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Jana S, Hamre AG, Wildberger P, Holen MM, Eijsink VGH, Beckham GT, Sørlie M, Payne CM. Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases. J Phys Chem B 2016; 120:1236-49. [PMID: 26824449 DOI: 10.1021/acs.jpcb.5b12610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microorganisms use a host of enzymes, including processive glycoside hydrolases, to deconstruct recalcitrant polysaccharides to sugars. Processive glycoside hydrolases closely associate with polymer chains and repeatedly cleave glycosidic linkages without dissociating from the crystalline surface after each hydrolytic step; they are typically the most abundant enzymes in both natural secretomes and industrial cocktails by virtue of their significant hydrolytic potential. The ubiquity of aromatic residues lining the enzyme catalytic tunnels and clefts is a notable feature of processive glycoside hydrolases. We hypothesized that these aromatic residues have uniquely defined roles, such as substrate chain acquisition and binding in the catalytic tunnel, that are defined by their local environment and position relative to the substrate and the catalytic center. Here, we investigated this hypothesis with variants of Serratia marcescens family 18 processive chitinases ChiA and ChiB. We applied molecular simulation and free energy calculations to assess active site dynamics and ligand binding free energies. Isothermal titration calorimetry provided further insight into enthalpic and entropic contributions to ligand binding free energy. Thus, the roles of six aromatic residues, Trp-167, Trp-275, and Phe-396 in ChiA, and Trp-97, Trp-220, and Phe-190 in ChiB, have been examined. We observed that point mutation of the tryptophan residues to alanine results in unfavorable changes in the free energy of binding relative to wild-type. The most drastic effects were observed for residues positioned at the "entrances" of the deep substrate-binding clefts and known to be important for processivity. Interestingly, phenylalanine mutations in ChiA and ChiB had little to no effect on chito-oligomer binding, in accordance with the limited effects of their removal on chitinase functionality.
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Affiliation(s)
- Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
| | - Anne Grethe Hamre
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Patricia Wildberger
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Matilde Mengkrog Holen
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Morten Sørlie
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
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Wildberger P, Pfeiffer M, Brecker L, Nidetzky B. Diastereoselektive Synthese von Glykosylphosphaten mit einem Phosphorylase‐Phosphatase‐Kombikatalysator. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Patricia Wildberger
- Institut für Biotechnologie und Bioprozesstechnik, Technische Universität Graz, Petersgasse 12, 8010 Graz (Österreich)
| | - Martin Pfeiffer
- Institut für Biotechnologie und Bioprozesstechnik, Technische Universität Graz, Petersgasse 12, 8010 Graz (Österreich)
| | - Lothar Brecker
- Institut für Organische Chemie, Universität Wien, Währingerstraße 38, 1090 Wien (Österreich)
| | - Bernd Nidetzky
- Institut für Biotechnologie und Bioprozesstechnik, Technische Universität Graz, Petersgasse 12, 8010 Graz (Österreich)
- acib – Austrian Centre of Industrial Biotechnology (Österreich)
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Wildberger P, Pfeiffer M, Brecker L, Nidetzky B. Diastereoselective Synthesis of Glycosyl Phosphates by Using a Phosphorylase-Phosphatase Combination Catalyst. Angew Chem Int Ed Engl 2015; 54:15867-71. [PMID: 26565075 PMCID: PMC4737314 DOI: 10.1002/anie.201507710] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 11/10/2022]
Abstract
Sugar phosphates play an important role in metabolism and signaling, but also as constituents of macromolecular structures. Selective phosphorylation of sugars is chemically difficult, particularly at the anomeric center. We report phosphatase-catalyzed diastereoselective "anomeric" phosphorylation of various aldose substrates with α-D-glucose 1-phosphate, derived from phosphorylase-catalyzed conversion of sucrose and inorganic phosphate, as the phosphoryl donor. Simultaneous and sequential two-step transformations by the phosphorylase-phosphatase combination catalyst yielded glycosyl phosphates of defined anomeric configuration in yields of up to 70 % based on the phosphate applied to the reaction. An efficient enzyme-assisted purification of the glycosyl phosphate products from reaction mixtures was established.
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Affiliation(s)
- Patricia Wildberger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, 8010 Graz (Austria)
| | - Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, 8010 Graz (Austria)
| | - Lothar Brecker
- Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090 Vienna (Austria)
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, 8010 Graz (Austria). .,acib - Austrian Centre of Industrial Biotechnology (Austria).
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Wildberger P, Aish GA, Jakeman DL, Brecker L, Nidetzky B. Interplay of catalytic subsite residues in the positioning of α-d-glucose 1-phosphate in sucrose phosphorylase. Biochem Biophys Rep 2015; 2:36-44. [PMID: 26380381 PMCID: PMC4554294 DOI: 10.1016/j.bbrep.2015.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 12/01/2022] Open
Abstract
Kinetic and molecular docking studies were performed to characterize the binding of α-d-glucose 1-phosphate (αGlc 1-P) at the catalytic subsite of a family GH-13 sucrose phosphorylase (from L. mesenteroides) in wild-type and mutated form. The best-fit binding mode of αGlc 1-P dianion had the phosphate group placed anti relative to the glucosyl moiety (adopting a relaxed 4C1 chair conformation) and was stabilized mainly by hydrogen bonds from residues of the enzyme׳s catalytic triad (Asp196, Glu237 and Asp295) and from Arg137. Additional feature of the αGlc 1-P docking pose was an intramolecular hydrogen bond (2.7 Å) between the glucosyl C2-hydroxyl and the phosphate oxygen. An inactive phosphonate analog of αGlc 1-P did not show binding to sucrose phosphorylase in different experimental assays (saturation transfer difference NMR, steady-state reversible inhibition), consistent with evidence from molecular docking study that also suggested a completely different and strongly disfavored binding mode of the analog as compared to αGlc 1-P. Molecular docking results also support kinetic data in showing that mutation of Phe52, a key residue at the catalytic subsite involved in transition state stabilization, had little effect on the ground-state binding of αGlc 1-P by the phosphorylase. However, when combined with a second mutation involving one of the catalytic triad residues, the mutation of Phe52 by Ala caused complete (F52A_D196A; F52A_E237A) or very large (F52A_D295A) disruption of the proposed productive binding mode of αGlc 1-P with consequent effects on the enzyme activity. Effects of positioning of αGlc 1-P for efficient glucosyl transfer from phosphate to the catalytic nucleophile of the enzyme (Asp196) are suggested. High similarity between the αGlc 1-P conformers bound to sucrose phosphorylase (modeled) and the structurally and mechanistically unrelated maltodextrin phosphorylase (experimental) is revealed.
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Affiliation(s)
- Patricia Wildberger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010 Graz, Austria
| | - Gaia A. Aish
- College of Pharmacy, Dalhousie University, PO Box 15,000, 5968 College Street, Halifax, Nova Scotia, Canada B3H 4R2
| | - David L. Jakeman
- College of Pharmacy, Dalhousie University, PO Box 15,000, 5968 College Street, Halifax, Nova Scotia, Canada B3H 4R2
| | - Lothar Brecker
- Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, A-1090 Vienna, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
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Pfeiffer M, Wildberger P, Nidetzky B. Yihx-encoded haloacid dehalogenase-like phosphatase HAD4 from Escherichia coli is a specific α-d-glucose 1-phosphate hydrolase useful for substrate-selective sugar phosphate transformations. ACTA ACUST UNITED AC 2014; 110:39-46. [PMID: 25484615 PMCID: PMC4251788 DOI: 10.1016/j.molcatb.2014.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 11/30/2022]
Abstract
Functional expression of Escherichia coli haloacid dehalogenase-like phosphatase 4 (HAD4). Characterization of HAD4 fusion to the cationic module Zbasic2. Single-step capture and polishing purification of Zbasic2_HAD4. Selective conversion of α-d-glucose 1-phosphate in mixture with glucose 6-phosphate. Oriented immobilization with high effectiveness of Zbasic2_HAD4 on porous support.
Phosphomonoester hydrolases (phosphatases; EC 3.1.3.) often exhibit extremely relaxed substrate specificity which limits their application to substrate-selective biotransformations. In search of a phosphatase catalyst specific for hydrolyzing α-d-glucose 1-phosphate (αGlc 1-P), we selected haloacid dehalogenase-like phosphatase 4 (HAD4) from Escherichia coli and obtained highly active recombinant enzyme through a fusion protein (Zbasic2_HAD4) that contained Zbasic2, a strongly positively charged three α-helical bundle module, at its N-terminus. Highly pure Zbasic2_HAD4 was prepared directly from E. coli cell extract using capture and polishing combined in a single step of cation exchange chromatography. Kinetic studies showed Zbasic2_HAD4 to exhibit 565-fold preference for hydrolyzing αGlc 1-P (kcat/KM = 1.87 ± 0.03 mM−1 s−1; 37 °C, pH 7.0) as compared to d-glucose 6-phosphate (Glc 6-P). Also among other sugar phosphates, αGlc 1-P was clearly preferred. Using different mixtures of αGlc 1-P and Glc 6-P (e.g. 180 mM each) as the substrate, Zbasic2_HAD4 could be used to selectively convert the αGlc 1-P present, leaving back all of the Glc 6-P for recovery. Zbasic2_HAD4 was immobilized conveniently using direct loading of E. coli cell extract on sulfonic acid group-containing porous carriers, yielding a recyclable heterogeneous biocatalyst that was nearly as effective as the soluble enzyme, probably because protein attachment to the anionic surface occurred in a preferred orientation via the cationic Zbasic2 module. Selective removal of αGlc 1-P from sugar phosphate preparations could be an interesting application of Zbasic2_HAD4 for which readily available broad-spectrum phosphatases are unsuitable.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, A-8010 Graz, Austria
| | - Patricia Wildberger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, A-8010 Graz, Austria ; ACIB - Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
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Wildberger P, Brecker L, Nidetzky B. Chiral resolution through stereoselective transglycosylation by sucrose phosphorylase: application to the synthesis of a new biomimetic compatible solute, (R)-2-O-α-D-glucopyranosyl glyceric acid amide. Chem Commun (Camb) 2014; 50:436-8. [PMID: 24253490 DOI: 10.1039/c3cc47249c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sucrose phosphorylase catalysed glycosylation of glyceric acid amide with complete regio- and diastereo-selectivity is studied. (R)-2-O-α-D-Glucopyranosyl glyceric acid amide was obtained in high yield from single-step transformation of racemic glyceric acid amide and sucrose. Non-productive binding of (S)-glyceric acid amide appeared to underlie strict enantiodiscrimination by the enzyme, thus supporting chiral resolutions based on stereoselective transglycosylation.
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Affiliation(s)
- Patricia Wildberger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, A-8010 Graz, Austria.
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Wildberger P, Todea A, Nidetzky B. Probing enzyme–substrate interactions at the catalytic subsite ofLeuconostoc mesenteroidessucrose phosphorylase with site-directed mutagenesis: the roles of Asp49and Arg395. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.674720] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Wildberger P, Luley-Goedl C, Nidetzky B. Aromatic interactions at the catalytic subsite of sucrose phosphorylase: Their roles in enzymatic glucosyl transfer probed with Phe52
→ Ala and Phe52
→ Asn mutants. FEBS Lett 2011; 585:499-504. [DOI: 10.1016/j.febslet.2010.12.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 12/23/2010] [Accepted: 12/29/2010] [Indexed: 10/18/2022]
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Luley-Goedl C, Sawangwan T, Brecker L, Wildberger P, Nidetzky B. Regioselective O-glucosylation by sucrose phosphorylase: a promising route for functional diversification of a range of 1,2-propanediols. Carbohydr Res 2010; 345:1736-40. [DOI: 10.1016/j.carres.2010.05.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 05/12/2010] [Accepted: 05/22/2010] [Indexed: 12/31/2022]
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Goedl C, Sawangwan T, Wildberger P, Nidetzky B. Sucrose phosphorylase: a powerful transglucosylation catalyst for synthesis of α-D-glucosides as industrial fine chemicals. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242420903411595] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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