Glycosidic Oxygen Research Articles

Synthesis and Evaluation of 1,5-Dithia-d-laminaribiose, Triose, and Tetraose as Truncated β-(1→3)-Glucan Mimetics.

The preparation and characterization of a series of di-, tri-, and tetrasaccharide analogues of β-(1→3)-glucans is described in which each pyranoside ring is replaced by a 5-thiopyranosyl ring and each glycosidic oxygen by a thioether. These oligomeric 1,5-dithio-d-glucopyranose derivatives were shown to inhibit the staining of human neutrophils and of mouse macrophages by fluorescent anti-CR3 and anti-Dectin-1 antibodies, respectively. The compounds were also demonstrated to stimulate phagocytosis and pinocytosis indicative of binding to the carbohydrate binding domains of complement receptor 3 (CR3) and Dectin-1. Activity in all three assays was optimum at the level of the trisaccharide mimic, suggesting that, while the replacement of ethereal oxygens by thioethers results in a greater affinity for the aromatic lined hydrophobic binding pockets, the presence of multiple longer C-S bonds eventually results in a mismatch and a loss of affinity.

Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide

Oligosaccharyltransferase (OST) is a key enzyme of the N-glycosylation pathway, where it catalyzes the transfer of a glycan from a lipid-linked oligosaccharide (LLO) to an acceptor asparagine within the conserved sequon N-X-T/S. A previous structure of a ternary complex of bacterial single subunit OST, PglB, bound to a non-hydrolyzable LLO analog and a wild type acceptor peptide showed how both substrates bind and how an external loop (EL5) of the enzyme provided specific substrate-binding contacts. However, there was a relatively large separation of the substrates at the active site. Here we present the X-ray structure of PglB bound to a reactive LLO analog and an inhibitory peptide, revealing previously unobserved interactions in the active site. We found that the atoms forming the N-glycosidic bond (C-1 of the GlcNAc moiety of LLO and the –NH2 group of the peptide) are closer than in the previous structure, suggesting that we have captured a conformation closer to the transition state of the reaction. We find that the distance between the divalent metal ion and the glycosidic oxygen of LLO is now 4 Å, suggesting that the metal stabilizes the leaving group of the nucleophilic substitution reaction. Further, the carboxylate group of a conserved aspartate of PglB mediates an interaction network between the reducing-end sugar of the LLO, the asparagine side chain of the acceptor peptide, and a bound divalent metal ion. The interactions identified in this novel state are likely to be relevant in the catalytic mechanisms of all OSTs.

Understanding the Rate-Limiting Step of Glycogenolysis by Using QM/MM Calculations on Human Glycogen Phosphorylase.

Liver glycogen phosphorylase (GP) is a key enzyme for human health, as its increased activity is associated with type 2 diabetes. The GP catalytic mechanism has been explored by quantum mechanics/molecular mechanics (QM/MM) methods. Herein, we propose a mechanism that proceeds by three steps: 1) it begins with transfer of a hydrogen atom from the phosphate group of the pyridoxal 5'-phosphate (HPO42- -PLP) cofactor to the phosphate substrate; 2) the glycosidic linkage is then cleaved through protonation of the glycosidic oxygen atom by a hydroxy group of the inorganic phosphate group; and 3) an oxygen atom of the phosphate performs a nucleophilic attack on the anomeric carbon atom of glucose, concomitant with the return of a proton from phosphate to PO43- -PLP, which finally leads to formation of the glucose-1-phosphate product and recovers the initial state of the PLP cofactor. The glycosidic bond cleavage and nucleophilic attack from the phosphate group to the glycosyl molecule have the highest activation free energies. The structural properties of the hereby characterized transition states could be very useful in structure-based drug design studies against liver GP.

A Full QM Computational Study of the Catalytic Mechanism of α-1,4-Glucan Lyases.

We investigated the catalytic mechanism of α-1,4-glucan lyases using a full QM DFT approach based on the M06-2X functional. The reaction profile of the whole catalytic process can be divided into three phases: glycosylation, deglycosylation-elimination and tautomerization. Glycosylation is a highly asynchronous SN 1-like process with an energy barrier of 10.2 kcal mol-1 . A proton moves from the Asp665 residue to the glycosidic oxygen. Asp553 acts as a nucleophile and attacks the anomeric carbon causing the cleavage of the glycosidic bond. Deglycosilation-elimination is the rate-determining step of the entire process with an overall barrier of 18.3 kcal mol-1 . The final step (restoring the catalyst and tautomerization) occurs rather easily, since the Asp553 carboxylate group "assists" the proton transfer in the tautomerization process. Our computations clearly indicate that tautomerization must occur inside the enzyme before leaving the active site rather than in the aqueous solution. Outside of the protein environment the enol-AF→keto-AF process "assisted" by a water molecule has a barrier of 35.8 kcal mol-1 .

A Buried Water Molecule Influences Reactivity in α-Amylase on a Subnanosecond Time Scale

The subset of catalytically competent conformations can be significantly small in comparison with the full conformational landscape of enzyme–substrate complexes. In some enzymes, the probability of finding a reactive conformation can account for up to 4 kcal/mol of activation barrier, even when the substrate remains tightly bound. In this study, we sampled conformations of human pancreatic α-amylase with bound substrate in a molecular dynamics (MD) simulation of over 100 ns and calculated energy profiles along the reaction coordinate. We found that reactive states require a hydrogen bond between a buried water molecule and E233, which is the general acid in the glycolysis mechanism. The effect of this single, nonreactive, intermolecular interaction is as important as the correct positioning and orientation of the reacting residues to achieve a competent energy barrier. This hydrogen bond increases the acidity of E233, facilitating proton transfer to the glycosidic oxygen. In the MD simulation, this requi...

Dry Thermotropic Glycolipid Self-Assembly:A Review

Also recognized as carbohydrate liquid crystals, glycolipids are amphiphiles whose basic unit comprises of a sugar group attached to an alkyl chain. Glycolipids are amphitropic, which means these materials form liquid crystal self-assemblies when dry (thermotropic) as well as when dissolved in solvents (lyotropic/surfactants) such as water. Many glycolipids are also naturally derived since these can be found in cell membranes. Their membrane and surfactant functions are largely understood through their lyotropic properties. While glycolipids are expected to play major roles as eco-friendly surfactants in the global surfactant market, their usefulness as thermotropic liquid crystal material is, to date, unknown, due to relatively lack of research performed and data reported in the literature. Understandably since glycolipids are hygroscopic with many hydroxy groups, removing the last trace water is very challenging. In recent time, with careful lyophilization and more consistent characterization technique, some researchers have attempted serious studies into "dry" or anhydrous glycolipids. Motivated by possible developments of novel thermotropic applications, some results from these studies also provide surprising new understanding to support conventional wisdom of the lyotropic systems. Here we review the dry state of glycosides, a family of glycolipids whose sugar headgroup is linked to the lipid chain via a glycosidic oxygen linker. The structure property relationship of both linear and anhydrous Guerbet glycosides will be examined. In particular, how the variation of sugar stereochemistry (e.g. anomer vs. epimer), the chain length and chain branching affect the formation of thermotropic liquid crystals phases, which not only located under equilibrium but also far from equilibrium conditions (glassy phase) are scrutinized. The dry glycolipid assembly has been subjected to electric and magnetic fields and the results show interesting behaviors including a possible transient current generation.

The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors

The α-N-acetylgalactosaminidase from the probiotic bacterium Bifidobacterium bifidum (NagBb) belongs to the glycoside hydrolase family 129 and hydrolyzes the glycosidic bond of Tn-antigen (GalNAcα1-Ser/Thr). NagBb is involved in assimilation of O-glycans on mucin glycoproteins by B. bifidum in the human gastrointestinal tract, but its catalytic mechanism has remained elusive because of a lack of sequence homology around putative catalytic residues and of other structural information. Here we report the X-ray crystal structure of NagBb, representing the first GH129 family structure, solved by the single-wavelength anomalous dispersion method based on sulfur atoms of the native protein. We determined ligand-free, GalNAc, and inhibitor complex forms of NagBb and found that Asp-435 and Glu-478 are located in the catalytic domain at appropriate positions for direct nucleophilic attack at the anomeric carbon and proton donation for the glycosidic bond oxygen, respectively. A highly conserved Asp-330 forms a hydrogen bond with the O4 hydroxyl of GalNAc in the -1 subsite, and Trp-398 provides a stacking platform for the GalNAc pyranose ring. Interestingly, a metal ion, presumably Ca2+, is involved in the recognition of the GalNAc N-acetyl group. Mutations at Asp-435, Glu-478, Asp-330, and Trp-398 and residues involved in metal coordination (including an all-Ala quadruple mutant) significantly reduced the activity, indicating that these residues and the metal ion play important roles in substrate recognition and catalysis. Interestingly, NagBb exhibited some structural similarities to the GH101 endo-α-N-acetylgalactosaminidases, but several critical differences in substrate recognition and reaction mechanism account for the different activities of these two enzymes.

New Human CD22/Siglec-2 Ligands with a Triazole Glycoside.

CD22 is a member of the Siglec family. Considerable attention has been drawn to the design and synthesis of new Siglec ligands to explore target biology and innovative therapies. In particular, CD22-ligand-targeted nanoparticles with therapeutic functions have proved successful in preclinical settings for blood cancers, autoimmune diseases, and tolerance induction. Here we report the design, synthesis and affinity evaluation of a new class of Siglec ligands: namely sialic acid derivatives with a triazole moiety replacing the natural glycoside oxygen atom. In addition, we describe important and surprising differences in binding to CD22 expressed at the cell surface for compounds with distinct valences. The new class of compounds might serve as a template for the design of ligands for other members of the Siglec family and next-generation CD22-ligand-based targeted therapies.

Cationized Carbohydrate Gas-Phase Fragmentation Chemistry.

We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms. Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies. Graphical Abstract ᅟ.

Improving the antioxidant functionality of Citrus junos Tanaka (yuzu) fruit juice by underwater shockwave pretreatment

Citrus junos Tanaka (yuzu) has a strong characteristic aroma, and hence, yuzu juice is used in a number of Japanese foods. We herein evaluated the functional compounds of yuzu juice to investigate whether underwater shockwave pretreatment affects its functionality. Employing the shockwave pretreatment at an increased discharge and energy of 3.5kV and 4.9kJ, respectively, resulted in an increase in the flavanone glycoside content and oxygen radical absorbance capacity (ORAC). The ORAC value of yuzu juice cultivated in Rikuzentakata increased approximately 1.7 times upon underwater shockwave pretreatment. The treatment method proposed herein exhibited reliable and good performance for the extraction of functional and antioxidant chemicals in yuzu fruits, and was comparable with traditional squeezing methods. The high applicability and reliability of this technique for improving the antioxidant functionality of yuzu fruit juice was demonstrated, confirming the potential for application to a wide range of food extraction processes.

Ring inversion properties of 1→2, 1→3 and 1→6-linked hexopyranoses and their correlation with the conformation of glycosidic linkages

Enhanced-sampling molecular dynamics simulations performed within the GROMOS 56a6CARBO_R force field were applied in order to elucidate ring-inversion properties of hexopyranose residues in a chain for the case of α(1→n) and β(1→n) glycosidic linkages (n = 2, 3 or 6). The results indicate that ring-inversion free energies calculated for residues in a chain are weakly correlated with those of corresponding monomers, except of the case of 1→6 linkages. This, in combination with the results for O1-methyl-hexopyranosides (Plazinski et al, 2016), suggests that both the type of functionalization (glycolysation vs. methylation) and the topology of glycosidic linkage play an important role in possible alterations of the hexopyranose ring flexibility. Additionally, the correlation of the ring shape with the preferred geometry of glycosidic linkages was investigated. The linkages of the 1→2, 1→3 and 1→6 types do not follow the trend found in the case of the 1→4 linkages, i.e. there is no correlation between the range of changes in the glycosidic linkage conformation and the topological orientation of the glycosidic oxygen atoms. Overall, the ring shape affects the glycosidic linkages of the 1→6 type to the least extent in comparison to the remaining ones.

Inclusion complexes of 2-methoxyestradiol with dimethylated and permethylated β-cyclodextrins: models for cyclodextrin-steroid interaction.

The interaction between the potent anticancer agent 2-methoxyestradiol (2ME) and a series of cyclodextrins (CDs) was investigated in the solid state using thermal analysis and X-ray diffraction, while the possibility of enhancing its poor aqueous solubility with CDs was probed by means of equilibrium solubility and dissolution rate measurements. Single crystal X-ray diffraction studies of the inclusion complexes between 2ME and the derivatised cyclodextrins heptakis(2,6-di-O-methyl)-β-CD (DIMEB) and heptakis(2,3,6-tri-O-methyl)-β-CD (TRIMEB) revealed for the first time the nature of the encapsulation of a bioactive steroid by representative CD host molecules. Inclusion complexation invariably involves insertion of the D-ring of 2ME from the secondary side of each CD molecule, with the 17-OH group generally hydrogen bonding to a host glycosidic oxygen atom within the CD cavity, while the A-ring and part of the B-ring of 2ME protrude from the secondary side. In the case of the TRIMEB·2ME complex, there is evidence that complexation proceeds with mutual conformational adaptation of host and guest molecules. The aqueous solubility of 2ME was significantly enhanced by CDs, with DIMEB, TRIMEB, randomly methylated β-CD and hydroxypropyl-β-CD being the most effective hosts. The 2:1 host–guest β-CD inclusion complex, prepared by two methods, yielded very rapid dissolution in water at 37 °C relative to untreated 2ME, attaining complete dissolution within 15 minutes (co-precipitated complex) and 45 minutes (complex from kneading).

Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism

O-Linked glycosylation is one of the most abundant post-translational modifications of proteins. Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. Glycoside hydrolases in family 101 are presently the only known enzymes to be able to hydrolyze this glycosidic linkage. Here we determine the high-resolution structures of the catalytic domain comprising a fragment of GH101 from Streptococcus pneumoniae TIGR4, SpGH101, in the absence of carbohydrate, and in complex with reaction products, inhibitor, and substrate analogues. Upon substrate binding, a tryptophan lid (residues 724-WNW-726) closes on the substrate. The closing of this lid fully engages the substrate in the active site with Asp-764 positioned directly beneath C1 of the sugar residue bound within the -1 subsite, consistent with its proposed role as the catalytic nucleophile. In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 Å) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. These same complexes, however, revealed a structurally conserved water molecule positioned between the catalytic acid/base and the glycosidic oxygen. On the basis of these structural observations we propose a new variation of the retaining glycoside hydrolase mechanism wherein the intervening water molecule enables a Grotthuss proton shuttle between Glu-796 and the glycosidic oxygen, permitting this residue to serve as the general acid/base catalytic residue.

Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD=pH+0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.

Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond.

Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

Understanding the Catalytic Mechanism of Laminaripentaose Producing β-1,3-Glucanase

Laminaripentaose-producing β-1,3-glucanase (LPHase) catalyzes the hydrolysis of a long chain polysaccharide β-1,3-glucan into specific pentasaccharide oligomers. LPHase is a member of the glycoside hydrolase family 64 (GH-64) that play important roles during biomass degradation. Experimentally, the enzymatic mechanism of LPHase remains to be determined although it has been reported that Glu154 and Asp170 may serve as the active site residues of LPHase. Molecular modelling may offer more insight into the reaction pathway. Several synthetic substrates of LPHase have been reported. We chose laminarihexaose as the substrate and docked one structure of laminarihexaose obtained from the Protein Data bank to the active site of LPHase. Molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) method have been employed to study the hydrolysis of the glycosidic bond catalyzed by LPHase. Our results on the current LPHase - substrate complex suggest that the proton transfer from the catalytic general acid to the glycosidic oxygen be concerted with the nucleophilic attack at the anomeric carbon, and the free energy of activation is about 30 kcal/mol. Additional simulations on LPHase - substrate complexes are underway to characterize the LPHase catalyzed reaction pathway.

Energy maps for glycosidic linkage conformations.

Glycosidic linkage conformations are the main factors in determining the shapes of disaccharide, oligosaccharide, and polysaccharide molecules. The conformations are expressed in terms of the torsion angles about the bonds from each ring of the disaccharide moiety to its glycosidic oxygen atom, and the probability of a given conformation is often expressed in terms of its free or potential energy. The energy surface or map for a disaccharide is a display of the energy plotted against the two torsion angles. Successful mapping allows a particular kind of energy calculation to provide the energy values for each conformation and avoids possible pitfalls. Although different methods are discussed, the main emphasis of this chapter is on the technical production of the maps and their exploitation in further understanding the shape of the molecule in question.

In Vitro Antimicrobial Screening of Metal Complexes of Schiff Base derived from Streptomycin and Amoxicillin: Synthesis, Characterization and Molecular Modelling

A series of three new metal (II) complexes of Schiff base were synthesized from the novel ligand derived from Streptomycin and Amoxicillin in stoichiometric ratio. They were characterized by elemental analysis and spectral techniques like IR, 1H NMR, electronic spectrum and mass spectrum. IR spectral data suggested that the tetradentate ligand has coordination to metal ions through azomethine nitrogen, glycosidic oxygen and two amine nitrogens. Electronic spectral measurement indicated square planar geometry of Ni and Zn-complexes and tetrahedral geometry of Cu-complex with diamagnetic behavior. Molar conductivity measurements revealed non-electrolyte nature of the complexes where metal ions have coordination through doubly negative charged anions of the Schiff base. The thermal behavior (TGA/DTA) of the complexes was studied and kinetic parameters were determined by Coats-Redfern method. XRPD technique revealed monoclinic crystal systems for Ni- and Zn-complexes and hexagonal crystal system for Cu-complex. The possible geometries of the metal complexes with their bond length were optimized by MM2 calculations using CsChem3D Ultra-11 program package software. Antibacterial sensitivity of the ligand and its metal complexes were assayed in vitro against four bacterial pathogens viz. E. coli, B. subtilis, S. aureus and K. pneumonia by Kirby Bauer paper disc diffusion method and showed moderate to better potency.

Umpolung Reactivity in the Stereoselective Synthesis of S‐Linked 2‐Deoxyglycosides

sugars play a critical role in the biological activity of these compounds as well as their stability and solubility. [10] As a result, considerable effort has been devoted to the stereoselective synthesis of 2-deoxyglycosides and the study of their structure–activity relationships. [11] Despite the significance of 2-deoxysugar subunits, the glycosidic linkage of 2deoxyglycosides has been found to be susceptible to hydrolysis in acid media or by glycosyl hydrolases. This reactivity has made it difficult to pinpoint the biological role of these 2deoxysugars, has resulted in toxicity [12] and reduced activity [13] of the parent molecules, and has limited their use as clinical agents. Thioglycosides (S-linked glycosides), [14] in which the glycosidic oxygen atom is replaced with a sulfur atom, are resistant towards enzymatic cleavage as well as chemical degradation. Furthermore, thioglycosides maintain the biological activity of their parent O-linked glycosides and are tolerated by most biological systems. Therefore, they are an important tool for structural biology [15] and attractive therapeutic agents. Because of these characteristics, the preparation of S-linked 2-deoxysugars for comparison of their physical, chemical, and biological properties with those of their natural O-linked counterparts is beneficial. Although a number of protocols are available for the synthesis of thioglycosides, [14, 16] there is no efficient method for the

A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 β1,6-N-Acetylglucosaminyltransferase

β1,6-GlcNAc-transferase (C2GnT) is an important controlling factor of biological functions for many glycoproteins and its activity has been found to be altered in breast, colon, and lung cancer cells, in leukemia cells, in the lymhomonocytes of multiple sclerosis patients, leukocytes from diabetes patients, and in conditions causing an immune deficiency. The result of the action of C2GnT is the core 2 structure that is essential for the further elongation of the carbohydrate chains of O-glycans. The catalytic mechanism of this metal-ion-independent glycosyltransferase is of paramount importance and is investigated here by using quantum mechanical (QM) (density functional theory (DFT))/molecular modeling (MM) methods with different levels of theory. The structural model of the reaction site used in this report is based on the crystal structures of C2GnT. The entire enzyme-substrate system was subdivided into two different subsystems: the QM subsystem containing 206 atoms and the MM region containing 5914 atoms. Three predefined reaction coordinates were employed to investigate the catalytic mechanism. The calculated potential energy surfaces discovered the existence of a concerted SN 2-like mechanism. In this mechanism, a nucleophilic attack by O6 facilitated by proton transfer to the catalytic base and the separation of the leaving group all occur almost simultaneously. The transition state for the proposed reaction mechanism at the M06-2X/6-31G** (with diffuse functions on the O1', O5', OGlu , and O6 atoms) level was located at C1-O6=1.74 Å and C1-O1=2.86 Å. The activation energy for this mechanism was estimated to be between 20 and 29 kcal mol⁻¹, depending on the method used. These calculations also identified a low-barrier hydrogen bond between the nucleophile O6H and the catalytic base Glu320, and a hydrogen bond between the N-acetamino group and the glycosidic oxygen of the donor in the TS. It is proposed that these interactions contribute to a stabilization of TS and participate in the catalytic mechanism.