PubMed Health⌕ Search

Biomedical subjects

M Hrmova

Publications and source records attributed to M Hrmova.

15 recordsLinked to original sources
PubMed2001

Barley arabinoxylan arabinofuranohydrolases: purification, characterization and determination of primary structures from cDNA clones.

A family 51 arabinoxylan arabinofuranohydrolase, designated AXAH-I, has been purified from extracts of 7-day-old barley (Hordeum vulgare L.) seedlings by fractional precipitation with (NH(4))(2)SO(4) and ion-exchange chromatography. The enzyme has an apparent molecular mass of 65 kDa and releases L-arabinose from cereal cell wall arabinoxylans with a pH optimum of 4.3, a catalytic rate constant (k(cat)) of 6.9 s(-1) and a catalytic efficiency factor (k(cat)/K(m)) of 0.76 (ml x s(-1) x mg(-1)). Whereas the hydrolysis of alpha-L-arabinofuranosyl residues linked to C(O)3 of backbone (1-->4)-beta-xylosyl residues proceeds at the fastest rate, alpha-L-arabinofuranosyl residues on doubly substituted xylosyl residues are also hydrolysed, at lower rates. A near full-length cDNA encoding barley AXAH-I indicates that the mature enzyme consists of 626 amino acid residues and has a calculated pI of 4.8. A second cDNA, which is 81% identical with that encoding AXAH-I, encodes another barley AXAH, which has been designated AXAH-II. The barley AXAHs are likely to have key roles in wall metabolism in cereals and other members of the Poaceae. Thus the enzymes could participate in the modification of the fine structure of arabinoxylan during wall deposition, maturation or expansion, or in wall turnover and the hydrolysis of arabinoxylans in germinated grain.

Amino Acid Sequence↗
PubMed2001

Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase.

BACKGROUND: Barley beta-D-glucan glucohydrolases represent family 3 glycoside hydrolases that catalyze the hydrolytic removal of nonreducing glucosyl residues from beta-D-glucans and beta-D-glucooligosaccharides. After hydrolysis is completed, glucose remains bound in the active site. RESULTS: When conduritol B epoxide and 2', 4'-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside are diffused into enzyme crystals, they displace the bound glucose and form covalent glycosyl-enzyme complexes through the Odelta1 of D285, which is thereby identified as the catalytic nucleophile. A nonhydrolyzable S-glycosyl analog, 4(I), 4(III), 4(V)-S-trithiocellohexaose, also diffuses into the active site, and a S-cellobioside moiety positions itself at the -1 and +1 subsites. The glycosidic S atom of the S-cellobioside moiety forms a short contact (2.75 A) with the Oepsilon2 of E491, which is likely to be the catalytic acid/base. The glucopyranosyl residues of the S-cellobioside moiety are not distorted from the low-energy 4C(1) conformation, but the glucopyranosyl ring at the +1 subsite is rotated and translated about the linkage. CONCLUSIONS: X-ray crystallography is used to define the three key intermediates during catalysis by beta-D-glucan glucohydrolase. Before a new hydrolytic event begins, the bound product (glucose) from the previous catalytic reaction is displaced by the incoming substrate, and a new enzyme-substrate complex is formed. The second stage of the hydrolytic pathway involves glycosidic bond cleavage, which proceeds through a double-displacement reaction mechanism. The crystallographic analysis of the S-cellobioside-enzyme complex with quantum mechanical modeling suggests that the complex might mimic the oxonium intermediate rather than the enzyme-substrate complex.

Catalytic Domain↗
PubMed2001

Binding interactions between barley thaumatin-like proteins and (1,3)-beta-D-glucans. Kinetics, specificity, structural analysis and biological implications.

The specificity and kinetics of the interaction between the pathogenesis-related group of thaumatin-like proteins (PR5) in higher plants and (1,3)-beta-D-glucans have been investigated. Two thaumatin-like proteins with 60% amino-acid sequence identity were purified from extracts of germinated barley grain, and were designated HvPR5b and HvPR5c. Purified HvPR5c interacted with insoluble (1,3)-beta-D-glucans, but not with cellulose, pustulan, xylan, chitin or a yeast mannoprotein. Tight binding was observed with unbranched and unsubstituted (1,3)-beta-D-glucans, and weaker binding was seen if (1,6)-beta-linked branch points or beta-glucosyl substituents were present in the substrate. The HvPR5b protein interacted weakly with insoluble (1,3)-beta-D-glucans and did not bind to any of the other polysaccharides tested. This indicated that only specific barley PR5 isoforms interact tightly with (1,3)-beta-D-glucans. The complete primary structures of HvPR5b and HvPR5c were determined and used to construct molecular models of HvPR5b and HvPR5c, based on known three-dimensional structures of related thaumatin-like proteins. The models were examined for features that may be associated with (1,3)-beta-D-glucan binding, and a potential (1,3)-beta-D-glucan-binding region was located on the surface of HvPR5c. No obvious structural features that would prevent binding of (1,3)-beta-D-glucan to HvPR5b were identified, but several of the amino acids in HvPR5c that are likely to interact with (1,3)-beta-D-glucans are not present in HvPR5b.

Adsorption↗
PubMed2001

Structure-function relationships of beta-D-glucan endo- and exohydrolases from higher plants.

(1-->3),(1-->4)-beta-D-Glucans represent an important component of cell walls in the Poaceae family of higher plants. A number of glycoside endo- and exohydrolases is required for the depolymerization of (1-->3),(1-->4)-beta-D-glucans in germinated grain or for the partial hydrolysis of the polysaccharide in elongating vegetative tissues. The enzymes include (1-->3),(1-->4)-beta-D-glucan endohydrolases (EC 3.2.1.73), which are classified as family 17 glycoside hydrolases, (1-->4)-beta-D-glucan glucohydrolases (family 1) and beta-D-glucan exohydrolases (family 3). Kinetic analyses of hydrolytic reactions enable the definition of action patterns, the thermodynamics of substrate binding, and the construction of subsite maps. Mechanism-based inhibitors and substrate analogues have been used to study the spatial orientation of the substrate in the active sites of the enzymes, at the atomic level. The inhibitors and substrate analogues also allow us to define the catalytic mechanisms of the enzymes and to identify catalytic amino acid residues. Three-dimensional structures of (1-->3),(1-->4)-beta-D-glucan endohydrolases, (1-->4)-beta-D-glucan glucohydrolases and beta-D-glucan exohydrolases are available or can be reliably modelled from the crystal structures of related enzymes. Substrate analogues have been diffused into crystals for solving of the three-dimensional structures of enzyme-substrate complexes. This information provides valuable insights into potential biological roles of the enzymes in the degradation of the barley (1-->3),(1-->4)-beta-D-glucans during endosperm mobilization and in cell elongation.

Cell Wall↗
PubMed2000

Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases.

There are approximately 100 known members of the family 3 group of glycoside hydrolases, most of which are classified as beta-glucosidases and originate from microorganisms. The only family 3 glycoside hydrolase for which a three-dimensional structure is available is a beta-glucan exohydrolase from barley. The structural coordinates of the barley enzyme is used here to model representatives from distinct phylogenetic clusters within the family. The majority of family 3 hydrolases have an NH(2)-terminal (alpha/beta)(8) barrel connected by a short linker to a second domain, which adopts an (alpha/beta)(6) sandwich fold. In two bacterial beta-glucosidases, the order of the domains is reversed. The catalytic nucleophile, equivalent to D285 of the barley beta-glucan exohydrolase, is absolutely conserved across the family. It is located on domain 1, in a shallow site pocket near the interface of the domains. The likely catalytic acid in the barley enzyme, E491, is on domain 2. Although similarly positioned acidic residues are present in closely related members of the family, the equivalent amino acid in more distantly related members is either too far from the active site or absent. In the latter cases, the role of catalytic acid is probably assumed by other acidic amino acids from domain 1.

Amino Acid Sequence↗
PubMed1999

Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase.

BACKGROUND: Cell walls of the starchy endosperm and young vegetative tissues of barley (Hordeum vulgare) contain high levels of (1-->3,1-->4)-beta-D-glucans. The (1-->3,1-->4)-beta-D-glucans are hydrolysed during wall degradation in germinated grain and during wall loosening in elongating coleoptiles. These key processes of plant development are mediated by several polysaccharide endohydrolases and exohydrolases. RESULTS: . The three-dimensional structure of barley beta-D-glucan exohydrolase isoenzyme ExoI has been determined by X-ray crystallography. This is the first reported structure of a family 3 glycosyl hydrolase. The enzyme is a two-domain, globular protein of 605 amino acid residues and is N-glycosylated at three sites. The first 357 residues constitute an (alpha/beta)8 TIM-barrel domain. The second domain consists of residues 374-559 arranged in a six-stranded beta sandwich, which contains a beta sheet of five parallel beta strands and one antiparallel beta strand, with three alpha helices on either side of the sheet. A glucose moiety is observed in a pocket at the interface of the two domains, where Asp285 and Glu491 are believed to be involved in catalysis. CONCLUSIONS: The pocket at the interface of the two domains is probably the active site of the enzyme. Because amino acid residues that line this active-site pocket arise from both domains, activity could be regulated through the spatial disposition of the domains. Furthermore, there are sites on the second domain that may bind carbohydrate, as suggested by previously published kinetic data indicating that, in addition to the catalytic site, the enzyme has a second binding site specific for (1-->3, 1-->4)-beta-D-glucans.

Amino Acid Sequence↗
PubMed1999

A single limit dextrinase gene is expressed both in the developing endosperm and in germinated grains of barley.

The single gene encoding limit dextrinase (pullulan 6-glucanohydrolase; EC 3.2.1.41) in barley (Hordeum vulgare) has 26 introns that range in size from 93 to 822 base pairs. The mature polypeptide encoded by the gene has 884 amino acid residues and a calculated molecular mass of 97,417 D. Limit dextrinase mRNA is abundant in gibberellic acid-treated aleurone layers and in germinated grain. Gibberellic acid response elements were found in the promoter region of the gene. These observations suggest that the enzyme participates in starch hydrolysis during endosperm mobilization in germinated grain. The mRNA encoding the enzyme is present at lower levels in the developing endosperm of immature grain, a location consistent with a role for limit dextrinase in starch synthesis. Enzyme activity was also detected in developing grain. The limit dextrinase has a presequence typical of transit peptides that target nascent polypeptides to amyloplasts, but this would not be expected to direct secretion of the mature enzyme from aleurone cells in germinated grain. It remains to be discovered how the enzyme is released from the aleurone and whether another enzyme, possibly of the isoamylase group, might be equally important for starch hydrolysis in germinated grain.

Amino Acid Sequence↗
PubMed1998

Crystallization and preliminary X-ray analysis of beta-glucan exohydrolase isoenzyme ExoI from barley (Hordeum vulgare).

Crystals of a beta-glucan exohydrolase purified from extracts of young barley seedlings have been obtained by vapour diffusion in the presence of ammonium sulfate and polyethylene glycol. The enzyme exhibits broad substrate specificity against (1,3)-, (1,3;1,4)- and (1,3;1,6)-beta-glucans, and related oligosaccharides. Crystal dimensions of up to 0.8 x 0.4 x 0.6 mm have been observed. The crystals belong to the tetragonal space group P41212 or P43212. Cell parameters are a = b = 102.1 and c = 184.5 A, and there appear to be eight molecules in the asymmetric unit. The crystals diffract to at least 2.2 A resolution using X-rays from a rotating-anode generator.

Crystallization↗
PubMed1998

Substrate binding and catalytic mechanism of a barley beta-D-Glucosidase/(1,4)-beta-D-glucan exohydrolase.

A beta-glucosidase, designated isoenzyme betaII, from germinated barley (Hordeum vulgare L.) hydrolyzes aryl-beta-glucosides and shares a high level of amino acid sequence similarity with beta-glucosidases of diverse origin. It releases glucose from the non-reducing termini of cellodextrins with catalytic efficiency factors, kcat/Km, that increase approximately 9-fold as the degree of polymerization of these substrates increases from 2 to 6. Thus, the enzyme has a specificity and action pattern characteristic of both beta-glucosidases (EC 3.2.1.21) and the polysaccharide exohydrolase, (1,4)-beta-glucan glucohydrolase (EC 3.2.1.74). At high concentrations (100 mM) of 4-nitrophenyl beta-glucoside, beta-glucosidase isoenzyme betaII catalyzes glycosyl transfer reactions, which generate 4-nitrophenyl-beta-laminaribioside, -cellobioside, and -gentiobioside. Subsite mapping with cellooligosaccharides indicates that the barley beta-glucosidase isoenzyme betaII has six substrate-binding subsites, each of which binds an individual beta-glucosyl residue. Amino acid residues Glu181 and Glu391 are identified as the probable catalytic acid and catalytic nucleophile, respectively. The enzyme is a family 1 glycoside hydrolase that is likely to adopt a (beta/alpha)8 barrel fold and in which the catalytic amino acid residues appear to be located at the bottom of a funnel-shaped pocket in the enzyme.

Amino Acid Sequence↗
PubMed1997

Purification and characterization of a (1-->3)-beta-D-glucan endohydrolase from rice (Oryza sativa) bran.

A (1-->3)-beta-glucanase with an apparent M(r) of 29,000 and an isoelectric point of 4.0 has been purified 2000-fold from extracts of rice bran, using fractional precipitation with ammonium sulfate, anion exchange chromatography, size-exclusion chromatography, chromatofocussing, and hydrophobic interaction chromatography. The enzyme can be classified with the EC 3.2.1.39 group, because it releases laminarabiose and higher laminara-oligosaccharides from linear (1-->3)-beta-D-glucans with an action pattern that is typical of (1-->3)-beta-D-glucan endohydrolases. However, the introduction of substituents or branching in the (1-->3)-beta-D-glucan substrates causes a marked decrease in the rate of hydrolysis. Thus, substituted or branched (1-->3)-beta-D-glucans of the kind commonly found in fungal cell walls are less susceptible to hydrolysis than essentially linear (1-->3)-beta-D-glucans. Kinetic analyses indicate an apparent Km of 42 microM, a kcat constant of 67 s-1, and a pH optimum of 5.0 during hydrolysis of the (1-->3)-beta-D-glucan, laminaran, from Laminaria digitata. The first 60 NH2-terminal amino acid residues of the purified rice (1-->3)-beta-glucanase contain blocks of amino acids that are conserved in other cereal (1-->3)-beta-glucanases. Although the precise tissue location and function of the enzyme in rice bran are not known, it is likely that it is concentrated in the aleurone layer and that it plays a preemptive role in the protection of ungerminated grain against pathogen attack.

Carbohydrate Conformation↗
PubMed1997

Polysaccharide hydrolases in germinated barley and their role in the depolymerization of plant and fungal cell walls.

Cell wall degradation is an important event during endosperm mobilization in the germinated barley grain. A battery of polysaccharide and oligosaccharide hydrolases is required for the complete depolymerization of the arabinoxylans and (1 --> 3,1 --> 4)-beta-glucans which comprise in excess of 90% by weight of these walls. The (1 --> 3,1 --> 4)-beta-glucan endohydrolases release oligosaccharides from their substrate and are probably of central importance for the initial solubilization of the (1 --> 3,1 --> 4)-beta-glucans, but beta-glucan exohydrolases and beta-glucosidases may be important additional enzymes for the conversion of released oligosaccharides to glucose. The latter enzymes have recently been purified from germinated barley and characterized. There is an increasing body of evidence to support the notion that the (1 --> 3,1 --> 4)-beta-glucan endohydrolases from germinated barley evolved from the pathogenesis-related (1 --> 3)-beta-glucanases which are widely distributed in plants and which hydrolyse polysaccharides that are abundant in fungal cell walls. Arabinoxylan depolymerization is also mediated by a family of enzymes, but these are less well characterized. (1 --> 4)-beta-Xylan endohydrolases have been purified and the corresponding cDNAs and genes isolated. While the presence of (1 --> 4)-beta-xylan exohydrolases and alpha-L-arabinofuranosidases has been reported many times, the enzymes have not yet been studied in detail. Here, recent advances in the enzymology and physiology of cell wall degradation in the germinated barley grain are briefly reviewed.

Carbohydrate Sequence↗
PubMed1996

Barley beta-D-glucan exohydrolases with beta-D-glucosidase activity. Purification, characterization, and determination of primary structure from a cDNA clone.

Two beta-glucan exohydrolases of apparent molecular masses 69,000 and 71,000 Da have been purified from extracts of 8-day germinated barley grains and are designated isoenzymes ExoI and ExoII, respectively. The sequences of their first 52 NH2-terminal amino acids show 64% positional identity. Both enzymes hydrolyze the (1,3)-beta-glucan, laminarin, but also hydrolyze (1,3;1,4)-beta-glucan and 4-nitrophenyl beta-D-glucoside. The complete sequence of 602 amino acid residues of the mature beta-glucan exohydrolase isoenzyme ExoII has been deduced by nucleotide sequence analysis of a near full-length cDNA. Two other enzymes of apparent molecular mass 62,000 Da, designated betaI and betaII, were also purified from the extracts. Their amino acid sequences are similar to enzymes classified as beta-glucosidases and although they hydrolyze 4-nitrophenyl beta-glucoside, their substrate specificities and action patterns are more typical of polysaccharide exohydrolases of the (1,4)-beta-glucan glucohydrolase type. Both the beta-glucan exohydrolase isoenzyme ExoI and the beta-glucosidase isoenzyme betaII release single glucosyl residues from the nonreducing ends of substrates and proton-NMR shows that anomeric configurations are retained during hydrolysis by both classes of enzyme. These results raise general questions regarding the distinction between polysaccharide exohydrolases and glucosidases, together with more specific questions regarding the functional roles of the two classes of enzyme in germinating barley grain.

Amino Acid Sequence↗
PubMed1995

Subsite affinities and disposition of catalytic amino acids in the substrate-binding region of barley 1,3-beta-glucanases. Implications in plant-pathogen interactions.

Oligo-1,3-beta-glucosides with degrees of polymerization of 2-9 were labeled at their reducing terminal residues by catalytic tritiation. These substrates were used in detailed kinetic and thermodynamic analyses to examine substrate binding in 1,3-beta-D-glucan glucanohydrolase (EC 3.2.1.39) isoenzymes GI, GII, and GIII from young seedlings of barley (Hordeum vulgare). Bond-cleavage frequencies, together with the kinetic parameter kcat/Km, have been calculated as a function of substrate chain length to define the number of subsites that accommodate individual beta-glucosyl residues and to estimate binding energies at each subsite. Each isoenzyme has eight beta-glucosyl-binding subsites. The catalytic amino acids are located between the third and fourth subsite from the nonreducing terminus of the substrate. Negative binding energies in subsites adjacent to the hydrolyzed glycosidic linkage suggest that some substrate distortion may occur in this region during binding and that the resultant strain induced in the substrate might facilitate hydrolytic cleavage. If the 1,3-beta-glucanases exert their function as pathogenesis-related proteins by hydrolyzing the branched or substituted 1,3;1,6-beta-glucans of fungal walls, it is clear that relatively extended regions of the cell wall polysaccharide must fit into the substrate-binding cleft of the enzyme.

Amino Acids↗
PubMed1993

Purification and properties of three (1-->3)-beta-D-glucanase isoenzymes from young leaves of barley (Hordeum vulgare).

Three (1-->3)-beta-D-glucan glucanohydrolase (EC 3.2.1.39) isoenzymes GI, GII and GIII were purified from young leaves of barley (Hordeum vulgare) using (NH4)2SO4 fractional precipitation, ion-exchange chromatography, chromatofocusing and gel-filtration chromatography. The three (1-->3)-beta-D-glucanases are monomeric proteins of apparent M(r)32,000 with pI values in the range 8.8-10.3. N-terminal amino-acid-sequence analyses confirmed that the three isoenzymes represent the products of separate genes. Isoenzymes GI and GII are less stable at elevated temperatures and are active over a narrower pH range than is isoenzyme GIII, which is a glycoprotein containing 20-30 mol of hexose equivalents/mol of enzyme. The preferred substrate for the enzymes is laminarin from the brown alga Laminaria digitata, an essentially linear (1-->3)-beta-D-glucan with a low degree of glucosyl substitution at 0-6 and a degree of polymerization of approx. 25. The three enzymes are classified as endohydrolases, because they yield (1-->3)-beta-D-oligoglucosides with degrees of polymerization of 3-8 in the initial stages of hydrolysis of laminarin. Kinetic analyses indicate apparent Km values in the range 172-208 microM, kcat. constants of 36-155 s-1 and pH optima of 4.8. Substrate specificity studies show that the three isoenzymes hydrolyse substituted (1-->3)-beta-D-glucans with degrees of polymerization of 25-31 and various high-M(r), substituted and side-branched fungal (1-->3;1-->6)-beta-D-glucans. However, the isoenzymes differ in their rates of hydrolysis of a (1-->3;1-->6)-beta-D-glucan from baker's yeast and their specific activities against laminarin vary significantly. The enzymes do not hydrolyse (1-->3;1-->4)-beta-D-glucans, (1-->6)-beta-D-glucan, CM-cellulose, insoluble (1-->3)-beta-D-glucans or aryl beta-D-glycosides.

Amino Acid Sequence↗