Catalytic Mechanisms and Reaction Intermediates along the Hydrolytic Pathway of a Plant β-D-glucan Glucohydrolase
Identifieur interne : 00B924 ( Main/Exploration ); précédent : 00B923; suivant : 00B925Catalytic Mechanisms and Reaction Intermediates along the Hydrolytic Pathway of a Plant β-D-glucan Glucohydrolase
Auteurs : Maria Hrmova [Australie] ; Joseph N. Varghese [Australie] ; Ross De Gori [Australie] ; Brian J. Smith [Australie] ; Hugues Driguez [France] ; Geoffrey B. Fincher [Australie]Source :
- Structure [ 0969-2126 ] ; 2001.
Descripteurs français
English descriptors
- KwdEn :
- 4iii, Acetate ions, Acid residues, Acta crystallogr, Active site, Amino, Amino acid residue, Amino acid residues, Analog, Anomeric configuration, Atomic structure, Barley glucohydrolase, Barley glucohydrolases, Biol, Bond angles, Catalysis, Catalytic, Catalytic mechanism, Catalytic nucleophile, Catalytic site, Ccoc, Ccoc angles, Cellulomonas fimi, Chem, Conduritol, Covalent, Crystal structure, Cyclitol ring, Cyclohexitol, Cyclohexitol ring, Data frames, Diffraction data, Dihedral, Electron density, Enzyme, Epoxide, Ester linkage, Exoi, Exposure times, Final refinement statistics, Fincher, Fourier, Fresh solution, Glucohydrolase, Glucohydrolase isoenzyme exoi, Glucohydrolases, Glucopyranosyl ring, Glucose, Glucose molecule, Glucose product, Glucosyl residue, Glycoside, Glycoside hydrolases, Glycosidic, Glycosidic linkage, Glycosyl, Higher plants, Hrmova, Hydrolases, Hydrolytic, Hydrolytic mechanism, Hydrolytic pathway, Hydroxyl, Hydroxyl group, Inhibitor, Isoenzyme, Linkage, Moiety, Nonhydrolyzable substrate analog, Nucleophile, Oxonium, Pathway, Reaction intermediates, Relative energies, Residue, Sodium acetate buffer, Subsite, Subsites, Substrate analog, Substrate distortion, Substrate specificity, Water molecules, Withers.
- Teeft :
- 4iii, Acetate ions, Acid residues, Acta crystallogr, Active site, Amino, Amino acid residue, Amino acid residues, Analog, Anomeric configuration, Atomic structure, Barley glucohydrolase, Barley glucohydrolases, Biol, Bond angles, Catalysis, Catalytic, Catalytic mechanism, Catalytic nucleophile, Catalytic site, Ccoc, Ccoc angles, Cellulomonas fimi, Chem, Conduritol, Covalent, Crystal structure, Cyclitol ring, Cyclohexitol, Cyclohexitol ring, Data frames, Diffraction data, Dihedral, Electron density, Enzyme, Epoxide, Ester linkage, Exoi, Exposure times, Final refinement statistics, Fincher, Fourier, Fresh solution, Glucohydrolase, Glucohydrolase isoenzyme exoi, Glucohydrolases, Glucopyranosyl ring, Glucose, Glucose molecule, Glucose product, Glucosyl residue, Glycoside, Glycoside hydrolases, Glycosidic, Glycosidic linkage, Glycosyl, Higher plants, Hrmova, Hydrolases, Hydrolytic, Hydrolytic mechanism, Hydrolytic pathway, Hydroxyl, Hydroxyl group, Inhibitor, Isoenzyme, Linkage, Moiety, Nonhydrolyzable substrate analog, Nucleophile, Oxonium, Pathway, Reaction intermediates, Relative energies, Residue, Sodium acetate buffer, Subsite, Subsites, Substrate analog, Substrate distortion, Substrate specificity, Water molecules, Withers.
Abstract
Abstract: Background: Barley β-D-glucan glucohydrolases represent family 3 glycoside hydrolases that catalyze the hydrolytic removal of nonreducing glucosyl residues from β-D-glucans and β-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-β-D-glucopyranoside are diffused into enzyme crystals, they displace the bound glucose and form covalent glycosyl-enzyme complexes through the Oδ1 of D285, which is thereby identified as the catalytic nucleophile. A nonhydrolyzable S-glycosyl analog, 4I, 4III, 4V-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 Å) with the Oϵ2 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 4C1 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 β-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.
Url:
DOI: 10.1016/S0969-2126(01)00673-6
Affiliations:
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<term>Acta crystallogr</term>
<term>Active site</term>
<term>Amino</term>
<term>Amino acid residue</term>
<term>Amino acid residues</term>
<term>Analog</term>
<term>Anomeric configuration</term>
<term>Atomic structure</term>
<term>Barley glucohydrolase</term>
<term>Barley glucohydrolases</term>
<term>Biol</term>
<term>Bond angles</term>
<term>Catalysis</term>
<term>Catalytic</term>
<term>Catalytic mechanism</term>
<term>Catalytic nucleophile</term>
<term>Catalytic site</term>
<term>Ccoc</term>
<term>Ccoc angles</term>
<term>Cellulomonas fimi</term>
<term>Chem</term>
<term>Conduritol</term>
<term>Covalent</term>
<term>Crystal structure</term>
<term>Cyclitol ring</term>
<term>Cyclohexitol</term>
<term>Cyclohexitol ring</term>
<term>Data frames</term>
<term>Diffraction data</term>
<term>Dihedral</term>
<term>Electron density</term>
<term>Enzyme</term>
<term>Epoxide</term>
<term>Ester linkage</term>
<term>Exoi</term>
<term>Exposure times</term>
<term>Final refinement statistics</term>
<term>Fincher</term>
<term>Fourier</term>
<term>Fresh solution</term>
<term>Glucohydrolase</term>
<term>Glucohydrolase isoenzyme exoi</term>
<term>Glucohydrolases</term>
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<term>Glucose molecule</term>
<term>Glucose product</term>
<term>Glucosyl residue</term>
<term>Glycoside</term>
<term>Glycoside hydrolases</term>
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<term>Hydrolytic mechanism</term>
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<term>Hydroxyl</term>
<term>Hydroxyl group</term>
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<term>Linkage</term>
<term>Moiety</term>
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<term>Pathway</term>
<term>Reaction intermediates</term>
<term>Relative energies</term>
<term>Residue</term>
<term>Sodium acetate buffer</term>
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<term>Subsites</term>
<term>Substrate analog</term>
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<term>Substrate specificity</term>
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<term>Acetate ions</term>
<term>Acid residues</term>
<term>Acta crystallogr</term>
<term>Active site</term>
<term>Amino</term>
<term>Amino acid residue</term>
<term>Amino acid residues</term>
<term>Analog</term>
<term>Anomeric configuration</term>
<term>Atomic structure</term>
<term>Barley glucohydrolase</term>
<term>Barley glucohydrolases</term>
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<term>Catalytic mechanism</term>
<term>Catalytic nucleophile</term>
<term>Catalytic site</term>
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<term>Ccoc angles</term>
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<term>Conduritol</term>
<term>Covalent</term>
<term>Crystal structure</term>
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<term>Cyclohexitol ring</term>
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<term>Diffraction data</term>
<term>Dihedral</term>
<term>Electron density</term>
<term>Enzyme</term>
<term>Epoxide</term>
<term>Ester linkage</term>
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<term>Exposure times</term>
<term>Final refinement statistics</term>
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<term>Fourier</term>
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<term>Glycosidic linkage</term>
<term>Glycosyl</term>
<term>Higher plants</term>
<term>Hrmova</term>
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<term>Inhibitor</term>
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<term>Linkage</term>
<term>Moiety</term>
<term>Nonhydrolyzable substrate analog</term>
<term>Nucleophile</term>
<term>Oxonium</term>
<term>Pathway</term>
<term>Reaction intermediates</term>
<term>Relative energies</term>
<term>Residue</term>
<term>Sodium acetate buffer</term>
<term>Subsite</term>
<term>Subsites</term>
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<term>Substrate distortion</term>
<term>Substrate specificity</term>
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<front><div type="abstract" xml:lang="en">Abstract: Background: Barley β-D-glucan glucohydrolases represent family 3 glycoside hydrolases that catalyze the hydrolytic removal of nonreducing glucosyl residues from β-D-glucans and β-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-β-D-glucopyranoside are diffused into enzyme crystals, they displace the bound glucose and form covalent glycosyl-enzyme complexes through the Oδ1 of D285, which is thereby identified as the catalytic nucleophile. A nonhydrolyzable S-glycosyl analog, 4I, 4III, 4V-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 Å) with the Oϵ2 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 4C1 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 β-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.</div>
</front>
</TEI>
<affiliations><list><country><li>Australie</li>
<li>France</li>
</country>
<region><li>Auvergne-Rhône-Alpes</li>
<li>Rhône-Alpes</li>
</region>
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<tree><country name="Australie"><noRegion><name sortKey="Hrmova, Maria" sort="Hrmova, Maria" uniqKey="Hrmova M" first="Maria" last="Hrmova">Maria Hrmova</name>
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<name sortKey="De Gori, Ross" sort="De Gori, Ross" uniqKey="De Gori R" first="Ross" last="De Gori">Ross De Gori</name>
<name sortKey="Fincher, Geoffrey B" sort="Fincher, Geoffrey B" uniqKey="Fincher G" first="Geoffrey B" last="Fincher">Geoffrey B. Fincher</name>
<name sortKey="Fincher, Geoffrey B" sort="Fincher, Geoffrey B" uniqKey="Fincher G" first="Geoffrey B" last="Fincher">Geoffrey B. Fincher</name>
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<name sortKey="Varghese, Joseph N" sort="Varghese, Joseph N" uniqKey="Varghese J" first="Joseph N" last="Varghese">Joseph N. Varghese</name>
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<country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Driguez, Hugues" sort="Driguez, Hugues" uniqKey="Driguez H" first="Hugues" last="Driguez">Hugues Driguez</name>
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