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Haataja T, Gado JE, Nutt A, Anderson NT, Nilsson M, Momeni MH, Isaksson R, Väljamäe P, Johansson G, Payne CM, Ståhlberg J. Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non-productive binding: insights from crystal structures and MD simulation. FEBS J 2023; 290:379-399. [PMID: 35997626 PMCID: PMC10087753 DOI: 10.1111/febs.16602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/30/2022] [Accepted: 08/17/2022] [Indexed: 02/05/2023]
Abstract
Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) (EC3.2.1.176) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p-nitrophenyl-β-d-cellobioside (pNPC), p-nitrophenyl-β-d-lactoside (pNPL) and methylumbelliferyl-β-d-cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o-nitrophenyl-β-d-cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium. Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non-productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non-productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates (kcat ) than TrCel7A, but higher Michaelis-Menten (KM ) constants as well. Furthermore, oNPC turned out to be useful as an active-site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.
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Affiliation(s)
- Topi Haataja
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Japheth E Gado
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA.,Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Anu Nutt
- Department of Chemistry, Uppsala University, Sweden.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Nolan T Anderson
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Mikael Nilsson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Majid Haddad Momeni
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roland Isaksson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | | | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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2
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Rabinovich ML, Melnik MS, Herner ML, Voznyi YV, Vasilchenko LG. Predominant Nonproductive Substrate Binding by Fungal Cellobiohydrolase I and Implications for Activity Improvement. Biotechnol J 2018; 14:e1700712. [PMID: 29781240 DOI: 10.1002/biot.201700712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/08/2018] [Indexed: 12/20/2022]
Abstract
Enzymatic conversion of the most abundant renewable source of organic compounds, cellulose to fermentable sugars is attractive for production of green fuels and chemicals. The major component of industrial enzyme systems, cellobiohydrolase I from Hypocrea jecorina (Trichoderma reesei) (HjCel7A) processively splits disaccharide units from the reducing ends of tightly packed cellulose chains. HjCel7A consists of a catalytic domain (CD) and a carbohydrate-binding module (CBM) separated by a linker peptide. A tunnel-shaped substrate-binding site in the CD includes nine subsites for β-d-glucose units, seven of which (-7 to -1) precede the catalytic center. Low catalytic activity of Cel7A is the bottleneck and the primary target for improvement. Here it is shown for the first time that, in spite of much lower apparent kcat of HjCel7A at the hydrolysis of β-1,4-glucosidic linkages in the fluorogenic cellotetra- and -pentaose compared to the structurally related endoglucanase I (HjCel7B), the specificity constants (catalytic efficiency) kcat /Km for both enzymes are almost equal in these reactions. The observed activity difference appears from strong nonproductive substrate binding by HjCel7A, particularly significant for MU-β-cellotetraose (MUG4 ). Interaction of substrates with the subsites -6 and -5 proximal to the nonconserved Gln101 residue in HjCel7A decreases Km,ap by >1500 times. HjCel7A can be nonproductively bound onto cellulose surface with Kd ≈2-9 nM via CBM and CD that captures six terminal glucose units of cellulose chain. Decomposition of this nonproductive complex can determine the rate of cellulose conversion. MUG4 is a promising substrate to select active cellobiohydrolase I variants with reduced nonproductive substrate binding.
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Affiliation(s)
- Mikhail L Rabinovich
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Maria S Melnik
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Mikhail L Herner
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Yakov V Voznyi
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| | - Lilia G Vasilchenko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
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3
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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4
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Najah M, Mayot E, Mahendra-Wijaya IP, Griffiths AD, Ladame S, Drevelle A. New Glycosidase Substrates for Droplet-Based Microfluidic Screening. Anal Chem 2013; 85:9807-14. [DOI: 10.1021/ac4022709] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Majdi Najah
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Ets J.
Soufflet,
division Biotechnologies-OSIRIS, quai
Sarrail, 10400 Nogent-sur-Seine, France
| | - Estelle Mayot
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Ets J.
Soufflet,
division Biotechnologies-OSIRIS, quai
Sarrail, 10400 Nogent-sur-Seine, France
| | - I Putu Mahendra-Wijaya
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Ets J.
Soufflet,
division Biotechnologies-OSIRIS, quai
Sarrail, 10400 Nogent-sur-Seine, France
| | - Andrew D. Griffiths
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), 10 rue Vauquelin, 75231 Paris Cedex, France
| | - Sylvain Ladame
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Department
of Bioengineering, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Antoine Drevelle
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Ets J.
Soufflet,
division Biotechnologies-OSIRIS, quai
Sarrail, 10400 Nogent-sur-Seine, France
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5
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Teugjas H, Väljamäe P. Product inhibition of cellulases studied with 14C-labeled cellulose substrates. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:104. [PMID: 23883520 PMCID: PMC3726336 DOI: 10.1186/1754-6834-6-104] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/11/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND As a green alternative for the production of transportation fuels, the enzymatic hydrolysis of lignocellulose and subsequent fermentation to ethanol are being intensively researched. To be economically feasible, the hydrolysis of lignocellulose must be conducted at a high concentration of solids, which results in high concentrations of hydrolysis end-products, cellobiose and glucose, making the relief of product inhibition of cellulases a major challenge in the process. However, little quantitative information on the product inhibition of individual cellulases acting on cellulose substrates is available because it is experimentally difficult to assess the hydrolysis of the heterogeneous polymeric substrate in the high background of added products. RESULTS The cellobiose and glucose inhibition of thermostable cellulases from Acremonium thermophilum, Thermoascus aurantiacus, and Chaetomium thermophilum acting on uniformly 14C-labeled bacterial cellulose and its derivatives, 14C-bacterial microcrystalline cellulose and 14C-amorphous cellulose, was studied. Cellulases from Trichoderma reesei were used for comparison. The enzymes most sensitive to cellobiose inhibition were glycoside hydrolase (GH) family 7 cellobiohydrolases (CBHs), followed by family 6 CBHs and endoglucanases (EGs). The strength of glucose inhibition followed the same order. The product inhibition of all enzymes was relieved at higher temperatures. The inhibition strength measured for GH7 CBHs with low molecular-weight model substrates did not correlate with that measured with 14C-cellulose substrates. CONCLUSIONS GH7 CBHs are the primary targets for product inhibition of the synergistic hydrolysis of cellulose. The inhibition must be studied on cellulose substrates instead of on low molecular-weight model substrates when selecting enzymes for lignocellulose hydrolysis. The advantages of using higher temperatures are an increase in the catalytic efficiency of enzymes and the relief of product inhibition.
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Affiliation(s)
- Hele Teugjas
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b – 202, Tartu 51010, Estonia
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b – 202, Tartu 51010, Estonia
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6
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Bu L, Nimlos MR, Shirts MR, Ståhlberg J, Himmel ME, Crowley MF, Beckham GT. Product binding varies dramatically between processive and nonprocessive cellulase enzymes. J Biol Chem 2012; 287:24807-13. [PMID: 22648408 DOI: 10.1074/jbc.m112.365510] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulases hydrolyze β-1,4 glycosidic linkages in cellulose, which are among the most prevalent and stable bonds in Nature. Cellulases comprise many glycoside hydrolase families and exist as processive or nonprocessive enzymes. Product inhibition negatively impacts cellulase action, but experimental measurements of product-binding constants vary significantly, and there is little consensus on the importance of this phenomenon. To provide molecular level insights into cellulase product inhibition, we examine the impact of product binding on processive and nonprocessive cellulases by calculating the binding free energy of cellobiose to the product sites of catalytic domains of processive and nonprocessive enzymes from glycoside hydrolase families 6 and 7. The results suggest that cellobiose binds to processive cellulases much more strongly than nonprocessive cellulases. We also predict that the presence of a cellodextrin bound in the reactant site of the catalytic domain, which is present during enzymatic catalysis, has no effect on product binding in nonprocessive cellulases, whereas it significantly increases product binding to processive cellulases. This difference in product binding correlates with hydrogen bonding between the substrate-side ligand and the cellobiose product in processive cellulase tunnels and the additional stabilization from the longer tunnel-forming loops. The hydrogen bonds between the substrate- and product-side ligands are disrupted by water in nonprocessive cellulase clefts, and the lack of long tunnel-forming loops results in lower affinity of the product ligand. These findings provide new insights into the large discrepancies reported for binding constants for cellulases and suggest that product inhibition will vary significantly based on the amount of productive binding for processive cellulases on cellulose.
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Affiliation(s)
- Lintao Bu
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA.
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7
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Excoffier G, Toussaint B, Vignon MR. Saccharification of steam-exploded poplar wood. Biotechnol Bioeng 2010; 38:1308-17. [PMID: 18600732 DOI: 10.1002/bit.260381108] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Effects of time, temperature, and pH during the steam explosion of poplar wood were studied with the aim of optimize both pentoses recovery and enzymatic hydrolysis efficiency. Steam explosion of acid impregnated wood chips allowed the recovery of 70% of potential xylose as monomers (217 degrees C, 120 s) Enzymatic hydrolysis of pretreated fiber with Trichoderma reesei CL-847 cellulase system increased progressively with the severity of the steam treatment conditions. The best yield in term of glucose recovery after 24 h of enzymatic hydrolysis was 70% of potential glucose (225 degrees C, 120 s). Deactivation by adsorption on lignin of Trichoderma reesei cellulases and inhibition of these enzymes by low-molecular-weight phenols and trihydroxybutyric acids were noticed.
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Affiliation(s)
- G Excoffier
- CREMAV-CNRS, BP 53 X, 38041 Grenoble Cedex, France
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8
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Kwok AC, Wong JT. The activity of a wall-bound cellulase is required for and is coupled to cell cycle progression in the dinoflagellate Crypthecodinium cohnii. THE PLANT CELL 2010; 22:1281-98. [PMID: 20407022 PMCID: PMC2879759 DOI: 10.1105/tpc.109.070243] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 03/23/2010] [Accepted: 04/03/2010] [Indexed: 05/29/2023]
Abstract
Cellulose synthesis, but not its degradation, is generally thought to be required for plant cell growth. In this work, we cloned a dinoflagellate cellulase gene, dCel1, whose activities increased significantly in G(2)/M phase, in agreement with the significant drop of cellulose content reported previously. Cellulase inhibitors not only caused a delay in cell cycle progression at both the G(1) and G(2)/M phases in the dinoflagellate Crypthecodinium cohnii, but also induced a higher level of dCel1p expression. Immunostaining results revealed that dCel1p was mainly localized at the cell wall. Accordingly, the possible role of cellulase activity in cell cycle progression was tested by treating synchronized cells with exogenous dCelp and purified antibody, in experiments analogous to overexpression and knockdown analyses, respectively. Cell cycle advancement was observed in cells treated with exogenous dCel1p, whereas the addition of purified antibody resulted in a cell cycle delay. Furthermore, delaying the G(2)/M phase independently with antimicrotubule inhibitors caused an abrupt and reversible drop in cellulase protein level. Our results provide a conceptual framework for the coordination of cell wall degradation and reconstruction with cell cycle progression in organisms with cell walls. Since cellulase activity has a direct bearing on the cell size, the coupling between cellulase expression and cell cycle progression can also be considered as a feedback mechanism that regulates cell size.
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Affiliation(s)
| | - Joseph T.Y. Wong
- Department of Biology, Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, People's Republic of China
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9
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Majumdar S, Pratt RF. Intramolecular cooperativity in the reaction of diacyl phosphates with serine beta-lactamases. Biochemistry 2009; 48:8293-8. [PMID: 19678666 DOI: 10.1021/bi900808x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asymmetric diaroyl phosphates (ArCOOPO(2)(-)OCOAr', where Ar = Ph, Ar' = 4-biphenyl, 2-benzothiophenyl and 2-benzofuranyl) have been prepared, evaluated as serine (classes A, C, and D) beta-lactamase inhibitors, and compared with respect to the latter with their symmetric parents, where Ar = Ar'. The asymmetric compounds, in general, were found to react with the beta-lactamases in two modes, corresponding to different orientations with respect to the active site, whereby either of the two aroyl groups may acylate the enzyme to form two different inert acyl-enzymes, E-COAr and E-COAr' . In all cases, the asymmetric compounds, in one orientation, react more rapidly with the enzymes tested than one symmetrical parent but not both. From comparisons of activation free energy differences, it was found that the changes in free energy on changing from one aryl group to another, in either the acyl group or the leaving group, were not additive, i.e., that the effect of changing one aroyl group to another depended on the leaving group and vice versa. Thus, intramolecular cooperativity between the aroyl groups must exist, arising either from direct interaction between them or from protein-mediated interaction or from a combination of both. Such cooperativity brings fresh opportunities and challenges to the search for novel beta-lactamase inhibitors.
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Affiliation(s)
- Sudipta Majumdar
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, USA
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10
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Faijes M, Saura-Valls M, Pérez X, Conti M, Planas A. Acceptor-dependent regioselectivity of glycosynthase reactions by Streptomyces E383A β-glucosidase. Carbohydr Res 2006; 341:2055-65. [PMID: 16716271 DOI: 10.1016/j.carres.2006.04.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 04/27/2006] [Accepted: 04/30/2006] [Indexed: 11/28/2022]
Abstract
The nonnucleophilic mutant E383A beta-glucosidase from Streptomyces sp. has proven to be an efficient glycosynthase enzyme, catalyzing the condensation of alpha-glucosyl and alpha-galactosyl fluoride donors to a variety of acceptors. The enzyme has maximal activity at 45 degrees C, and a pH-dependence reflecting general base catalysis with an apparent kinetic pKa of 7.2. The regioselectivity of the new glycosidic linkage depends unexpectedly on the acceptor substrate. With aryl monosaccharide acceptors, beta-(1-->3) disaccharides are obtained in good to excellent yields, thus expanding the synthetic products available with current exo-glycosynthases. With xylopyranosyl acceptor, regioselectivity is poorer and results in the formation of a mixture of beta-(1-->3) and beta-(1-->4) linkages. In contrast, disaccharide acceptors produce exclusively beta-(1-->4) linkages. Therefore, the presence of a glycosyl unit in subsite +II redirects regioselectivity from beta-(1-->3) to beta-(1-->4). To improve operational performance, the E383A mutant was immobilized on a Ni2+-chelating Sepharose resin. Immobilization did not increase stability to pH and organic solvents, but the operational stability and storage stability were clearly enhanced for recycling and scaling-up.
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Affiliation(s)
- Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
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11
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Abel M, Iversen K, Planas A, Christensen U. Pre-steady-state kinetics of Bacillus licheniformis 1,3-1,4-beta-glucanase: evidence for a regulatory binding site. Biochem J 2003; 371:997-1003. [PMID: 12568655 PMCID: PMC1223346 DOI: 10.1042/bj20021504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2002] [Revised: 01/17/2003] [Accepted: 02/04/2003] [Indexed: 11/17/2022]
Abstract
In a previous paper, we reported the first stopped-flow experiments on a Bacillus licheniformis 1,3-1,4-beta-glucanase [Abel, Planas and Christensen (2001) Biochem. J. 357, 195-202]. It was shown that the pre-steady-state kinetics of the 1,3-1,4-beta-glucanase using the substrate 4-methylumbelliferyl 3-O-beta-cellobiosyl-beta-D-glucoside may be explained by a reaction scheme involving an induced fit and the binding of two substrates as well as a second enzymic conformational change, whereas the results definitely could not be explained in terms of the simple double-displacement scheme. In the present study, we report further stopped-flow kinetic results on the glucanase using a series of low-molecular-mass substrates with various leaving groups and varying chain length. The analysis of the resulting data leads to the conclusion that the free enzyme exists in two conformations, one of which binds the substrates rather strongly in a regulatory site, before any productive interactions can take place. This corresponds to an allosteric activation mechanism. With these substrates, however, the productive enzyme-substrate species are also able to change into less active or inactive forms. This may be seen as a feedback inhibitory mechanism.
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Affiliation(s)
- Mireia Abel
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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12
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Desmet T, Nerinckx W, Stals I, Callewaert N, Contreras R, Claeyssens M. Novel tools for the study of class I alpha-mannosidases: a chromogenic substrate and a substrate-analog inhibitor. Anal Biochem 2002; 307:361-7. [PMID: 12202255 DOI: 10.1016/s0003-2697(02)00039-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The use of chromogenic substrates for evaluation of class I alpha-mannosidase is described. 2('),4(')-Dinitrophenyl-alpha-D-mannopyranoside allows rapid and sensitive assays of enzymatic activities, e.g., of heterologously expressed alpha-1,2-mannosidase from Trichoderma reesei. Interaction constants of several ligands with alpha-mannosidases from class I and II could also be determined. Furthermore, novel types of inhibitors derived from D-lyxose are presented. Methyl-alpha-D-lyxopyranosyl-(1(')-->2)-alpha-D-mannopyranoside is a potent inhibitor of the alpha-1,2-mannosidase from T. reesei (K(i)=600 microM) and since it probably spans subsites -1/+1, this disaccharide could be valuable in crystallographic studies of class I alpha-mannosidases.
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Affiliation(s)
- T Desmet
- Laboratory for Biochemistry, Department of Biochemistry, Physiology, and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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13
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Abel M, Planas A, Christensen U. Presteady-state kinetics of Bacillus 1,3-1,4-beta-glucanase: binding and hydrolysis of a 4-methylumbelliferyl trisaccharide substrate. Biochem J 2001; 357:195-202. [PMID: 11415449 PMCID: PMC1221941 DOI: 10.1042/0264-6021:3570195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the present study the first stopped-flow experiments performed on Bacillus 1,3-1,4-beta-glucanases are reported. The presteady-state kinetics of the binding of 4-methylumbelliferyl 3-O-beta-cellobiosyl-beta-D-glucoside to the inactive mutant E134A, and the wild-type-catalysed hydrolysis of the same substrate, were studied by measuring changes in the fluorescence of bound substrate or 4-methylumbelliferone produced. The presteady-state traces all showed an initial lag phase followed by a fast monoexponential phase leading to equilibration (for binding to E134A) or to steady state product formation (for the wild-type reaction). The lag phase, with a rate constant of the order of 100 s(-1), was independent of the substrate concentration; apparently an induced-fit mechanism governs the formation of enzyme-substrate complexes. The concentration dependencies of the observed rate constant of the second presteady-state phase were analysed according to a number of reaction models. For the reaction of the wild-type enzyme, it is shown that the fast product formation observed before steady state is not due to a rate-determining deglycosylation step. A model that can explain the observed results involves, in addition to the induced fit, a conformational change of the productive ES complex into a form that binds a second substrate molecule in a non-productive mode.
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Affiliation(s)
- M Abel
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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14
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Irwin DC, Zhang S, Wilson DB. Cloning, expression and characterization of a family 48 exocellulase, Cel48A, from Thermobifida fusca. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:4988-97. [PMID: 10931180 DOI: 10.1046/j.1432-1327.2000.01546.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The gene for a 104-kDa exocellulase, Cel48A, formerly E6, was cloned from Thermobifida fusca into Escherichia coli and Streptomyces lividans. The DNA sequence revealed a type II cellulose-binding domain at the N-terminus, followed by a FNIII-like domain and ending with a glycosyl hydrolase Family 48 catalytic domain. The enzyme and catalytic domain alone were each expressed in and purified from S. lividans and had very low catalytic activity on swollen cellulose, carboxymethyl cellulose, bacterial microcrystalline cellulose and filter paper. However, in synergistic assays on filter paper, the addition of Cel48A to a balanced mixture of T. fusca endocellulase and exocellulase increased the specific activity from 7.9 to 11.7 micromol cellobiose.min-1.mL-1, more than 15-fold higher than any single enzyme alone. Cel48A retained > 50% of its maximum activity from pH 5 to 9 and from 40 to 60 degrees C. Using SWISSMODEL, the amino-acid sequence of the Cel48Acd was modeled to the known structure of Clostridium cellulolyticum CelF. Family 48 enzymes are remarkably homologous at 35% identity for all their catalytic domains and some of the properties of the 10 members are discussed.
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Affiliation(s)
- D C Irwin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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Zhang S, Irwin DC, Wilson DB. Site-directed mutation of noncatalytic residues of Thermobifida fusca exocellulase Cel6B. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:3101-15. [PMID: 10824094 DOI: 10.1046/j.1432-1327.2000.01315.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fifteen mutant genes in six loop residues and eight mutant genes in five conserved noncatalytic active site residues of Thermobifida fusca Cel6B were constructed, cloned and expressed in Escherichia coli or Streptomyces lividans. The mutant enzymes were assayed for catalytic activity on carboxymethyl cellulose (CMC), swollen cellulose (SC), filter paper (FP), and bacterial microcrystalline cellulose (BMCC) as well as cellotetraose, cellopentaose, and 2, 4-dinitrophenyl-beta-D-cellobioside. They were also assayed for ligand binding, enzyme processivity, thermostability, and cellobiose feedback inhibition. Two double Cys mutations that formed disulfide bonds across two tunnel forming loops were found to significantly weaken binding to ligands, lower all activities, and processivity, demonstrating that the movement of these loops is important but not essential for Cel6B function. Two single mutant enzymes, G234S and G284P, had higher activity on SC and FP, and the double mutant enzyme had threefold and twofold higher activity on these substrates, respectively. However, synergism with endocellulase T. fusca Cel5A was not increased with these mutant enzymes. All mutant enzymes with lower activity on filter paper, BMCC, and SC had lower processivity. This trend was not true for CMC, suggesting that processivity in Cel6B is a key factor in the hydrolysis of insoluble and crystalline cellulose. Three mutations (E495D, H326A and W329C) located near putative glycosyl substrate subsites -2, +1 and +2, were found to significantly increase resistance to cellobiose feedback inhibition. Both the A229V and L230C mutations specifically decreased activity on BMCC, suggesting that BMCC hydrolysis has a different rate limiting step than the other substrates. Most of the mutant enzymes had reduced thermostability although Cel6B G234S maintained wild-type thermostability. The properties of the different mutant enzymes provide insight into the catalytic mechanism of Cel6B.
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Affiliation(s)
- S Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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von Ossowski I, Teeri T, Kalkkinen N, Oker-Blom C. Expression of a fungal cellobiohydrolase in insect cells. Biochem Biophys Res Commun 1997; 233:25-9. [PMID: 9144389 DOI: 10.1006/bbrc.1997.6391] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The gene for Trichoderma reesei cellobiohydrolase I (CBHI) was expressed with a recombinant baculovirus and high levels of secreted protein were produced in Spodoptera frugiperda and Trichoplusia ni insect cells. Electrophoretic analysis indicated that the recombinant CBHI (rCBHI) was similar in apparent molecular weight to the native form and immunoblotting with anti-CBHI monoclonal antibodies confirmed its identity. The rCBHI was easily purified by affinity and hydrophobic interaction chromatography and demonstrated enzymatic activity on soluble substrate.
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Harjunpää V, Teleman A, Koivula A, Ruohonen L, Teeri TT, Teleman O, Drakenberg T. Cello-oligosaccharide hydrolysis by cellobiohydrolase II from Trichoderma reesei. Association and rate constants derived from an analysis of progress curves. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 240:584-91. [PMID: 8856058 DOI: 10.1111/j.1432-1033.1996.0584h.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The hydrolysis of soluble cello-oligosaccharides, with a degree of polymerisation of 4-6, catalysed by cellobiohydrolase II from Trichoderma reesei was studied using 1H-NMR spectroscopy and HPLC. The experimental progress curves were analysed by fitting numerically integrated kinetic equations, which provided cleavage patterns and kinetic constants for each oligosaccharide. This analysis procedure accounts for product inhibition and avoids the initial slope approximation. No glucose was detected at the beginning of the reaction indicating that only the internal glycosidic linkages are attacked. For cellotetraose only the second glycosidic linkage was cleaved. For cellopentaose and cellohexaose the second and the third glycosidic linkage from the non-reducing end were cleaved with approximately equal probability. The degradation rates of these cello-oligosaccharides, 1-12 s-1 at 27 degrees C, are about 10-100 times faster than for the 4-methylumbelliferyl substituted analogs or for collotriose. No intermediate products larger than cellotriose were released. The degradation rate for cellotetraose were higher than its off-rate, which accounts for the processive degradation of cellohexaose. A high cellohexaose/enzyme ratio caused slow reversible inactivation of the enzyme.
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Kleman-Leyer KM, Siika-Aho M, Teeri TT, Kirk TK. The Cellulases Endoglucanase I and Cellobiohydrolase II of Trichoderma reesei Act Synergistically To Solubilize Native Cotton Cellulose but Not To Decrease Its Molecular Size. Appl Environ Microbiol 1996; 62:2883-7. [PMID: 16535380 PMCID: PMC1388918 DOI: 10.1128/aem.62.8.2883-2887.1996] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Degradation of cotton cellulose by Trichoderma reesei endoglucanase I (EGI) and cellobiohydrolase II (CBHII) was investigated by analyzing the insoluble cellulose fragments remaining after enzymatic hydrolysis. Changes in the molecular-size distribution of cellulose after attack by EGI, alone and in combination with CBHII, were determined by size exclusion chromatography of the tricarbanilate derivatives. Cotton cellulose incubated with EGI exhibited a single major peak, which with time shifted to progressively lower degrees of polymerization (DP; number of glucosyl residues per cellulose chain). In the later stages of degradation (8 days), this peak was eventually centered over a DP of 200 to 300 and was accompanied by a second peak (DP, (apprx=)15); a final weight loss of 34% was observed. Although CBHII solubilized approximately 40% of bacterial microcrystalline cellulose, the cellobiohydrolase did not depolymerize or significantly hydrolyze native cotton cellulose. Furthermore, molecular-size distributions of cellulose incubated with EGI together with CBHII did not differ from those attacked solely by EGI. However, a synergistic effect was observed in the reducing-sugar production by the cellulase mixture. From these results we conclude that EGI of T. reesei degrades cotton cellulose by selectively cleaving through the microfibrils at the amorphous sites, whereas CBHII releases soluble sugars from the EGI-degraded cotton cellulose and from the more crystalline bacterial microcrystalline cellulose.
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Damude HG, Ferro V, Withers SG, Warren RA. Substrate specificity of endoglucanase A from Cellulomonas fimi: fundamental differences between endoglucanases and exoglucanases from family 6. Biochem J 1996; 315 ( Pt 2):467-72. [PMID: 8615816 PMCID: PMC1217219 DOI: 10.1042/bj3150467] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Values of kcat. and Km for the hydrolysis of cellotetraose, cellotriose, beta-cellobiosyl fluoride and various beta-aryl cellobiosides by endoglucanase A (CenA) from Cellulomonas fimi indicate that specific binding interactions between the reducing-end glucose residues of cellotetraose and cellotriose and the enzyme at the transition state provide enormous stabilization, endowing glucose with the "effective leaving group ability' of 2,4-dinitrophenol. As has been seen with several other inverting glycosidases, CenA hydrolyses the "wrong' anomer of its glycosyl fluoride substrate, alpha-cellobiosyl fluoride, according to non-Michaelian kinetics. This indicates that CenA carries out this hydrolysis by a mechanism involving binding of two substrate molecules in the active site (Hehre, Brewer and Genghof (1979) J. Biol. Chem. 254, 5942-5950] in contrast with that reported for cellobiohydrolase II, another family-6 enzyme [Konstantinidis, Marsden and Sinnott (1993) Biochem. J. 291, 833-838]. The pH profiles for wild-type CenA indicate that kcat. for CenA depends on the presence of both a protonated group and a deprotonated group for full activity, consistent with the presence of an acid and a base catalyst at the active site. By contrast, the profile for the Asp252Ala mutant of CenA shows a dependence only on a base-catalytic group, thereby confirming the role of Asp-252 as an acid catalyst. These results show that hydrolysis by CenA occurs by a typical inverting mechanism involving both acid and base catalysis, as first proposed by Koshland. It also suggests that endoglucanases from family 6 may function by fundamentally different mechanisms for exoglucanases in this family.
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Affiliation(s)
- H G Damude
- Protein Engineering Network of Centres of Excellence, University of British Columbia, Vancouver, Canada
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Teleman A, Koivula A, Reinikainen T, Valkeajärvi A, Teeri TT, Drakenberg T, Teleman O. Progress-curve analysis shows that glucose inhibits the cellotriose hydrolysis catalysed by cellobiohydrolase II from Trichoderma reesei. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 231:250-8. [PMID: 7628478 DOI: 10.1111/j.1432-1033.1995.tb20694.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
NMR spectroscopy and HPLC were used to investigate the hydrolysis of cellotriose by cellobiohydrolase II from Trichoderma reesei. Substrate and product concentrations were followed as a function of time. Progress curves were calculated by forward numerical integration of the full kinetic equations and were fitted to the experimental data. Binding and rate constants were obtained from this fit, whereby no initial slope or Michaelis-Menten approximation was used. The progress curves from a single experiment sufficed to produce agreement with the Michaelis-Menten model (eight experiments). The absence of a kinetic isotope effect was proven. The progress-curve analysis showed that a simple degradation model cannot describe the experimental time-courses at substrate concentrations greater than 1 mM. A model containing competitive inhibition from cellobiose as well as non-competitive inhibition from glucose was developed. This four-parameter model accurately reproduces about 1000 experimental data points covering five orders of magnitude in oligosaccharide concentrations. Glucose binding to the enzyme/cellotriose complex retards, in a non-competitive fashion, cellotriose hydrolysis by at least a factor of 30. A structural model for the non-competitive inhibition is discussed. The NMR experiment also produced individual progress curves for the alpha and beta anomers. The beta anomer of cellotriose was degraded 2.5-times faster than the alpha anomer.
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Affiliation(s)
- A Teleman
- VTT Chemical Technology, Espoo, Finland
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Modes of action of two Trichoderma reesei cellobiohydrolases. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s0921-0423(06)80105-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Singh A, Hayashi K. Microbial cellulases: protein architecture, molecular properties, and biosynthesis. ADVANCES IN APPLIED MICROBIOLOGY 1995; 40:1-44. [PMID: 7604736 DOI: 10.1016/s0065-2164(08)70362-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- A Singh
- Biomaterials Conversion Laboratory, National Food Research Institute, Ibaraki, Japan
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Engle AR, Purdie N, Hyatt JA. Induced circular dichroism study of the aqueous solution complexation of cello-oligosaccharides and related polysaccharides with aromatic dyes. Carbohydr Res 1994; 265:181-95. [PMID: 7842441 DOI: 10.1016/0008-6215(94)00235-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Acetobacter xylinum, grown in the presence of low levels of the water-soluble dye Calcofluor White ST produces a pellicle of cellulose that has no detectable crystallinity. Biological factors of this sort are probably more important than physical factors in controlling the higher order structures of celluloses. Circular dichroism (CD) is induced by complexes that are formed by specific interactions between chiral oligosaccharides and dye molecules. Using CD, equilibrium constants were measured for the association reactions between various dyes with a series of cello-oligosaccharides (n = 2-6), methylcellulose, hydroxypropylcellulose (HPC), amylose, cyclomalto-oligosaccharides (cyclodextrins), and the linear malto-oligosaccharides (n = 3-7). Possible structural features of the complexes are discussed. Dyes that are capable of binding to the higher cello-oligomers in aqueous solutions are the same dyes that modify the solid structure of bacterial cellulose. An analogy between the binding of water-soluble dyes to cello-oligosaccharides and the binding of the cellulose-degrading enzyme, cellobiohydrolase I, to cellulose is discussed.
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Affiliation(s)
- A R Engle
- Chemistry Department, Oklahoma State University, Stillwater 74078-0447
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Activity studies of eight purified cellulases: Specificity, synergism, and binding domain effects. Biotechnol Bioeng 1993; 42:1002-13. [DOI: 10.1002/bit.260420811] [Citation(s) in RCA: 270] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Teeri TT, Penttilä M, Keränen S, Nevalainen H, Knowles JK. Structure, function, and genetics of cellulases. BIOTECHNOLOGY (READING, MASS.) 1992; 21:417-45. [PMID: 1576482 DOI: 10.1016/b978-0-7506-9115-4.50020-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Studies of the cellulolytic system of the filamentous fungus Trichoderma reesei QM 9414. Substrate specificity and transfer activity of endoglucanase I. Biochem J 1990; 270:251-6. [PMID: 2396985 PMCID: PMC1131706 DOI: 10.1042/bj2700251] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Endoglucanase I from the filamentous fungus Trichoderma reesei catalyses hydrolysis and glycosyl-transfer reactions of cello-oligosaccharides. Initial bond-cleaving frequencies determined with 1-3H-labelled cello-oligosaccharides proved to be substrate-concentration-dependent. Using chromophoric glycosides and analysing the reaction products by h.p.l.c., kinetic data are obtained and, as typical for an endo-type depolymerase, apparent hydrolytic parameters (kcat., kcat./Km) increase steadily as a function of the number of glucose residues. At high substrate concentrations, and for both free cellodextrins and their aromatic glycosides, complex patterns (transfer reactions) are, however, evident. In contrast with the corresponding lactosides and 1-thiocellobiosides, and in conflict with the expected specificity, aromatic 1-O-beta-cellobiosides are apparently hydrolysed at both scissile bonds, yielding the glucoside as one of the main reaction products. Its formation rate is clearly non-hyperbolically related to the substrate concentration and, since the rate of D-glucose formation is substantially lower, strong indications for dismutation reactions (self-transfer) are again obtained. Evidence for transfer reactions catalysed by endoglucanase I further results from experiments using different acceptor and donor substrates. A main transfer product accumulating in a digest containing a chromophoric 1-thioxyloside was isolated and its structure elucidated by proton n.m.r. spectrometry (500 MHz). The beta 1-4 configuration of the newly formed bond was proved.
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