antoni; Nieto, Juan Miguel; Abel, Mireia; Segade, Antoni

doi:10.1080/10242420310001618500

Cited by 2 publications

(3 citation statements)

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“…The subtle change in the position of O5 has little mechanistic consequence other than to allow development of the partial double bond. Interactions at C2 are usually (but not always, see: [ 8 ]) significant and for the β-glucosidase Abg from Agrobacterium sp. or for α-glucosidase of Saccharomyces cerevisiae [ 9 ] have been shown to contribute 18–22 kJ mol −1 to transition state stabilization [ 10 ], highlighting that the repositioning of C2 and its substituent and other electronic changes accompanying formation of the oxocarbenium ion-like transition state can provide substantial amounts of stabilization energy.…”

Section: Contortions Along the Reaction Coordinatementioning

confidence: 99%

Dissecting conformational contributions to glycosidase catalysis and inhibition

Speciale

Thompson

Davies

et al. 2014

Current Opinion in Structural Biology

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Section: Contortions Along the Reaction Coordinatementioning

confidence: 99%

Dissecting conformational contributions to glycosidase catalysis and inhibition

Speciale

Thompson

Davies

et al. 2014

Current Opinion in Structural Biology

120

141

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“…The substrate chosen for the analysis is the 4-methylumbelliferyl tetrasaccharide shown in Fig. 3, which is a good substrate extensively used in enzyme kinetics (32)(33)(34). To the best of our knowledge, the conformational itinerary of the substrate in GHs has not yet been investigated by the first principles methods.…”

mentioning

confidence: 99%

“…In the framework of our structure/function studies of bacterial 1,3-1,4-␤-glucanases (7,(32)(33)(34), we investigate here the conformation of the substrate in the Michaelis complex of Bacillus 1,3-1,4-␤-glucanase by means of hybrid quantum mechanics/molecular mechanics (QM/MM) simulations (35). In this approach, the atoms of the QM region evolve in time under the effect of the quantum mechanical forces, computed using density functional theory (DFT), and the electronic cloud adapts instantaneously to the chemical environment, whereas the forces on the MM region are ruled by a force field.…”

mentioning

confidence: 99%

Substrate Distortion in the Michaelis Complex of Bacillus 1,3–1,4-β-Glucanase

Biarnés

Nieto

Planas

et al. 2006

Journal of Biological Chemistry

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The structure and dynamics of the enzyme-substrate complex of Bacillus 1,3-1,4-␤-glucanase, one of the most active glycoside hydrolases, is investigated by means of Car-Parrinello molecular dynamics simulations (CPMD) combined with force field molecular dynamics (QM/MM CPMD). It is found that the substrate sugar ring located at the ؊1 subsite adopts a distorted 1 S 3 skew-boat conformation upon binding to the enzyme. With respect to the undistorted 4 C 1 chair conformation, the 1 S 3 skew-boat conformation is characterized by: (a) an increase of charge at the anomeric carbon (C1), (b) an increase of the distance between C1 and the leaving group, and (c) a decrease of the intraring O5-C1 distance. Therefore, our results clearly show that the distorted conformation resembles both structurally and electronically the transition state of the reaction in which the substrate acquires oxocarbenium ion character, and the glycosidic bond is partially broken. Together with analysis of the substrate conformational dynamics, it is concluded that the main determinants of substrate distortion have a structural origin. To fit into the binding pocket, it is necessary that the aglycon leaving group is oriented toward the ␤ region, and the skew-boat conformation naturally fulfills this premise. Only when the aglycon is removed from the calculation the substrate recovers the all-chair conformation, in agreement with the recent determination of the enzyme product structure. The QM/MM protocol developed here is able to predict the conformational distortion of substrate binding in glycoside hydrolases because it accounts for polarization and charge reorganization at the ؊1 sugar ring. It thus provides a powerful tool to model E⅐S complexes for which experimental information is not yet available. Glycoside hydrolases (GHs)2 are the enzymes responsible for the hydrolysis of glycosidic bonds and play important biological functions such as glycan processing in glycoproteins, remodeling the cell walls, and polysaccharide modification and degradation. The reaction mechanism, a classical textbook example of enzymatic reaction, has attracted much interest because genetically inherited disorders of glycoside hydrolysis often occur and because inhibitors of these enzymes can act as new therapeutic agents for the treatment of viral infections (1, 2). Despite the large number of GHs known, classified into more than 90 families (1), the catalytic mechanism is similar. They typically operate by means of acid/base catalysis with retention or inversion of the anomeric configuration, although a different mechanism has recently been proposed for the GH family 4 (3). The acid/base reaction is assisted by two essential residues: a proton donor and a nucleophile or general base residue (4). Inverting enzymes operate by a single nucleophilic substitution, whereas retaining glycosidases follow a double displacement mechanism via formation and hydrolysis of a covalent glycosyl-enzyme intermediate. Both steps involve oxocarbenium ion-like transition states (F...

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Unusual Role of the 3-OH Group of Oligosaccharide Substrates in the Mechanism ofBacillus1,3-1,4-β-glucanase

Cited by 2 publications

References 37 publications

Dissecting conformational contributions to glycosidase catalysis and inhibition

Dissecting conformational contributions to glycosidase catalysis and inhibition

Substrate Distortion in the Michaelis Complex of Bacillus 1,3–1,4-β-Glucanase

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