On the biosynthesis of alternating alpha-2,9/alpha-2,8 heteropolymer of sialic acid catalyzed by the sialyltransferase of Escherichia coli Bos-12.

Escherichia coli Bos-12 synthesizes a heteropolymer of sialic acids with alternating alpha-2,9/alpha-2,8 glycosidic linkages (1). In this study, we have shown that the polysialyltransferase of the E. coli Bos-12 recognizes an alpha-2,8 glycosidic linkage of sialic acid at the nonreducing end of an exogenous acceptor of either the alpha-2,8 homopolymer of sialic acid or the alternating alpha-2,9/alpha-2,8 heteropolymer of sialic acid and catalyzes the transfer of Neu5Ac from CMP-Neu5Ac to this residue. When the exogenous acceptor is an alpha-2,8-linked oligomer of sialic acid, the main product synthesized is derived from the addition of a single residue of [14C]Neu5Ac to form either an alpha-2,8 glycosidic linkage or an alpha-2,9 glycosidic linkage at the nonreducing end, at an alpha-2, 8/alpha-2,9 ratio of approximately 2:1. When the acceptor is the alternating alpha-2,9/alpha-2,8 heteropolymer of sialic acid, chain elongation takes place four to five times more efficiently than the alpha-2,8-linked homopolymer of sialic acid as an acceptor. It was found that the alpha-2,9-linked homopolymer of sialic acid and the alpha-2,8/alpha-2,9-linked hetero-oligomer of sialic acid with alpha-2,9 at the nonreducing end not only failed to serve as an acceptor for the E. coli Bos-12 polysialyltransferase for the transfer of [14C]Neu5Ac, but they inhibited the de novo synthesis of polysialic acid catalyzed by this enzyme. The results obtained in this study favor the proposal that the biosynthesis of the alpha-2, 9/alpha-2,8 heteropolymer of sialic acid catalyzed by the E. coli Bos-12 polysialyltransferase involves a successive transfer of a preformed alpha-2,8-linked dimer of sialic acid at the nonreducing terminus of the acceptor to form an alpha-2,9 glycosidic linkage between the incoming dimer and the acceptor. The glycosidic linkage at the nonreducing end of the alternating alpha-2,9/alpha-2,8 heteropolymer of sialic acid produced by E. coli Bos-12 should be an alpha-2,8 glycosidic bond and not an alpha-2,9 glycosidic linkage.     

核糖体RNA拓扑学与RNA N－糖苷酶研究进展（上）

核糖体RNA拓扑学的研究对阐明核糖体RNA(rRNA)在蛋白质生物合成中的作用具有重要的意义.RNA N-糖苷酶是一类核糖体失活蛋白.它只水解rRNA特定位置上一个腺苷酸的糖苷键,释放一个腺嘌呤碱基,使核糖体失活.Ricin A链是研究得最早和最详细的RNA N-糖苷酶,迄今已发现有二十五种核糖体失活蛋白具有RNA N-糖苷酶活性.RNA N-糖苷酶作用于28S rRNA的α-sarcin结构域,改变核糖体的构象而使其失活.     

Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages

Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) has unique hydrolyzing activities for pullulan with sequence repeats of alpha-(1,4), alpha-(1,4), and alpha-(1,6) glycosidic linkages, as well as for starch. TVAI mainly hydrolyzes alpha-(1,4) glycosidic linkages to produce a panose, but it also hydrolyzes alpha-(1,6) glycosidic linkages with a lesser efficiency. X-ray structures of three complexes comprising an inactive mutant TVAI (D356N or D356N/E396Q) and a pullulan model oligosaccharide (P2; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]2 or P5; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]5) were determined. The complex D356N/P2 is a mimic of the enzyme/product complex in the main catalytic reaction of TVAI, and a structural comparison with Aspergillus oryzaealpha-amylase showed that the (-) subsites of TVAI are responsible for recognizing both starch and pullulan. D356N/E396Q/P2 and D356N/E396Q/P5 provided models of the enzyme/substrate complex recognizing the alpha-(1,6) glycosidic linkage at the hydrolyzing site. They showed that only subsites -1 and -2 at the nonreducing end of TVAI are effective in the hydrolysis of alpha-(1,6) glycosidic linkages, leading to weak interactions between substrates and the enzyme. Domain N of TVAI is a starch-binding domain acting as an anchor in the catalytic reaction of the enzyme. In this study, additional substrates were also found to bind to domain N, suggesting that domain N also functions as a pullulan-binding domain.     

Biosynthesis of ganglioside mimics in Campylobacter jejuni OH4384. Identification of the glycosyltransferase genes, enzymatic synthesis of model compounds, and characterization of nanomole amounts by 600-mhz (1)h and (13)c NMR analysis

We have applied two strategies for the cloning of four genes responsible for the biosynthesis of the GT1a ganglioside mimic in the lipooligosaccharide (LOS) of a bacterial pathogen, Campylobacter jejuni OH4384, which has been associated with Guillain-Barré syndrome. We first cloned a gene encoding an alpha-2, 3-sialyltransferase (cst-I) using an activity screening strategy. We then used nucleotide sequence information from the recently completed sequence from C. jejuni NCTC 11168 to amplify a region involved in LOS biosynthesis from C. jejuni OH4384. The LOS biosynthesis locus from C. jejuni OH4384 is 11.47 kilobase pairs and encodes 13 partial or complete open reading frames, while the corresponding locus in C. jejuni NCTC 11168 spans 13.49 kilobase pairs and contains 15 open reading frames, indicating a different organization between these two strains. Potential glycosyltransferase genes were cloned individually, expressed in Escherichia coli, and assayed using synthetic fluorescent oligosaccharides as acceptors. We identified genes encoding a beta-1, 4-N-acetylgalactosaminyl-transferase (cgtA), a beta-1, 3-galactosyltransferase (cgtB), and a bifunctional sialyltransferase (cst-II), which transfers sialic acid to O-3 of galactose and to O-8 of a sialic acid that is linked alpha-2,3- to a galactose. The linkage specificity of each identified glycosyltransferase was confirmed by NMR analysis at 600 MHz on nanomole amounts of model compounds synthesized in vitro. Using a gradient inverse broadband nano-NMR probe, sequence information could be obtained by detection of (3)J(C,H) correlations across the glycosidic bond. The role of cgtA and cst-II in the synthesis of the GT1a mimic in C. jejuni OH4384 were confirmed by comparing their sequence and activity with corresponding homologues in two related C. jejuni strains that express shorter ganglioside mimics in their LOS.     

The crystal structure and catalytic mechanism of cellobiohydrolase CelS,the major enzymatic component of the Clostridium thermocellum Cellulosome

Cellobiohydrolase CelS plays an important role in the cellulosome, an active cellulase system produced by the thermophilic anaerobe Clostridium thermocellum. The structures of the catalytic domain of CelS in complex with substrate (cellohexaose) and product (cellobiose) were determined at 2.5 and 2.4 A resolution, respectively. The protein folds into an (alpha/alpha)(6) barrel with a tunnel-shaped substrate-binding region. The conformation of the loops defining the tunnel is intrinsically stable in the absence of substrate, suggesting a model to account for the processive mode of action of family 48 cellobiohydrolases. Structural comparisons with other (alpha/alpha)(6) barrel glycosidases indicate that CelS and endoglucanase CelA, a sequence-unrelated family 8 glycosidase with a groove-shaped substrate-binding region, use the same catalytic machinery to hydrolyze the glycosidic linkage, despite a low sequence similarity and a different endo/exo mode of action. A remarkable feature of the mechanism is the absence, from CelS, of a carboxylic group acting as the base catalyst. The nearly identical arrangement of substrate and functionally important residues in the two active sites strongly suggests an evolutionary relationship between the cellobiohydrolase and endoglucanase families, which can therefore be classified into a new clan of glycoside hydrolases.     

Structure and evolution of mammalian maltase-glucoamylase and sucrase-isomaltase genes

Maltase-glucoamylase and sucrase-isomaltase are two human glycosidases responsible for starch digestion. We have performed a comparative analysis of their amino acid sequences from several species of mammals and their orthologues from other chordates. This allowed us to determine the evolutionary history of the enzymes. Both glycosidases are paralogues and contain GH31 family catalytic domains. The common evolutionary precursor of these genes has arisen by a tandem duplication. As a consequence, sucrase-isomaltase consists of two homologous parts. The maltase-glucoamylase gene was a subject of several additional duplications, which number was not the same in different mammals. The locus, containing this gene, consists of 4-7 tandem repeats. The amino acid sequence, encoded by each of them, is similar to both parts of sucrase-isomaltase.     

Theory and computation show that Asp463 is the catalytic proton donor in human endoplasmic reticulum alpha-(1-->2)-mannosidase I

It has been difficult to identify the proton donor and nucleophilic assistant/base of endoplasmic reticulum alpha-(1-->2)-mannosidase I, a member of glycoside hydrolase Family 47, which cleaves the glycosidic bond between two alpha-(1-->2)-linked mannosyl residues by the inverting mechanism, trimming Man(9)GlcNAc(2) to Man(8)GlcNAc(2) isomer B. Part of the difficulty is caused by the enzyme's use of a water molecule to transmit the proton that attacks the glycosidic oxygen atom. We earlier used automated docking to conclusively determine that Glu435 in the yeast enzyme (Glu599 in the corresponding human enzyme) is the nucleophilic assistant. The commonly accepted proton donor has been Glu330 in the human enzyme (Glu132 in the yeast enzyme). However, for theoretical reasons this conclusion is untenable. Theory, automated docking of alpha-d-(3)S(1)-mannopyranosyl-(1-->2)-alpha-d-(4)C(1)-mannopyranose and water molecules associated with candidate proton donors, and estimation of dissociation constants of the latter have shown that the true proton donor is Asp463 in the human enzyme (Asp275 in the yeast enzyme).     

Substrate competition and specificity at the active site of amylopullulanase from Clostridium thermohydrosulfuricum

A highly thermostable pullulanase purified from Clostridium thermohydrosulfuricum strain 39E displayed dual activity with respect to glycosidic bond cleavage. The enzyme cleaved alpha-1,6 bonds in pullulan, while it showed alpha-1,4 activity against malto-oligosaccharides. Kinetic analysis of the purified enzyme in a system which contained both pullulan and amylose as the two competing substrates were used to distinguish the dual specificity of the enzyme from the single substrate specificity known for pullulanases and alpha-amylases.     

Unexpected alpha-stereochemical outcomes of attempted beta-glycosylations

In an effort to prepare complex oligosaccharide derivatives, a series of unexpected alpha glycosides were predominantly formed in the presence of neighboring group participation using imidates or thioglycosides as glycosyl donors under standard glycosylation conditions. The observations are especially suitable in the case of alpha-(1-->3) glycosidic bond formation.     

Transglycosylation reactions of Bacillus stearothermophilus maltogenic amylase with acarbose and various acceptors

It was observed that Bacillus stearothermophilus maltogenic amylase cleaved the first glycosidic bond of acarbose to produce glucose and a pseudotrisaccharide (PTS) that was transferred to C-6 of the glucose to give an alpha-(1-->6) glycosidic linkage and the formation of isoacarbose. The addition of a number of different carbohydrates to the digest gave transfer products in which PTS was primarily attached alpha-(1-->6) to D-glucose, D-mannose, D-galactose, and methyl alpha-D-glucopyranoside. With D-fructopyranose and D-xylopyranose, PTS was linked alpha-(1-->5) and alpha-(1-->4), respectively. PTS was primarily transferred to C-6 of the nonreducing residue of maltose, cellobiose, lactose, and gentiobiose. Lesser amounts of alpha-(1-->3) and/or alpha-(1-->4) transfer products were also observed for these carbohydrate acceptors. The major transfer product to sucrose gave PTS linked alpha-(1-->4) to the glucose residue. alpha,alpha-Trehalose gave two major products with PTS linked alpha-(1-->6) and alpha-(1-->4). Maltitol gave two major products with PTS linked alpha-(1-->6) and alpha-(1-->4) to the glucopyranose residue. Raffinose gave two major products with PTS linked alpha-(1-->6) and alpha-(1-->4) to the D-galactopyranose residue. Maltotriose gave two major products with PTS linked alpha-(1-->6) and alpha-(1-->4) to the nonreducing end glucopyranose residue. Xylitol gave PTS linked alpha-(1-->5) as the major product and D-glucitol gave PTS linked alpha-(1-->6) as the only product. The structures of the transfer products were determined using thin-layer chromatography, high-performance ion chromatography, enzyme hydrolysis, methylation analysis and 13C NMR spectroscopy. The best acceptor was gentiobiose, followed closely by maltose and cellobiose, and the weakest acceptor was D-glucitol.     

糖苷酶耐热性改造策略与应用

糖苷酶作为绿色温和的生物催化剂,能够水解包含糖苷、寡糖、多糖等在内的各种含糖化合物的糖苷键生成具有高生理和药理活性的衍生物,在食品、医药等工业领域应用广泛.而工业应用的糖苷酶经常需在高温条件下进行催化,以提高反应效率并减少污染,但大多数糖苷酶属于中温酶,在实际生产条件下的活性较低且损失较快,因此,提高糖苷酶在高温下的稳...     

How pyridoxal 5'-phosphate could function in glycogen phosphorylase catalysis.

A mechanism for the phosphorylase reaction is proposed which offers a plausible explanation for the essential role of pyridoxal 5'-phosphate in glycogen phosphorylases: in the forward direction, phosphorolysis of alpha-1,4-glycosidic bonds in oligo- or polysaccharides is started by protonation of the glycosidic oxygen by the substrate orthophosphate followed by stabilization of the incipient oxocarbonium ion and subsequent covalent binding to form alpha-glucose 1-phosphate. In the reverse direction, protonation of the phosphate of glucose 1-phosphate destabilizes the glycosidic bond and promotes formation of a glucosyl oxocarbonium ion-phosphate anion pair. In the subsequent step the phosphate anion facilitates the nucleophilic attack of a terminal glucosyl residue on the carbonium ion bringing about alpha-1,4-glycosidic bond formation and primer elongation. Both in the forward and reverse reactions, the phosphate of the cofactor pyridoxal 5'-phosphate acts as a general acid (PL-OPO3H- or PL-OPO3(2-) and protonates the substrate phosphate functioning as proton shuttle. Thus in glycogen phosphorylases, phosphates which directly interact with each other have replaced a pair of amino acid carboxyl groups functioning in catalysis of carbohydrases.     

Mechanisms of glycosyl transferases and hydrolases

Glycosidases and glycosyl transferases fall into two major mechanistic classes; those that hydrolyse the glycosidic bond with retention of anomeric configuration and those that do so with inversion. There are, however, two classes of transferases: those that use nucleotide phosphosugars (NP-sugar-dependent) and those that simply transglycosylate between oligosaccharides or polysaccharides (transglycosylases). The latter are mechanistically similar to retaining glycosidases while the mechanisms of NP-sugar-dependent transferases are far from clear.

Retaining glycosidases and the transglycosylases employ a mechanism involving a covalent glycosyl–enzyme intermediate formed and hydrolysed with acid/base catalytic assistance via oxocarbenium ion-like transition states. This intermediate has been trapped on glycosidases in two distinct ways, either by modification of the substrate through fluorination, or of the enzyme through mutation of key residues. A third method has been developed for trapping the intermediate on transglycosylases involving the use of incompetent substrates that allow formation of the intermediate, but prohibit its transfer as a consequence of their acceptor hydroxyl group being removed.

Three-dimensional structures of several of these glycosyl–enzyme complexes, along with those of Michaelis complexes, have been determined through X-ray crystallographic analysis, revealing the identities of important amino acid residues involved in catalysis. In particular they reveal the involvement of the carbonyl oxygen of the catalytic nucleophile in strong hydrogen bonding to the sugar 2-hydroxyl for the β-retainers or in interactions with the ring oxygen for -retainers. The glucose ring in the −1 (cleavage) site in the intermediates formed on several cellulases and a β-glucosidase adopts a normal ⁴C₁ chair conformation. By contrast the xylose ring at this site in a xylanase is substantially distorted into a ^2,5B boat conformation, an observation that bears significant stereoelectronic implications. Substantial distortion is also observed in the substrate upon binding to several β-glycosidases, this time to a ¹S₃ skew boat conformation. Much less distortion is seen in the substrate bound on an -transglycosylase.

Finally an efficient catalyst for synthesis, but not hydrolysis, of glycosidic bonds has been generated by mutation of the glutamic acid catalytic nucleophile of a β-glucosidase to an alanine. When used with -glucosyl fluoride as a glycosyl donor, along with a suitable acceptor, oligosaccharides up to five sugars in length have been made with yields of up to 90% on individual steps. These new enzymes have been named Glycosynthases.     

Molecular characterization of the beta-N-acetylglucosaminidase of Escherichia coli and its role in cell wall recycling

The beta-N-acetylglucosaminidase of Escherichia coli was found to have a novel specificity and to be encoded by a gene (nagZ) that maps at 25.1 min. It corresponds to an open reading frame, ycfO, whose predicted amino acid sequence is 57% identical to that of Vibrio furnissii ExoII. NagZ hydrolyzes the beta-1,4 glycosidic bond between N-acetylglucosamine and anhydro-N-acetylmuramic acid in cell wall degradation products following their importation into the cell during the process for recycling cell wall muropeptides. From amino acid sequence comparisons, the novel beta-N-acetylglucosaminidase appears to be conserved in all 12 gram-negative bacteria whose complete or partial genome sequence data are available.     

Temperature dependent vibrational modes of glycosidic bond in disaccharide sugars

We studied the temperature dependent vibrational modes of the glycosidic bond in trehalose, sucrose, and maltose at wavenumbers ranging from 1000 to 1200 cm(-1). We found that the slope of temperature dependent Raman shifts of the glycosidic bond in trehalose and sucrose changed at temperatures around 120 degrees C, indicating a bond length or a bond angle (dihedral and torsional angles) change. However, we did not observe any slope change in maltose because the melting temperature of maltose is very close to 120 degrees C. We also found, at temperatures below 120 degrees C, that Raman shifts of the vibrational modes of the glycosidic bond in trehalose showed the strongest temperature dependence among the three disaccharides.     

A 13C NMR study of poly(adenosine diphosphate ribose) and its monomers: evidence of alpha-(1'''' leads to 2'') ribofuranosy1 ribofuranoside risidue.

The 13C NMR spectra of poly(adenosine diphosphate ribose), ribosyl adenosine 5', 5'-bis(phosphate) and related compounds were analyzed. The structure of the ribose-ribose linkage was determined as alpha-(1' leads to 2')ribofuranosyl ribofuranoside, from the 13C chemical shifts of methyl-alpha- and methyl-beta-D-ribofuranosides, and from the downfield displacements of 13C NMR signals by glycosidic bond formation.     

Remote control of alpha- or beta-stereoselectivity in (1-->3)-glucosylations in the presence of a C-2 ester capable of neighboring-group participation

In (1-->3)-glucosylation the glycosyl bond originally present in either donor or acceptor is shown to control the stereoselectivity of the forthcoming bond, i.e., the newly formed glycosidic linkage has the opposite anomeric configuration of that of either the donor or acceptor. Therefore, with alpha-(1-->3)-linked disaccharides with nonreducing ends that have the 3-OH free as the acceptor and an acetylated glucosyl trichloroacetimidate as the donor, or with an alpha-(1-->3)-linked acetylated disaccharide trichloroacetimidate as the donor and a glucoside with 3-OH free as the acceptor, beta-linked trisaccharides were obtained. Meanwhile, with beta-(1-->3)-linked disaccharides that have nonreducing ends with the 3-OH free as the acceptor and an acetylated glucosyl trichloroacetimidate as the donor, or with a beta-(1-->3)-linked acetylated disaccharide trichloroacetimidate as the donor and a glucoside with the 3-OH free as the acceptor, alpha-linked trisaccharides were obtained in spite of the C-2 neighboring group participation.     

Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation

The synucleins are a family of intrinsically disordered proteins involved in various human diseases. alpha-Synuclein has been extensively characterized due to its role in Parkinson's disease where it forms intracellular aggregates, while gamma-synuclein is overexpressed in a majority of late-stage breast cancers. Despite fairly strong sequence similarity between the amyloid-forming regions of alpha- and gamma-synuclein, gamma-synuclein has only a weak propensity to form amyloid fibrils. We hypothesize that the different fibrillation tendencies of alpha- and gamma-synuclein may be related to differences in structural propensities. Here we have measured chemical shifts for gamma-synuclein and compared them to previously published shifts for alpha-synuclein. In order to facilitate direct comparison, we have implemented a simple new technique for re-referencing chemical shifts that we have found to be highly effective for both disordered and folded proteins. In addition, we have developed a new method that combines different chemical shifts into a single residue-specific secondary structure propensity (SSP) score. We observe significant differences between alpha- and gamma-synuclein secondary structure propensities. Most interestingly, gamma-synuclein has an increased alpha-helical propensity in the amyloid-forming region that is critical for alpha-synuclein fibrillation, suggesting that increased structural stability in this region may protect against gamma-synuclein aggregation. This comparison of residue-specific secondary structure propensities between intrinsically disordered homologs highlights the sensitivity of transient structure to sequence changes, which we suggest may have been exploited as an evolutionary mechanism for fast modulation of protein structure and, hence, function.     

Acid glycosidases in the isthmus of the hen oviduct and egg shell membranes

Specific activities of seven acid glycosidases: beta-hexosaminidase, alpha- and beta-galactosidase, alpha- and beta-mannosidase, alpha-glucosidase and alpha-fucosidase were determined in various parts of the domestic hen oviduct (infundibulum, isthmus, shell gland and vagina). The activity of most enzymes was the highest in the isthmus. Multiple forms of all acid glycosidases from the isthmus were separated by strong anion exchange chromatography at pH 6.0. The isoelectric points of the isthmus forms of beta-hexosaminidase, beta-galactosidase and alpha- and beta-mannosidase were determined by chromatofocusing. For the first time the high beta-galactosidase activity was found in hen egg shell membranes.