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Identification of the nucleophile catalytic residue of GH51 α-L-arabinofuranosidase from Pleurotus ostreatus. AMB Express 2015; 5:79. [PMID: 26690659 PMCID: PMC4686458 DOI: 10.1186/s13568-015-0164-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/12/2015] [Indexed: 11/21/2022] Open
Abstract
In this study, the recombinant α-l-arabinofuranosidase from the fungus Pleurotus ostreatus (rPoAbf) was subjected to site-directed mutagenesis in order to identify the catalytic nucleophile residue. Based on bioinformatics and homology modelling analyses, E449 was revealed to be the potential nucleophilic residue. Thus, the mutant E449G of PoAbf was recombinantly expressed in Pichia pastoris and its recombinant expression level and reactivity were investigated in comparison to the wild-type. The design of a suitable set of hydrolysis experiments in the presence or absence of alcoholic arabinosyl acceptors and/or formate salts allowed to unambiguously identify the residue E449 as the nucleophile residue involved in the retaining mechanism of this GH51 arabinofuranosidase. 1H NMR analysis was applied for the identification of the products and the assignement of their anomeric configuration.
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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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Teze D, Dion M, Daligault F, Tran V, André-Miral C, Tellier C. Alkoxyamino glycoside acceptors for the regioselective synthesis of oligosaccharides using glycosynthases and transglycosidases. Bioorg Med Chem Lett 2013; 23:448-51. [DOI: 10.1016/j.bmcl.2012.11.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/13/2012] [Accepted: 11/18/2012] [Indexed: 12/01/2022]
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Tiwari MK, Lee KM, Kalyani D, Singh RK, Kim H, Lee JK, Ramachandran P. Role of Glu445 in the substrate binding of β-glucosidase. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cobucci-Ponzano B, Moracci M. Glycosynthases as tools for the production of glycan analogs of natural products. Nat Prod Rep 2012; 29:697-709. [DOI: 10.1039/c2np20032e] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Cobucci-Ponzano B, Perugino G, Strazzulli A, Rossi M, Moracci M. Thermophilic Glycosynthases for Oligosaccharides Synthesis. Methods Enzymol 2012; 510:273-300. [DOI: 10.1016/b978-0-12-415931-0.00015-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Ramachandran P, Tiwari MK, Singh RK, Haw JR, Jeya M, Lee JK. Cloning and characterization of a putative β-glucosidase (NfBGL595) from Neosartorya fischeri. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.10.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Molecular characterization of endo-1,3-β-glucanase from Cellulosimicrobium cellulans: Effects of carbohydrate-binding module on enzymatic function and stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1713-9. [DOI: 10.1016/j.bbapap.2011.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 09/07/2011] [Accepted: 09/19/2011] [Indexed: 11/21/2022]
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D’Almeida A, Ionata M, Tran V, Tellier C, Dion M, Rabiller C. An expeditious and efficient synthesis of β-d-galactopyranosyl-(1→3)-d-N-acetylglucosamine (lacto-N-biose) using a glycosynthase from Thermus thermophilus as a catalyst. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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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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12
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Benzoate methanolysis catalyzed by α-cyclosophorohexadecaose isolated from Xanthomonas oryzae. Carbohydr Polym 2007. [DOI: 10.1016/j.carbpol.2007.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Wan CF, Chen WH, Chen CT, Chang MT, Lo LC, Li YK. Mutagenesis and mechanistic study of a glycoside hydrolase family 54 alpha-L-arabinofuranosidase from Trichoderma koningii. Biochem J 2007; 401:551-8. [PMID: 17002602 PMCID: PMC1820808 DOI: 10.1042/bj20060717] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 09/27/2006] [Accepted: 09/27/2006] [Indexed: 11/17/2022]
Abstract
A GH (glycoside hydrolase) family 54 alpha-L-arabinofuranosidase from Trichoderma koningii G-39 (termed Abf) was successfully expressed in Pichia pastoris and purified to near homogeneity by cation-exchange chromatography. To determine the amino acid residues essential for the catalytic activity of Abf, extensive mutagenesis of 24 conserved glutamate and aspartate residues was performed. Among the mutants, D221N, E223Q and D299N were found to decrease catalytic activity significantly. The kcat values of the D221N and D299N mutants were 7000- and 1300-fold lower respectively, than that of the wild-type Abf. E223Q was nearly inactive. These results are consistent with observations obtained from the Aspergillus kawachii alpha-L-arabinofuranosidase three-dimensional structure. This structure indicates that Asp221 of T. koningii Abf is significant for substrate binding and that Glu223 as well as Asp299 function as a nucleophile and a general acid/base catalyst for the enzymatic reaction respectively. The catalytic mechanism of wild-type Abf was further investigated by NMR spectroscopy and kinetic analysis. The results showed that Abf is a retaining enzyme. It catalyses the hydrolysis of various substrates via the formation of a common intermediate that is probably an arabinosyl-enzyme intermediate. A two-step, double-displacement mechanism involving first the formation, and then the breakdown, of an arabinosyl-enzyme intermediate was proposed. Based on the kcat values of a series of aryl-alpha-L-arabinofuranosides catalytically hydrolysed by wild-type Abf, a relatively small Brønsted constant, beta(lg)=-0.18, was obtained, suggesting that the rate-limiting step of the enzymatic reaction is the dearabinosylation step. Further kinetic studies with the D299G mutant revealed that the catalytic activity of this mutant depended largely on the pK(a) values (>6) of leaving phenols, with beta(lg)=-1.3, indicating that the rate-limiting step of the reaction becomes the arabinosylation step. This kinetic outcome supports the idea that Asp299 is the general acid/base residue. The pH activity profile of D299N provided further evidence strengthening this suggestion.
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Key Words
- α-l-arabinofuranosidase
- brønsted plot
- catalytic mechanism
- glycoside hydrolase
- site-directed mutagenesis
- trichoderma koningii
- abf, glycoside hydrolase family 54 α-l-arabinofuranosidase from trichoderma koningii g-39
- gh, glycoside hydrolase
- cnpaf, 4-chloro-2-nitrophenyl-α-l-arabinofuranoside
- 2,5-dnpaf, 2,5-dinitrophenyl-α-l-arabinofuranoside
- maf, methyl-α-l-arabinofuranoside
- mnpaf, m-nitrophenyl-α-l-arabinofuranoside
- paf, phenyl-α-l-arabinofuranoside
- pcpaf, p-cyanophenyl-α-l-arabinofuranoside
- pnpaf, p-nitrophenyl-α-l-arabinofuranoside
- p.p.m., parts per million
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Affiliation(s)
- Chin-Feng Wan
- *Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
| | - Wei-Hong Chen
- *Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
| | - Cheng-Ta Chen
- *Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
| | | | - Lee-Chiang Lo
- ‡Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yaw-Kuen Li
- *Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
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Neustroev KN, Golubev AM, Sinnott ML, Borriss R, Krah M, Brumer H, Eneyskaya EV, Shishlyannikov S, Shabalin KA, Peshechonov VT, Korolev VG, Kulminskaya AA. Transferase and hydrolytic activities of the laminarinase from rhodothermus marinus and its M133A, M133C, and M133W mutants. Glycoconj J 2006; 23:501-11. [PMID: 17006642 DOI: 10.1007/s10719-006-6733-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 11/14/2005] [Accepted: 12/21/2005] [Indexed: 10/24/2022]
Abstract
Comparative studies of the transglycosylation and hydrolytic activities have been performed on the Rhodothermus marinus beta-1,3-glucanase (laminarinase) and its M133A, M133C, and M133W mutants. The M133C mutant demonstrated near 20% greater rate of transglycosylation activity in comparison with the M133A and M133W mutants that was measured by NMR quantitation of nascent beta(1-4) and beta(1-6) linkages. To obtain kinetic probes for the wild-type enzyme and Met-133 mutants, p-nitrophenyl beta-laminarin oligosaccharides of degree of polymerisation 2-8 were synthesized enzymatically. Catalytic efficiency values, k (cat)/K (m), of the laminarinase catalysed hydrolysis of these oligosaccharides suggested possibility of four negative and at least three positive binding subsites in the active site. Comparison of action patterns of the wild-type and M133C mutant in the hydrolysis of the p-nitrophenyl-beta-D-oligosac- charides indicated that the increased transglycosylation activity of the M133C mutant did not result from altered subsite affinities. The stereospecificity of the transglycosylation reaction also was unchanged in all mutants; the major transglycosylation products in hydrolysis of p-nitrophenyl laminaribioside were beta-glucopyranosyl-beta-1,3-D-glucopy- ranosyl-beta-1,3-D-glucopyranose and beta-glucopyranosyl-beta-1, 3-D-glucopyranosyl-beta-1,3-D-glucpyranosyl-beta-1,3-D- glucopyranoxside.
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Affiliation(s)
- Kirill N Neustroev
- Molecular and Radiation Biology Division, Petersburg Nuclear Physics Institute, Russian Academy of Science, Gatchina, 188300, Russia
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Saura-Valls M, Fauré R, Ragàs S, Piens K, Brumer H, Teeri T, Cottaz S, Driguez H, Planas A. Kinetic analysis using low-molecular mass xyloglucan oligosaccharides defines the catalytic mechanism of a Populus xyloglucan endotransglycosylase. Biochem J 2006; 395:99-106. [PMID: 16356166 PMCID: PMC1409682 DOI: 10.1042/bj20051396] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Plant XETs [XG (xyloglucan) endotransglycosylases] catalyse the transglycosylation from a XG donor to a XG or low-molecular-mass XG fragment as the acceptor, and are thought to be important enzymes in the formation and remodelling of the cellulose-XG three-dimensional network in the primary plant cell wall. Current methods to assay XET activity use the XG polysaccharide as the donor substrate, and present limitations for kinetic and mechanistic studies of XET action due to the polymeric and polydisperse nature of the substrate. A novel activity assay based on HPCE (high performance capillary electrophoresis), in conjunction with a defined low-molecular-mass XGO {XG oligosaccharide; (XXXGXXXG, where G=Glcbeta1,4- and X=[Xylalpha1,6]Glcbeta1,4-)} as the glycosyl donor and a heptasaccharide derivatized with ANTS [8-aminonaphthalene-1,3,6-trisulphonic acid; (XXXG-ANTS)] as the acceptor substrate was developed and validated. The recombinant enzyme PttXET16A from Populus tremula x tremuloides (hybrid aspen) was characterized using the donor/acceptor pair indicated above, for which preparative scale syntheses have been optimized. The low-molecular-mass donor underwent a single transglycosylation reaction to the acceptor substrate under initial-rate conditions, with a pH optimum at 5.0 and maximal activity between 30 and 40 degrees C. Kinetic data are best explained by a ping-pong bi-bi mechanism with substrate inhibition by both donor and acceptor. This is the first assay for XETs using a donor substrate other than polymeric XG, enabling quantitative kinetic analysis of different XGO donors for specificity, and subsite mapping studies of XET enzymes.
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Affiliation(s)
- Marc Saura-Valls
- *Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Régis Fauré
- †CERMAV-ICMG-FR-CNRS 2607, 38041 Grenoble Cedex 9, France
| | - Sergi Ragàs
- *Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Kathleen Piens
- ‡School of Biotechnology, Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Harry Brumer
- ‡School of Biotechnology, Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Tuula T. Teeri
- ‡School of Biotechnology, Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Sylvain Cottaz
- †CERMAV-ICMG-FR-CNRS 2607, 38041 Grenoble Cedex 9, France
| | - Hugues Driguez
- †CERMAV-ICMG-FR-CNRS 2607, 38041 Grenoble Cedex 9, France
| | - Antoni Planas
- *Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain
- To whom correspondence should be addressed (email )
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