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PubMed1994

The N-glycosidase mechanism of ribosome-inactivating proteins implied by crystal structures of alpha-momorcharin.

BACKGROUND: alpha-Momorcharin (alpha MMC) is a type I ribosome-inactivating protein. It inhibits protein synthesis by hydrolytically removing a specific adenine residue from a highly conserved, single-stranded loop of rRNA. RESULTS: Here we describe the determination and refinement of the crystal structures of alpha MMC in the native state and in complexes with the product, adenine, and a substrate analogue, formycin 5'-monophosphate (FMP) at high resolution. Both adenine and the base of FMP are tightly bound; the ribose of bound FMP adopts a strained, high-energy conformation, which may mimic the structure of the transition state. CONCLUSIONS: These structures indicate that residues Tyr70, Glu160 and Arg163 of alpha MMC are the most critical for catalysis. We propose that the strained conformation of the ribose in the target adenosine weakens the glycoside bond. Partial protonation mediated by Arg163 then facilitates N-glycoside bond cleavage, leading to the formation of an oxycarbonium ion intermediate which is stabilized by the negatively-charged Glu160. Tyr70 adopts subtly different conformations in the three structures implying that it may be important in substrate recognition and perhaps catalysis.

Amino Acid Sequence↗

PubMed2003

Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex.

Dextranase catalyzes the hydrolysis of the alpha-1,6-glycosidic linkage in dextran polymers. The structure of dextranase, Dex49A, from Penicillium minioluteum was solved in the apo-enzyme and product-bound forms. The main domain of the enzyme is a right-handed parallel beta helix, which is connected to a beta sandwich domain at the N terminus. In the structure of the product complex, isomaltose was found to bind in a crevice on the surface of the enzyme. The glycosidic oxygen of the glucose unit in subsite +1 forms a hydrogen bond to the suggested catalytic acid, Asp395. By NMR spectroscopy the reaction course was shown to occur with net inversion at the anomeric carbon, implying a single displacement mechanism. Both Asp376 and Asp396 are suitably positioned to activate the water molecule that performs the nucleophilic attack. A new clan that links glycoside hydrolase families 28 and 49 is suggested.

Amino Acid Sequence↗

PubMed1997

The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix.

BACKGROUND: Pectic substances are the major polysaccharide components of the middle lamella and primary cell wall of dicotyledonous plants. They consist of homogalacturonan 'smooth' regions and highly rhamnified 'hairy' regions of rhamnogalacturonan. The backbone in rhamnogalacturonan-l (RG-l), which is composed of alternating galacturonic acid and rhamnose residues, is the substrate for a new class of enzymes known as rhamnogalacturnoases (RGases). RGase A is a novel enzyme implicated in the enzymatic degradation of RG-l. RESULTS: The structure of RGase A from Aspergillus aculeatus has been solved by the single isomorphous replacement method including anomalous scattering (SIRAS method) to 2.0 A resolution. The enzyme folds into a large right-handed parallel beta helix, with a core composed of 13 turns of beta strands. Four parallel beta sheets (PB1, PB1a, PB2 and PB3), formed by the consecutive turns, are typically separated by a residue in the conformation of a left-handed alpha helix. As a consequence of the consecutive turns, 32% of all residues have their sidechains aligned at the surface or in the interior of the parallel beta helix. The aligned residues at the surface are dominated by threonine, aspartic acid and asparagine, whereas valine, leucine and isoleucine are most frequently found in the interior. A very large hydrophobic cavity is found in the interior of the parallel beta helix. The potential active site is a groove, oriented almost perpendicular to the helical axis, containing a cluster of three aspartic acid residues and one glutamic acid residue. The enzyme is highly glycosylated; two N-linked and eighteen O-linked glycosylation sites have been found in the structure. CONCLUSIONS: Rhamnogalacturonase A from A. aculeatus is the first three-dimensional structure of an enzyme hydrolyzing glycoside bonds within the backbone of RG-l. The large groove, which is the potential active site of RGase A, is also seen in the structures of pectate lyases. Two catalytic aspartic acid residues, which have been proposed to have a catalytic role, reside in this area of RGase A. The distance between the aspartic acid residues is consistent with the inverting mechanism of catalysis. The glycan groups bound to RGase A are important to the stability of the crystal, as the carbohydrate moiety is involved in most of the intermolecular hydrogen bonds.

Amino Acid Sequence↗

PubMed2003

Anatomy of glycosynthesis: structure and kinetics of the Humicola insolens Cel7B E197A and E197S glycosynthase mutants.

The formation of glycoconjugates and oligosaccharides remains one of the most challenging chemical syntheses. Chemo-enzymatic routes using retaining glycosidases have been successfully harnessed but require tight kinetic or thermodynamic control. "Glycosynthases," specifically engineered glycosidases that catalyze the formation of glycosidic bonds from glycosyl donor and acceptor alcohol, are an emerging range of synthetic tools in which catalytic nucleophile mutants are harnessed together with glycosyl fluoride donors to generate powerful and versatile catalysts. Here we present the structural and kinetic dissection of the Humicola insolens Cel7B glycosynthases in which the nucleophile of the wild-type enzyme is mutated to alanine and serine (E197A and E197S). 3-D structures reveal the acceptor and donor subsites and the basis for substrate inhibition. Kinetic analysis shows that the E197S mutant is considerably more active than the corresponding alanine mutant due to a 40-fold increase in k(cat).

Cellobiose↗

PubMed1998

Glycosidases and glycosyl transferases in glycoside and oligosaccharide synthesis.

Remarakable advances in glycobiology in recent years have stimulated a resurgence of interest in carbohydrate chemistry. The challenge of producing the complex glycosides and oligosaccharides needed for research in glycobiology has led to the development of enzymatic methods that are now firmly established as part of the synthetic repertoire of the carbohydrate chemist.

Catalysis↗

PubMed2003

Purification and characterization of a novel extracellular beta-1,3-glucanase produced by Bacillus clausii NM-1 isolated from ezo abalone Haliotis discus hannai.

A novel extracellular alkaline stable beta-1,3-glucanase produced by Bacillus clausii NM-1 isolated from the ezo abalone Haliotis discus hannai was purified by ammonium sulfate precipitation, DEAE-Sepharose FF ion exchange chromatography and Sephacryl S-200HR gel filtration. The molecular weight of the purified enzyme was estimated to be 71 kDa from sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The enzyme was very stable at pH 5.3 to 11.5 but unstable at pH 4.0 to 4.5. The optimum temperature and thermostability of the enzyme increased in the presence of CaC1, The enzyme hydrolyzed R-1,3-glucan from marine organisms, but did not show activity against any other beta-1,3-glucans. The major hydrolysis products of beta-1,3-glucan from Laminaria digitata and Eisenia bicyclis were laminaritriose and laminaritetraose, respectively. The N-terminal amino acid sequence of the purified enzyme was similar to that of several beta-1,3-glucanases in the glycoside hydrolase family 16.

Journal Article↗

PubMed2003

Family 3 beta-glucosidase from cellulose-degrading culture of the white-rot fungus Phanerochaete chrysosporium is a glucan 1,3-beta-glucosidase.

The substrate specificity of an extracellular beta-glucosidase (BGL) from cellulose-degrading culture of the white-rot fungus Phanerochaete chrysosporium was investigated, using a variety of compounds with beta-glucosidic linkages. Amino acid sequencing data for the purified BGL showed that the enzyme is identical to the glycoside hydrolase (GH) family 3 BGL of the same fungus previously reported [Li, B. and Renganathan, V, Appl. Environ. Microbiol., 64, 2748-2754 (1998)]. The BGL can hydrolyze both cellobiose and cellobionolactone, but cellobionolactone was hydrolyzed very much more slowly than cellobiose. Moreover, cellobionolactone inhibited cellobiose hydrolysis by the BGL, suggesting that this enzyme cannot cooperate with cellobiose dehydrogenase (CDH) in cellulose degradation by P. chrysosporium. In addition to cellobiose, BGL utilized various glucosyl-beta-glucosides, such as sophorose, laminaribiose and gentiobiose, as substrates. Among the four substrates, laminaribiose (beta-1,3-glucosidic linkage) was hydrolyzed most effectively. Moreover, the hydrolytic rate of laminarioligosaccharides increased proportionally to the degree of polymerization (DP), and the activity of BGL even towards laminarin with an average DP of 25 was similar to that towards laminaripentaose (DP 5). Therefore, we conclude that the extracellular BGL from P. chrysosporium is primarily a glucan 1,3-beta-glucosidase (EC 3.2.1.58), which might play a role on fungal cell wall metabolism, rather than a beta-glucosidase (EC 3.2.1.21), which might be involved in the hydrolysis of beta-1,4-glucosidic compounds during cellulose degradation.

Journal Article↗

PubMed2003

Cross-inhibitory activity of cereal protein inhibitors against alpha-amylases and xylanases.

The purification and characterisation of a xylanase inhibitor (XIP-I) from wheat was reported previously. In our current work, XIP-I is also demonstrated to have the capacity to inhibit the two barley alpha-amylase isozymes (AMY1 and AMY2). XIP-I completely inhibited the activity of AMY1 and AMY2 towards insoluble Blue Starch and a soluble hepta-oligosaccharide derivative. A ternary complex was formed between insoluble starch, a catalytically inactive mutant of AMY1 (D180A), and XIP-I, suggesting that the substrate-XIP-I interaction is necessary for inhibition of barley alpha-amylases. K(i) values for alpha-amylase inhibition, however, could not be calculated due to the nonlinear nature of the inhibition pattern. Furthermore, surface plasmon resonance and gel electrophoresis did not indicate interaction between XIP-I and the alpha-amylases. The inhibition was abolished by CaCl(2), indicating that the driving force for the interaction is different from that of complexation between the barley alpha-amylase/subtilisin inhibitor (BASI) and AMY2. This is the first report of a proteinaceous inhibitor of AMY1. BASI, in addition, was demonstrated to partially inhibit the endo-1,4-beta-D-xylanase from Aspergillus niger (XylA) of glycoside hydrolase family 11. Taken together, the data demonstrate for the first time the dual target enzyme specificity of BASI and XIP-I inhibitors for xylanase and alpha-amylase.

Animals↗

PubMed2004

Glycosidase activity in the excretory-secretory products of the liver fluke, Fasciola hepatica.

Fasciola hepatica secretes proteolytic enzymes and other molecules that are essential for host penetration and migration. This mixture may include enzymes required for the degradation of supramucosal gels, which defend epithelial surfaces against pathogen entry. These contain hydrated mucins that are heavily glycosylated. Excretory-secretory products (ES) from F. hepatica were examined for a range of glycosidase activities, using synthetic 4-methylumbelliferyl glycosides as substrates. The ES product contained at least 8 different glycosidase activities, the most abundant of which were beta-N-acetylhexosaminidase, beta-galactosidase and beta-glucosidase. Alpha-fucosidase, beta-glucuronidase, alpha-galactosidase, alpha-mannosidase and neuraminidase were also present. Beta-N-acetylhexosaminidase and beta-galactosidase were present in multiple isoforms (at least 4), whereas beta-glucosidase appeared to exist as one isoenzyme with a pI < 3.8. All three enzymes had acidic pH optima (4.5-5.0). Ovine small intestinal mucin was degraded by ES at pH 4.5 or 7.0, with or without active cathepsin L, the major protease found in F. hepatica ES. The ability of F. hepatica ES to degrade mucin in the presence or absence of active cathepsin L suggests that cathepsin L is not essential for mucin degradation. The abundance of beta-galactosidase and beta-hexosaminidase in ES supports a role for these enzymes in mucin degradation.

Animals↗

PubMed2026

Structural Characterization and Engineering of a GH134 β-Mannanase from Aspergillus nidulans for Enhancement of Activity and Stability.

Mannans are abundant plant hemicelluloses, and endo-β-mannanases are important biocatalysts for their conversion into functional manno-oligosaccharides. Here, we report the structural and functional characterization of a glycoside hydrolase family 134 β-mannanase from Aspergillus nidulans (AnGH134) and a structure-guided engineering strategy to improve its performance on locust bean gum. The 1.75 Å crystal structure reveals the conserved lysozyme-like fold of GH134 enzymes and supports an inverting catalytic mechanism with Glu43 and Asp55 as the putative catalytic residues. Docking, mutational, and molecular dynamics analyses indicate that AnGH134 uses an extended substrate-binding groove and that groove-exit residues and the C-terminal region contribute to productive catalysis. Guided by these findings, N-terminal fusion of CBM10 enhanced catalytic efficiency and thermal stability, whereas C-terminal fusion was detrimental. These results provide a framework for engineering GH134 mannanases.

Aspergillus nidulans↗

PubMed1995

Substrate-induced inactivation of a crippled beta-glucosidase mutant: identification of the labeled amino acid and mutagenic analysis of its role.

The beta-glucosidase from Agrobacterium sp. catalyzes the hydrolysis of beta-glucosides via a covalent alpha-D-glucopyranosyl-enzyme intermediate involving Glu358. Hydrolysis of 2,4-dinitrophenyl beta-D-glucopyranoside by the low activity Glu358Asp mutant of Agrobacterium beta-glucosidase is accompanied by time-dependent inactivation of the enzyme. Through kinetic studies, labeling, and sequence analysis, inactivation is shown to be a consequence of the occasional (1 time in 1100) attack of Tyr298 on the anomeric center of the substrate, in place of the catalytic nucleophile, with formation of a stable alpha-D-glucopyranosyl tyrosine residue. Tyr298 is conserved throughout family 1 of glycoside hydrolases, an indication of a possible role in catalysis. Results of a kinetic analysis of the Tyr298Phe mutant are consistent with a function of Tyr298 in both orienting the nearby nucleophile Glu358 and stabilizing its deprotonated state in the free enzyme.

Amino Acids↗

PubMed1995

Identification of the acid/base catalyst in Agrobacterium faecalis beta-glucosidase by kinetic analysis of mutants.

The catalytic mechanism of the retaining beta-glucosidase (Abg) from Agrobacterium faecalis involves a double-displacement process in which an alpha-glucosyl-enzyme intermediate is formed with general acid catalytic assistance and then hydrolyzed with general base assistance. Glu170 was identified as an important residue, possibly the acid/base catalyst, on the basis of sequence alignments. This glutamate is conserved in almost all enzymes in family 1 of glycoside hydrolases. Detailed pre-steady-state and steady-state kinetic analyses of the mutant E170G suggested very strongly that Glu170 is the acid/base catalyst. First, kcat values were invariant with pH over the range of 5.0-9.0. Secondly, rates of formation of the glycosyl-enzyme, calculated from kcat/Km and k2, were similar to those of wild-type enzyme for substrates not requiring protonic assistance but dramatically reduced for those needing acid catalysis. Thirdly, addition of azide as a competitive nucleophile increased kcat values 100-300-fold for substrates whose rate-limiting step is deglycosylation, yielding beta-glucosyl azide, but had no effect on the wild-type enzyme. Other anionic nucleophiles had similar, but less dramatic effects. Previous results [Gebler, J.C., et al. (1995) 34, 14547-14553] had indicated that Tyr298F is important for catalysis. The kinetic consequences of the mutations in the double mutant E170G-Y298F are additive, resulting in a 10(6)-fold reduction in kcat values and allowing the accumulation of a stable (t1/2 > 7 h) glucosyl-enzyme intermediate. Thus, Glu170 and Tyr298 function independently, and a possible role for Tyr298 in modulating the pKa of the catalytic nucleophile is proposed.

Amino Acid Sequence↗

PubMed1982

Trehalase: stereocomplementary hydrolytic and glucosyl transfer reactions with alpha- and beta-D-glucosyl fluoride.

A new understanding has been obtained of the catalytic capabilities of trehalase, an enzyme heretofore held to be strictly specific for hydrolyzing alpha, alpha-trehalose and devoid of transglycosylative ability. Highly purified rabbit renal cortical trehalase and a partly purified Candida tropicalis yeast trehalase were found to utilize both alpha- and beta-D-glucosyl fluoride as substrates. In each case, the reactions were competitively inhibited by alpha, alpha-trehalose. Both enzymes catalyzed rapid hydrolysis of alpha-D-glucosyl fluoride to form beta-D-glucose (also, of alpha, alpha-trehalose to form equimolar alpha- and beta-D-glucose). In addition, digests of beta-D-glucosyl fluoride plus alpha-D-[14C]-glucopyranose with either trehalase (but not controls of enzyme with alpha-D-[14C]glucopyranose alone) yielded small amounts of radioactive trehalose (alpha-D-glucopyranosyl alpha-D-[14C]glucopyranoside) which does not accumulate since it is rapidly hydrolyzed. Trehalase thus catalyzes two stereocomplementary types of glycosylation reactions: (I) alpha-D-glucosyl fluoride (or alpha, alpha-trehalose) + H2O leads to beta-D-glucose + HF (or alpha-D-glucose); (II) beta-D-glucosyl fluoride + alpha-D-glucopyranose leads to alpha, alpha-trehalose + HF. Such behavior shows that the catalytic groups of trehalase, as recently found for other glycosylases, are functionally flexible. The results illustrate the inadequacy of conventional views of carbohydrase specificity and the rigor, as a basic guiding principle, of the concept that glycoside hydrolases and glycosyltransferases form a class of glycosylases effecting glycosyl/proton interchange.

Animals↗

PubMed2001

Influence of the aglycone region of the substrate binding cleft of Pseudomonas xylanase 10A on catalysis.

Pseudomonas cellulosa xylanase 10A (Pc Xyn10A) contains an extended substrate binding cleft comprising three glycone (-1 to -3) and four aglycone (+1 to +4) subsites and, typical of retaining glycoside hydrolases, exhibits transglycosylation activity at elevated substrate concentrations. In a previous study [Charnock, S. J., et al. (1997) J. Biol. Chem. 272, 2942-2951], it was demonstrated that the -2 subsite mutations E43A and N44A caused a 100-fold reduction in activity against xylooligosaccharides, but did not influence xylanase activity. This led to the proposal that the low activity of these mutants against xylooligosaccharides was due to nonproductive complex formation between these small substrates and the extended aglycone region of the active site. To test this hypothesis, key residues at the +2 (Asn182), +3 (Tyr255), and +4 (Tyr220) subsites were substituted for alanine, and the activity of the mutants against polysaccharides and oligosaccharides was evaluated. All the aglycone mutants exhibited greatly reduced or no transglycosylating activity, and the triple mutants, E43A/Y220A/Y255A and E43A/N182A/Y255A, had activity against xylotriose similar to that of E43A. The aglycone mutations caused an increase in both k(cat) and K(m) against xylan, with N182A/Y220A/Y255A and N182A/Y255A exhibiting 25- and 15-fold higher k(cat) values, respectively, than wild-type Pc Xyn10A. These data indicate that Glu43 plays a role in binding xylooligosaccharides, but not xylan, suggesting that the mechanisms by which Pc Xyn10A binds polysaccharides and oligosaccharides are distinct. The increased k(cat) of the mutants against xylan indicates that the aglycone region of wild-type Pc Xyn10A restricts the rate of catalysis by limiting diffusion of the cleaved substrate, generated at the completion of the k(2) step, out of the active site.

Alanine↗

PubMed1974