1
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Jain N, Tamura K, Déjean G, Van Petegem F, Brumer H. Orthogonal Active-Site Labels for Mixed-Linkage endo-β-Glucanases. ACS Chem Biol 2021; 16:1968-1984. [PMID: 33988963 DOI: 10.1021/acschembio.1c00063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecule irreversible inhibitors are valuable tools for determining catalytically important active-site residues and revealing key details of the specificity, structure, and function of glycoside hydrolases (GHs). β-glucans that contain backbone β(1,3) linkages are widespread in nature, e.g., mixed-linkage β(1,3)/β(1,4)-glucans in the cell walls of higher plants and β(1,3)glucans in yeasts and algae. Commensurate with this ubiquity, a large diversity of mixed-linkage endoglucanases (MLGases, EC 3.2.1.73) and endo-β(1,3)-glucanases (laminarinases, EC 3.2.1.39 and EC 3.2.1.6) have evolved to specifically hydrolyze these polysaccharides, respectively, in environmental niches including the human gut. To facilitate biochemical and structural analysis of these GHs, with a focus on MLGases, we present here the facile chemo-enzymatic synthesis of a library of active-site-directed enzyme inhibitors based on mixed-linkage oligosaccharide scaffolds and N-bromoacetylglycosylamine or 2-fluoro-2-deoxyglycoside warheads. The effectiveness and irreversibility of these inhibitors were tested with exemplar MLGases and an endo-β(1,3)-glucanase. Notably, determination of inhibitor-bound crystal structures of a human-gut microbial MLGase from Glycoside Hydrolase Family 16 revealed the orthogonal labeling of the nucleophile and catalytic acid/base residues with homologous 2-fluoro-2-deoxyglycoside and N-bromoacetylglycosylamine inhibitors, respectively. We anticipate that the selectivity of these inhibitors will continue to enable the structural and mechanistic analyses of β-glucanases from diverse sources and protein families.
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Affiliation(s)
- Namrata Jain
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
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2
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Novel substrates for the automated and manual assay of endo-1,4-β-xylanase. Carbohydr Res 2017; 445:14-22. [PMID: 28384512 DOI: 10.1016/j.carres.2017.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/22/2017] [Accepted: 02/26/2017] [Indexed: 11/20/2022]
Abstract
endo-1,4-β-Xylanase (EC 3.2.1.8) is employed across a broad range of industries including animal feed, brewing, baking, biofuels, detergents and pulp (paper). Despite its importance, a rapid, reliable, reproducible, automatable assay for this enzyme that is based on the use of a chemically defined substrate has not been described to date. Reported herein is a new enzyme coupled assay procedure, termed the XylX6 assay, that employs a novel substrate, namely 4,6-O-(3-ketobutylidene)-4-nitrophenyl-β-45-O-glucosyl-xylopentaoside. The development of the substrate and associated assay is discussed here and the relationship between the activity values obtained with the XylX6 assay versus traditional reducing sugar assays and its specificity and reproducibility were thoroughly investigated.
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3
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Mangan D, Liadova A, Ivory R, McCleary B. Novel approaches to the automated assay of β-glucanase and lichenase activity. Carbohydr Res 2016; 435:162-172. [DOI: 10.1016/j.carres.2016.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/19/2016] [Indexed: 11/28/2022]
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4
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A novel automatable enzyme-coupled colorimetric assay for endo-1,4-β-glucanase (cellulase). Anal Bioanal Chem 2016; 408:4159-68. [PMID: 27052773 PMCID: PMC4873538 DOI: 10.1007/s00216-016-9507-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/21/2016] [Indexed: 11/07/2022]
Abstract
endo-1,4-β-Glucanase (endo-cellulase, EC 3.2.1.4) is one of the most widely used enzymes in industry. Despite its importance, improved methods for the rapid, selective, quantitative assay of this enzyme have been slow to emerge. In 2014, a novel enzyme-coupled assay that addressed many of the limitations of the existing assay methodology was reported. This involved the use of a bifunctional substrate chemically derived from cellotriose. Reported herein is a much improved version of this assay employing a novel substrate, namely 4,6-O-(3-ketobutylidene)-4-nitrophenyl-β-d-cellopentaoside. Principle of the CELLG5 assay ![]()
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5
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Cornaggia C, Ivory R, Mangan D, McCleary BV. Novel assay procedures for the measurement of α-amylase in weather-damaged wheat. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:404-412. [PMID: 25645152 DOI: 10.1002/jsfa.7103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 01/12/2015] [Accepted: 01/17/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND The measurement of α-amylase (EC 3.2.1.1) in sprout-damaged grains is a crucial analysis yet a problematic one owing to the typically low α-amylase levels in ground wheat samples. A number of standardised methods such as the Falling Number method and the Ceralpha method exist which are routinely used for the assay of α-amylase. These methods, however, are either highly substrate-dependent or lack the required sensitivity to assess sprout damage. RESULTS Novel colorimetric and fluorometric reagents have been prepared (Amylase HR, Amylase SD, BzCNPG7 reagent and BzMUG7 reagent) for the direct and specific assay of α-amylase activity in sprout-damaged wheat. Assays employing these reagents have been developed and optimised to include a decolourisation step using activated charcoal. When used in a convenient assay format, Amylase SD--containing EtNPG7 (II) as the colorimetric substrate and α-glucosidase as the ancillary enzyme--was found to be an excellent reagent for the assessment of sprout damage in wheat with incubation times as short as 5 min. CONCLUSION The assay using Amylase SD is completely specific for α-amylase. The use of the Amylase SD assay represents a sensitive and valid alternative to the traditionally used Falling Number values for the assessment of sprout damage in wheat samples.
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Affiliation(s)
- Claudio Cornaggia
- Megazyme International, IDA Business Park, Southern Cross Road, Bray, Co. Wicklow, Ireland
| | - Ruth Ivory
- Megazyme International, IDA Business Park, Southern Cross Road, Bray, Co. Wicklow, Ireland
| | - David Mangan
- Megazyme International, IDA Business Park, Southern Cross Road, Bray, Co. Wicklow, Ireland
| | - Barry V McCleary
- Megazyme International, IDA Business Park, Southern Cross Road, Bray, Co. Wicklow, Ireland
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6
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Ardèvol A, Rovira C. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations. J Am Chem Soc 2015; 137:7528-47. [DOI: 10.1021/jacs.5b01156] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Albert Ardèvol
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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7
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Mangan D, McCleary BV, Cornaggia C, Ivory R, Rooney E, McKie V. Colourimetric and fluorimetric substrates for the assay of limit dextrinase. J Cereal Sci 2015. [DOI: 10.1016/j.jcs.2014.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Mangan D, McCleary B, Liadova A, Ivory R, McCormack N. Quantitative fluorometric assay for the measurement of endo-1,4-β-glucanase. Carbohydr Res 2014; 395:47-51. [DOI: 10.1016/j.carres.2014.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/25/2014] [Accepted: 05/04/2014] [Indexed: 10/25/2022]
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9
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Colourimetric and fluorometric substrates for measurement of pullulanase activity. Carbohydr Res 2014; 393:60-9. [DOI: 10.1016/j.carres.2014.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/16/2014] [Accepted: 04/18/2014] [Indexed: 11/23/2022]
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10
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A transitional hydrolase to glycosynthase mutant by Glu to Asp substitution at the catalytic nucleophile in a retaining glycosidase. Carbohydr Res 2014; 389:85-92. [DOI: 10.1016/j.carres.2014.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 02/01/2014] [Accepted: 02/02/2014] [Indexed: 11/21/2022]
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11
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McCleary BV, Mangan D, Daly R, Fort S, Ivory R, McCormack N. Novel substrates for the measurement of endo-1,4-β-glucanase (endo-cellulase). Carbohydr Res 2014; 385:9-17. [DOI: 10.1016/j.carres.2013.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/02/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
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12
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Biarnés X, Ardèvol A, Iglesias-Fernández J, Planas A, Rovira C. Catalytic Itinerary in 1,3-1,4-β-Glucanase Unraveled by QM/MM Metadynamics. Charge Is Not Yet Fully Developed at the Oxocarbenium Ion-like Transition State. J Am Chem Soc 2011; 133:20301-9. [DOI: 10.1021/ja207113e] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Carme Rovira
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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13
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Planas A, Nieto J, Abel M, Segade A. Unusual Role of the 3-OH Group of Oligosaccharide Substrates in the Mechanism ofBacillus1,3-1,4-β-glucanase. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001618500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Greig IR, Macauley MS, Williams IH, Vocadlo DJ. Probing synergy between two catalytic strategies in the glycoside hydrolase O-GlcNAcase using multiple linear free energy relationships. J Am Chem Soc 2010; 131:13415-22. [PMID: 19715310 DOI: 10.1021/ja904506u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human O-GlcNAcase plays an important role in regulating the post-translational modification of serine and threonine residues with beta-O-linked N-acetylglucosamine monosaccharide unit (O-GlcNAc). The mechanism of O-GlcNAcase involves nucleophilic participation of the 2-acetamido group of the substrate to displace a glycosidically linked leaving group. The tolerance of this enzyme for variation in substrate structure has enabled us to characterize O-GlcNAcase transition states using several series of substrates to generate multiple simultaneous free-energy relationships. Patterns revealing changes in mechanism, transition state, and rate-determining step upon concomitant variation of both nucleophilic strength and leaving group abilities are observed. The observed changes in mechanism reflect the roles played by the enzymic general acid and the catalytic nucleophile. Significantly, these results illustrate how the enzyme synergistically harnesses both modes of catalysis; a feature that eludes many small molecule models of catalysis. These studies also suggest the kinetic significance of an oxocarbenium ion intermediate in the O-GlcNAcase-catalyzed hydrolysis of glucosaminides, probing the limits of what may be learned using nonatomistic investigations of enzymic transition-state structure and offering general insights into how the superfamily of retaining glycoside hydrolases act as efficient catalysts.
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Affiliation(s)
- Ian R Greig
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6
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15
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Greig IR. The analysis of enzymic free energy relationships using kinetic and computational models. Chem Soc Rev 2010; 39:2272-301. [DOI: 10.1039/b902741f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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16
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Abel M, Segade A, Planas A. Synthesis of an aryl 2-deoxy-β-glycosyl tetrasaccharide to probe retaining endo-glycosidase mechanism. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Li X, Huang L, Hu X, Huang X. Thio-arylglycosides with various aglycon para-substituents: a probe for studying chemical glycosylation reactions. Org Biomol Chem 2009; 7:117-27. [PMID: 19081954 PMCID: PMC2677192 DOI: 10.1039/b813048e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three series of thioglycosyl donors differing only in their respective aglycon substituents within each series have been prepared as representatives of typical glycosyl donors. The relative anomeric reactivities of these donors were quantified under competitive glycosylation conditions with various reaction time, promoters, solvents and acceptors. Over three orders of magnitude reactivity difference were generated by simple transformation of the para-substituent on the aglycon with methanol as the acceptor, while chemoselectivities became lower with carbohydrate acceptors. Excellent linear correlations were attained between relative reactivity values of donors and sigma(p) values of the substituents in the Hammett plots. This indicates that the glycosylation mechanism remains the same over a wide range of reactivities and glycosylation conditions. The negative slopes of the Hammett plots suggested that electron donating substituents expedite the reactions and the magnitudes of slopes can be rationalized by neighboring group participation as well as electronic properties of the glycon protective groups. Within the same series of donors, less nucleophilic acceptors gave smaller slopes in their Hammett plots. This is consistent with the notion that acceptor nucleophilic attack onto the reactive intermediate is part of the rate limiting step of the glycosylation reaction.
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Affiliation(s)
- Xiaoning Li
- Department of Chemistry, The University of Toledo, 2801 W. Bancroft Street, MS 602, Toledo, OH 43606
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18
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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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19
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Trincone A, Giordano A, Perugino G, Rossi M, Moracci M. Glycosynthase-Catalysed syntheses at pH below neutrality. Bioorg Med Chem Lett 2003; 13:4039-42. [PMID: 14592503 DOI: 10.1016/j.bmcl.2003.08.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The use of the new glycosynthase Ta-beta-GlyE386G and of the already known Ss-beta-GlyE387G for the synthesis of interesting 4-methylumbelliferyl disaccharides and for the galactosylation of alpha- and beta-xylosides of 4-penten-1-ol is reported. The results show satisfactory yields of reaction in presence of low excesses of acceptors and demonstrated that the high activity of these enzymes at pH below neutrality is applicable in the transfer of glucose as well as of galactose from the preferred 2-NP-based donors.
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Affiliation(s)
- Antonio Trincone
- Istituto di Chimica Biomolecolare C.N.R., Via Campi Flegrei 34, 80072 Pozzuoli, Naples, Italy.
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20
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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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21
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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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22
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Viladot JL, Canals F, Batllori X, Planas A. Long-lived glycosyl-enzyme intermediate mimic produced by formate re-activation of a mutant endoglucanase lacking its catalytic nucleophile. Biochem J 2001; 355:79-86. [PMID: 11256951 PMCID: PMC1221714 DOI: 10.1042/0264-6021:3550079] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mutant E134A 1,3-1,4-beta-glucanase from Bacillus licheniformis, in which the catalytic nucleophilic residue has been removed by mutation to alanine, has its hydrolytic activity rescued by exogenous formate in a concentration-dependent manner. A long-lived alpha-glycosyl formate is detected and identified by (1)H-NMR and matrix-assisted laser desorption ionization-time-of-flight-MS. The intermediate is kinetically competent, since it is, at least partially, enzymically hydrolysed, and able to act as a glycosyl donor in transglycosylation reactions. This transient compound represents a true covalent glycosyl-enzyme intermediate mimic of the proposed covalent intermediate in the reaction mechanism of retaining glycosidases.
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Affiliation(s)
- J L Viladot
- Laboratori de Bioquímica, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain
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23
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Planas A. Bacterial 1,3-1,4-beta-glucanases: structure, function and protein engineering. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1543:361-382. [PMID: 11150614 DOI: 10.1016/s0167-4838(00)00231-4] [Citation(s) in RCA: 197] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
1,3-1,4-beta-Glucanases (or lichenases, EC 3.2.1.73) hydrolyse linear beta-glucans containing beta-1,3 and beta-1,4 linkages such as cereal beta-glucans and lichenan, with a strict cleavage specificity for beta-1,4 glycosidic bonds on 3-O-substituted glucosyl residues. The bacterial enzymes are retaining glycosyl hydrolases of family 16 with a jellyroll beta-sandwich fold and a substrate binding cleft composed of six subsites. The present paper reviews the structure-function aspects of the enzymatic action including mechanistic enzymology, protein engineering and X-ray crystallographic studies.
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Affiliation(s)
- A Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta, 390, 08017, Barcelona, Spain.
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24
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Piotukh K, Serra V, Borriss R, Planas A. Protein-carbohydrate interactions defining substrate specificity in Bacillus 1,3-1,4-beta-D-glucan 4-glucanohydrolases as dissected by mutational analysis. Biochemistry 1999; 38:16092-104. [PMID: 10587432 DOI: 10.1021/bi991690q] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The carbohydrate-binding site of Bacillus macerans 1,3-1, 4-beta-D-glucan 4-glucanohydrolase has been analyzed through a mutational analysis to probe the role of protein-carbohydrate interactions defining substrate specificity. Amino acid residues involved in substrate binding were proposed on the basis of a modeled enzyme-substrate complex [Hahn, M., Keitel, T., and Heinemann, U. (1995) Eur. J. Biochem. 232, 849-859]. The effects of the mutations at 15 selected residues on catalysis and binding were determined by steady-state kinetics using a series of chromogenic substrates of different degree of polymerization to assign the individual H-bond and hydrophobic contributions to individual subsites in the binding site cleft. The glucopyranose rings at subsites -III and -II are tightly bound by a number of H-bond interactions to Glu61, Asn24, Tyr92, and Asn180. From k(cat)/K(M) values, single H-bonds account for 1.8-2.2 kcal mol(-)(1) transition-state (TS) stabilization, and a charged H-bond contributes up to 3.5 kcal mol(-)(1). Glu61 forms a bidentated H-bond in subsites -III and -II, and provides up to 6.5 kcal mol(-)(1) TS stabilization. With a disaccharide substrate that fills subsites -I and -II, activation kinetics were observed for the wild-type and mutant enzymes except for mutations on Glu61, pointing to an important role of the bidentate interaction of Glu61 in two subsites. Whereas removal of the hydroxyl group of Tyr121, initially proposed to hydrogen-bond with the 2OH of Glcp-I, has essentially no effect (Y121F mutant), side-chain removal (Y121A mutant) gave a 100-fold reduction in k(cat)/K(M) and a 10-fold lower K(I) value with a competitive inhibitor. In subsite -IV, only a stacking interaction with Tyr22 (0.7 kcal mol(-)(1) TS stabilization) is observed.
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Affiliation(s)
- K Piotukh
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
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Viladot JL, Stone B, Driguez H, Planas A. Expeditious synthesis of a new hexasaccharide using transglycosylation reaction catalyzed by Bacillus (1-->3),(1-->4)-Beta-D-glucan 4-glucanohydrolase. Carbohydr Res 1998; 311:95-9. [PMID: 9821269 DOI: 10.1016/s0008-6215(98)00212-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Enzymatic hydrolysis of barley (1-->3),(1-->4)-beta-D-glucan using a recombinant (1-->3),(1-->4)-beta-glucanase from Bacillus licheniformis gives Glc beta 4Glc beta 3Glc isolated after acetylation in 49% yield. Conventional treatment produced the corresponding beta-fluoride which was carefully de-O-acetylated. A transglycosylation reaction with this substrate, catalyzed by the title enzyme, gave Glc beta 4Glc beta 3Glc beta 4Glc beta 4Glc beta 3Glc in 20% yield.
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Affiliation(s)
- J L Viladot
- Laboratori de Bioquímica, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
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