(S)- and (R)-1-cyano-2-hydroxy-3-butene from myrosinase hydrolysis of epi-progoitrin and progoitrin.
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Antithyroid Agents↗
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Crystal structures of amylosucrase from Neisseria polysaccharea in complex with D-glucose and the active site mutant Glu328Gln in complex with the natural substrate sucrose.
The structure of amylosucrase from Neisseria polysaccharea in complex with beta-D-glucose has been determined by X-ray crystallography at a resolution of 1.66 A. Additionally, the structure of the inactive active site mutant Glu328Gln in complex with sucrose has been determined to a resolution of 2.0 A. The D-glucose complex shows two well-defined D-glucose molecules, one that binds very strongly in the bottom of a pocket that contains the proposed catalytic residues (at the subsite -1), in a nonstrained (4)C(1) conformation, and one that binds in the packing interface to a symmetry-related molecule. A third weaker D-glucose-binding site is located at the surface near the active site pocket entrance. The orientation of the D-glucose in the active site emphasizes the Glu328 role as the general acid/base. The binary sucrose complex shows one molecule bound in the active site, where the glucosyl moiety is located at the alpha-amylase -1 position and the fructosyl ring occupies subsite +1. Sucrose effectively blocks the only visible access channel to the active site. From analysis of the complex it appears that sucrose binding is primarily obtained through enzyme interactions with the glucosyl ring and that an important part of the enzyme function is a precise alignment of a lone pair of the linking O1 oxygen for hydrogen bond interaction with Glu328. The sucrose specificity appears to be determined primarily by residues Asp144, Asp394, Arg446, and Arg509. Both Asp394 and Arg446 are located in an insert connecting beta-strand 7 and alpha-helix 7 that is much longer in amylosucrase compared to other enzymes from the alpha-amylase family (family 13 of the glycoside hydrolases).
Amino Acid Substitution↗
Specificity modulation of barley alpha-amylase through biased random mutagenesis involving a conserved tripeptide in beta --> alpha loop 7 of the catalytic (beta/alpha)(8)-barrel domain.
The relative specificity and bond cleavage pattern of barley alpha-amylase 1 (AMY1) were dramatically changed by mutation in F(286)VD that connected beta-strand 7 of the catalytic (beta/alpha)(8)-barrel to a succeeding 3(10)-helix. This conserved tripeptide of the otherwise variable beta --> alpha segment 7 lacked direct ligand contact, but the nearby residues His290 and Asp291 participated in transition-state stabilization and catalysis. On the basis of sequences of glycoside hydrolase family 13, a biased random mutagenesis protocol was designed which encoded 174 putative F(286)VD variants of C95A-AMY1, chosen as the parent enzyme to avoid inactivating glutathionylation by the yeast host. The FVG, FGG, YVD, LLD, and FLE mutants showed 12-380 and 1.8-33% catalytic efficiency (k(cat)/K(m)) toward 2-chloro-4-nitrophenyl beta-D-maltoheptaoside and amylose DP17, respectively, and 0.5-50% activity for insoluble starch compared to that of C95A-AMY1. K(m) and k(cat) were decreased 2-9- and 1.3-83-fold, respectively, for the soluble substrates. The starch:oligosaccharide and amylose:oligosaccharide specificity ratios were 13-172 and 2.4-14 for mutants and 520 and 27 for C95A-AMY1, respectively. The FVG mutant released 4-nitrophenyl alpha-D-maltotrioside (PNPG(3)) from PNPG(5), whereas C95A-AMY1 produced PNPG and PNPG(2). The mutation thus favored interaction with the substrate aglycon part, while products from PNPG(6) reflected the fact that the mutation restored binding at subsite -6 which was lost in C95A-AMY1. The outcome of this combined irrational and rational protein engineering approach was evaluated considering structural accommodation of mutant side chains. FVG and FGG, present in the most active variants, represented novel sequences. This emphasized the worth of random mutagenesis and launched flexibility as a goal for beta --> alpha loop 7 engineering in family 13.
Amino Acid Sequence↗
Substrate specificity engineering of beta-mannosidase and beta-glucosidase from Pyrococcus by exchange of unique active site residues.
A beta-mannosidase gene (PH0501) was identified in the Pyrococcus horikoshii genome and cloned and expressed in E. coli. The purified enzyme (BglB) was most specific for the hydrolysis of p-nitrophenyl-beta-D-mannopyranoside (pNP-Man) (Km: 0.44 mM) with a low turnover rate (kcat: 4.3 s(-1)). The beta-mannosidase has been classified as a member of family 1 of glycoside hydrolases. Sequence alignments and homology modeling showed an apparent conservation of its active site region with, remarkably, two unique active site residues, Gln77 and Asp206. These residues are an arginine and asparagine residue in all other known family 1 enzymes, which interact with the catalytic nucleophile and equatorial C2-hydroxyl group of substrates, respectively. The unique residues of P. horikoshii BglB were introduced in the highly active beta-glucosidase CelB of Pyrococcus furiosus and vice versa, yielding two single and one double mutant for each enzyme. In CelB, both substitutions R77Q and N206D increased the specificity for mannosides and reduced hydrolysis rates 10-fold. In contrast, BglB D206N showed 10-fold increased hydrolysis rates and 35-fold increased affinity for the hydrolysis of glucosides. In combination with inhibitor studies, it was concluded that the substituted residues participate in the ground-state binding of substrates with an equatorial C2-hydroxyl group, but contribute most to transition-state stabilization. The unique activity profile of BglB seems to be caused by an altered interaction between the enzyme and C2-hydroxyl of the substrate and a specifically increased affinity for mannose that results from Asp206.
Amino Acid Sequence↗
Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis.
Around 80 enzymes are implicated in the generic starch and sucrose pathways. One of these enzymes is sucrose phosphorylase, which reversibly catalyzes the conversion of sucrose and orthophosphate to d-Fructose and alpha-d-glucose 1-phosphate. Here, we present the crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis (BiSP) refined at 1.77 A resolution. It represents the first 3D structure of a sucrose phosphorylase and is the first structure of a phosphate-dependent enzyme from the glycoside hydrolase family 13. The structure of BiSP is composed of the four domains A, B, B', and C. Domain A comprises the (beta/alpha)(8)-barrel common to family 13. The catalytic active-site residues (Asp192 and Glu232) are located at the tips of beta-sheets 4 and 5 in the (beta/alpha)(8)-barrel, as required for family 13 members. The topology of the B' domain disfavors oligosaccharide binding and reduces the size of the substrate access channel compared to other family 13 members, underlining the role of this domain in modulating the function of these enzymes. It is remarkable that the fold of the C domain is not observed in any other known hydrolases of family 13. BiSP was found as a homodimer in the crystal, and a dimer contact surface area of 960 A(2) per monomer was calculated. The majority of the interactions are confined to the two B domains, but interactions between the loop 8 regions of the two barrels are also observed. This results in a large cavity in the dimer, including the entrance to the two active sites.
Amino Acid Sequence↗
Structure and function of the long pentraxin PTX3 glycosidic moiety: fine-tuning of the interaction with C1q and complement activation.
The prototypic long pentraxin PTX3 is a unique fluid-phase pattern recognition receptor that plays a nonredundant role in innate immunity and female fertility. The PTX3 C-terminal domain is required for C1q recognition and complement activation and contains a single N-glycosylation site on Asn 220. In the present study, we characterized the structure of the human PTX3 glycosidic moiety and investigated its relevance in C1q interaction and activation of the complement classical pathway. By specific endo and exoglycosidases digestion and direct mass spectrometric analysis, we found that both recombinant and naturally occurring PTX3 were N-linked to fucosylated and sialylated complex-type sugars. Interestingly, glycans showed heterogeneity mainly in the relative amount of bi, tri, and tetrantennary structures depending on the cell type and inflammatory stimulus. Enzymatic removal of sialic acid or the entire glycosidic moiety equally enhanced PTX3 binding to C1q compared to that in the native protein, thus indicating that glycosylation substantially contributes to modulate PTX3/C1q interaction and that sialic acid is the main determinant of this contribution. BIAcore kinetic measurements returned decreasing K(off) values as sugars were removed, pointing to a stabilization of the PTX3/C1q complex. No major rearrangement of PTX3 quaternary structure was observed after desialylation or deglycosylation as established by size exclusion chromatography. Consistent with C1q binding, PTX3 desialylation enhanced the activation of the classical complement pathway, as assessed by C4 and C3 deposition. In conclusion, our results provided evidence of an involvement of the PTX3 sugar moiety in C1q recognition and complement activation.
Animals↗
X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution.
The three-dimensional structure of the Bacillus stearothermophilus "maltogenic" alpha-amylase, Novamyl, has been determined by X-ray crystallography at a resolution of 1.7 A. Unlike conventional alpha-amylases from glycoside hydrolase family 13, Novamyl exhibits the five-domain structure more usually associated with cyclodextrin glycosyltransferase. Complexes of the enzyme with both maltose and the inhibitor acarbose have been characterized. In the maltose complex, two molecules of maltose are found in the -1 to -2 and +2 to +3 subsites of the active site, with two more on the C and E domains. The C-domain maltose occupies a position identical to one previously observed in the Bacillus circulans CGTase structure [Lawson, C. L., et al. (1994) J. Mol. Biol. 236, 590-600], suggesting that the C-domain plays a genuine biological role in saccharide binding. In the acarbose-maltose complex, the tetrasaccharide inhibitor acarbose is found as an extended hexasaccharide species, bound in the -3 to +3 subsites. The transition state mimicking pseudosaccharide is bound in the -1 subsite of the enzyme in a 2H3 half-chair conformation, as expected. The active site of Novamyl lies in an open gully, fully consistent with its ability to perform internal cleavage via an endo as opposed to an exo activity.
Acarbose↗
Structural changes of the active site tunnel of Humicola insolens cellobiohydrolase, Cel6A, upon oligosaccharide binding.
The mechanisms of crystalline cellulose degradation by cellulases are of paramount importance for the exploitation of these enzymes in applied processes, such as biomass conversion. Cellulases have traditionally been classified into cellobiohydrolases, which are effective in the degradation of crystalline materials, and endoglucanases, which appear to act on "soluble" regions of the substrate. Humicola insolensCel6A (CBH II) is a cellobiohydrolase from glycoside hydrolase family 6 whose native structure has been determined at 1.9 A resolution [Varrot, A., Hastrup, S., Schülein, M., and Davies, G. J. (1999) Biochem. J. 337, 297-304]. Here we present the structure of the catalytic core domain of Humicola insolens cellobiohydrolase II Cel6A in complex with glucose/cellotetraose at 1.7 A resolution. Crystals of Cel6A, grown in the presence of cellobiose, reveal six binding subsites, with a single glucose moiety bound in the -2 subsite and cellotetraose in the +1 to +4 subsites. The complex structure is strongly supportive of the assignment of Asp 226 as the catalytic acid and consistent with proposals that Asp 405 acts as the catalytic base. The structure undergoes several conformational changes upon substrate binding, the most significant of which is a closing of the two active site loops (residues 174-196 and 397-435) with main-chain movements of up to 4.5 A observed. This complex not only defines the polysaccharide-enzyme interactions but also provides the first three-dimensional demonstration of conformational change in this class of enzymes.
Binding Sites↗
Protein-carbohydrate interactions defining substrate specificity in Bacillus 1,3-1,4-beta-D-glucan 4-glucanohydrolases as dissected by mutational analysis.
The carbohydrate-binding site of Bacillus macerans 1,3-1, 4-beta-D-glucan 4-glucanohydrolase has been analyzed through a mutational analysis to probe the role of protein-carbohydrate interactions defining substrate specificity. Amino acid residues involved in substrate binding were proposed on the basis of a modeled enzyme-substrate complex [Hahn, M., Keitel, T., and Heinemann, U. (1995) Eur. J. Biochem. 232, 849-859]. The effects of the mutations at 15 selected residues on catalysis and binding were determined by steady-state kinetics using a series of chromogenic substrates of different degree of polymerization to assign the individual H-bond and hydrophobic contributions to individual subsites in the binding site cleft. The glucopyranose rings at subsites -III and -II are tightly bound by a number of H-bond interactions to Glu61, Asn24, Tyr92, and Asn180. From k(cat)/K(M) values, single H-bonds account for 1.8-2.2 kcal mol(-)(1) transition-state (TS) stabilization, and a charged H-bond contributes up to 3.5 kcal mol(-)(1). Glu61 forms a bidentated H-bond in subsites -III and -II, and provides up to 6.5 kcal mol(-)(1) TS stabilization. With a disaccharide substrate that fills subsites -I and -II, activation kinetics were observed for the wild-type and mutant enzymes except for mutations on Glu61, pointing to an important role of the bidentate interaction of Glu61 in two subsites. Whereas removal of the hydroxyl group of Tyr121, initially proposed to hydrogen-bond with the 2OH of Glcp-I, has essentially no effect (Y121F mutant), side-chain removal (Y121A mutant) gave a 100-fold reduction in k(cat)/K(M) and a 10-fold lower K(I) value with a competitive inhibitor. In subsite -IV, only a stacking interaction with Tyr22 (0.7 kcal mol(-)(1) TS stabilization) is observed.
Amino Acid Sequence↗
Heat-resistant oxygen-carrying hemoproteins consist of recombinant xylanases and synthetic iron(II) porphyrin.
Synthetic iron(II) porphyrin (FeP) is equivalently incorporated into recombinant Thermotoga maritima xylanase B (TMX; family F/10 of glycoside hydrolase), producing a heat-resistant artificial hemoprotein (TMX-FeP) that can bind and release oxygen (O(2)) in aqueous medium (pH 7.3, 25 degrees C) in the same manner as hemoglobin and myoglobin. The oxygenated species was sufficiently stable; the half-lifetime against the ferric state (tau(1/2)) was 5 h. This O(2)-carrying hemoprotein showed a high degree of thermal stability over a wide range of temperatures up to 90 degrees C (tau(1/2) = 5 min at 90 degrees C and 9 min at 75 degrees C). Dictyoglomus thermophilum xylanase B (DTX; family G/11) also incorporates FeP, and DTX-FeP showed identical O(2)-binding parameters and thermostability. TMX-FeP is capable of catalyzing the beta-1,4-d-xylan hydrolysis reaction. Its larger K(m) value compared to that of TMX itself suggested competitive FeP binding to the active site of the host enzyme.
Endo-1,4-beta Xylanases↗
Chitinase-catalyzed synthesis of alternatingly N-deacetylated chitin: a chitin-chitosan hybrid polysaccharide.
A chitin-chitosan hybrid polysaccharide (2) having a beta(1-->4)-linked alternating structure of an N-acetyl-D-glucosamine (GlcNAc) unit and a D-glucosamine (GlcN) unit was synthesized via chitinase-catalyzed polymerization of an oxazoline derivative of a GlcNbeta(1-->4)GlcNAc monomer (1). Monomer 1 was designed as a transition-state analogue substrate (TSAS) monomer for chitinase catalysis, which belongs to the glycoside hydrolase family 18. Monomer 1 was effectively polymerized by the catalysis of enzymes from Bacillus sp., Serratia marcescens and Streptomyces griseus, under weak alkaline conditions, giving rise to a water-soluble hybrid polysaccharide (2) in good yields. Molecular weights of 2 reached 2,020 with using chitinase from Serratia marcescens, which corresponds to 10-12 saccharide units.
Acetylation↗
Toward a detailed understanding of base excision repair enzymes: transition state and mechanistic analyses of N-glycoside hydrolysis and N-glycoside transfer.
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Binding Sites↗
Synthesis of 5-fluoro N-acetylglucosamine glycosides and pyrophosphates via epoxide fluoridolysis: versatile reagents for the study of glycoconjugate biochemistry.
Numerous carbohydrate-processing enzymes facilitate catalysis via stabilization of positive charges on or near the C-1, C-4, C-5, or C-6 positions. Substrate analogues differing only in the substitution of a fluorine for the axial C-5 hydrogen would possess reduced electron density at these positions and could be useful mechanistic probes of these enzymes. Introduction of this 5-fluoro substituent after radical halogenation was problematic because of the incompatibility of many protecting groups to the radical halogenation and the instability of the subsequent 5-fluoro hexosamines. Thus, to allow easy access to a wide variety of 5-fluoro glycosides and glycosyl phosphates, a versatile method for the introduction of the 5-fluoro group has been developed, the key step being the fluoridolysis of C-5, 6 epoxides. By use of this method, two fluorinated carbohydrates, uridine 5'-diphospho-5-fluoro-N-acetylglucosamine and octyl 5-fluoro-N-acetylglucosamine, have been synthesized. Initial biochemical investigations of these compounds show that 5-fluoro analogues are useful probes of transition-state charge development in several enzyme-catalyzed reactions.
Acetylglucosamine↗
Remarkable supramolecular catalysis of glycoside hydrolysis by a cyclodextrin cyanohydrin.
(6AR,6DR)-6A,6D-di-C-cyano-beta-cyclodextrin (3) was synthesized and shown to catalyze hydrolysis of nitrophenyl glycosides with the reaction following Michaelis-Menten kinetics. At pH 7.4 and 25 degrees C, hydrolysis of 4-nitrophenyl-beta-glucopyranoside (2) was catalyzed with KM = 15 mM, kcat = 8.2 x 10-6 s-1, and kcat/kuncat = 1217. Catalysis was observed with concentration of 3 as low as 10 muM. Hydrolysis of the corresponding alpha-glucoside, alpha-galactoside, alpha-mannoside, and 2-nitrophenyl-beta-galactoside was also catalyzed by 3, with kcat/kuncat ranging from 283 to 2147. A series of analogues of 3 was prepared and investigated for catalysis of the hydrolysis of 2: (6AR,6DR)-6A,6D-di-C-propyl-beta-cyclodextrin (9) was not catalytic, while 6A,6D-di-C-cyano-6A,6D-dideoxy-beta-cyclodextrin (12) had a low catalytic activity (kcat/kuncat = 4). A kcat/kuncat = 48 was found for 6A,6D-dialdehydo-beta-cyclodextrin dihydrate (11). It was proposed that 3 acts by general acid catalysis on the bound substrate.
Biomimetic Materials↗
Analysis of glycosidically bound aroma precursors in tea leaves. 2. Changes in glycoside contents and glycosidase activities in tea leaves during the black tea manufacturing process.
Glycosides are known to be precursors of the alcoholic aroma compounds of black tea. They are hydrolyzed by endogenous glycosidases during the manufacturing process. Changes in the amounts of these glycosides during the manufacturing process were investigated by using a capillary gas chromatographic--mass spectrometric analysis after trifluoroacetyl derivatization of the tea glycosidic fractions. Primeverosides were 3-fold more abundant than glucosides in fresh leaves, but they decreased greatly during the manufacturing process, especially during the stage of rolling. After the final stage of fermentation, primeverosides had almost disappeared, whereas glucosides were substantially unchanged. These results show that hydrolysis of the glycosides mainly occurred during the stage of rolling and confirm that primeverosides are the main black tea aroma precursors. This was also supported by the changes in the glycosidase activities in tea leaves. The glycosidase activities remained at a high level during withering but decreased drastically after rolling.
Fermentation↗
Specific fluctuations in the composition of lipoxygenase- and glycosidase-generated flavors in some cultivated teas of Assam.
Variations of fatty acid compositions, glycosides precursors, and lipoxygenase and glycosidase enzymatic activities were used simultaneously to differentiate for nine genetically different cultivated teas, four seasonal changes, and the affect of leaf maturity. The muscatel flavor of second-flush teas was associated with increased activities of glycosidase and several terpenes, phenolics, and aliphatic compounds bound to glycosides, whereas high levels of fatty acids and lipoxygenase activity biosynthesized more green volatiles in monsoon teas. Sequential hydrolysis of lipids and lipoxygenase-mediated reactions, during withering and rolling, showed a 3-fold increase of hexenol, hexenal, and related volatiles, but they decreased to the levels of fresh leaf during drying. However, a 4-fold increase of the floral bend of volatiles found in black tea developed due to the hydrolysis of the glycoside precursors throughout processing stages. About 45 key volatiles were monitored for flavor superiority among different clones. Various parameters affecting yield of volatiles were optimized and recommended.
Fatty Acids↗
Enzymic degradability of hull-less barley flour alkali-solubilized arabinoxylan fractions by endoxylanases.
The impacts of the arabinose to xylose (A/X) ratio of arabinoxylans (AX) and the endoxylanase substrate specificity on the enzymic degradability of hull-less barley flour AX by endoxylanases were studied by using alkali-solubilized AX (AS-AX) fractions with different A/X ratio, on the one hand, and glycoside hydrolase family 10 and 11 endoxylanases of Aspergillus aculeatus (XAA) and Bacillus subtilis (XBS), respectively, on the other hand. AS-AX were obtained by saturated barium hydroxide treatment of hull-less barley flour water-unextractable AX. Fractionation of AS-AX by stepwise ethanol precipitation resulted in structurally different hull-less barley flour AS-AX fractions. Their A/X ratios increased with increasing ethanol concentration, and this increase in A/X ratio was reflected in their xylose substitution levels. For both XAA and XBS, the enzymic degradability of AX and apparent specific endoxylanase activity decreased with increasing A/X ratio of the AS-AX substrates, implying that both endoxylanases were sterically hindered by arabinose substituents. However, for all AS-AX fractions, hydrolysis end products of lower average degree of polymerization were obtained after incubation with XAA than with XBS, indicating that the former enzyme has a lower substrate specificity toward hull-less barley flour AS-AX than the latter. In addition, apparent specific endoxylanase activities indicated that XBS was approximately 2 times more sensitive to variations in the A/X ratio of AS-AX fractions than XAA. Furthermore, AS-AX with higher A/X ratio were relatively resistant to degradation by XBS.
Aspergillus↗
Purine thioglycosides. I. S-Glycosides of 6-mercaptopurine.
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Chemical Phenomena↗