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Cuxart I, Coines J, Esquivias O, Faijes M, Planas A, Biarnés X, Rovira C. Enzymatic Hydrolysis of Human Milk Oligosaccharides. The Molecular Mechanism of Bifidobacterium Bifidum Lacto- N-biosidase. ACS Catal 2022; 12:4737-4743. [PMID: 35465242 PMCID: PMC9016705 DOI: 10.1021/acscatal.2c00309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/26/2022] [Indexed: 12/22/2022]
Abstract
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Bifidobacterium
bifidum lacto-N-biosidase (LnbB)
is a critical enzyme for the degradation
of human milk oligosaccharides in the gut microbiota of breast-fed
infants. Guided by recent crystal structures, we unveil its molecular
mechanism of catalysis using QM/MM metadynamics. We show that the
oligosaccharide substrate follows 1S3/1,4B → [4E]‡ → 4C1/4H5 and 4C1/4H5 → [4E/4H5]‡ → 1,4B conformational itineraries for the two
successive reaction steps, with reaction free energy barriers in agreement
with experiments. The simulations also identify a critical histidine
(His263) that switches between two orientations to modulate the pKa of the acid/base residue, facilitating catalysis.
The reaction intermediate of LnbB is best depicted as an oxazolinium
ion, with a minor population of neutral oxazoline. The present study
sheds light on the processing of oligosaccharides of the early life
microbiota and will be useful for the engineering of LnbB and similar
glycosidases for biocatalysis.
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Affiliation(s)
- Irene Cuxart
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Oriol Esquivias
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08020 Barcelona, Spain
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2
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Coines J, Cuxart I, Teze D, Rovira C. Computer Simulation to Rationalize “Rational” Engineering of Glycoside Hydrolases and Glycosyltransferases. J Phys Chem B 2022; 126:802-812. [PMID: 35073079 PMCID: PMC8819650 DOI: 10.1021/acs.jpcb.1c09536] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
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Glycoside hydrolases
and glycosyltransferases are the main classes
of enzymes that synthesize and degrade carbohydrates, molecules essential
to life that are a challenge for classical chemistry. As such, considerable
efforts have been made to engineer these enzymes and make them pliable
to human needs, ranging from directed evolution to rational design,
including mechanism engineering. Such endeavors fall short and are
unreported in numerous cases, while even success is a necessary but
not sufficient proof that the chemical rationale behind the design
is correct. Here we review some of the recent work in CAZyme mechanism
engineering, showing that computational simulations are instrumental
to rationalize experimental data, providing mechanistic insight into
how native and engineered CAZymes catalyze chemical reactions. We
illustrate this with two recent studies in which (i) a glycoside hydrolase
is converted into a glycoside phosphorylase and (ii) substrate specificity
of a glycosyltransferase is engineered toward forming O-, N-, or S-glycosidic bonds.
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Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Irene Cuxart
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - David Teze
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
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3
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Discovery of Octahydroisoindolone as a Scaffold for the Selective Inhibition of Chitinase B1 from Aspergillus fumigatus: In Silico Drug Design Studies. Molecules 2021; 26:molecules26247606. [PMID: 34946697 PMCID: PMC8705689 DOI: 10.3390/molecules26247606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 11/21/2022] Open
Abstract
Chitinases represent an alternative therapeutic target for opportunistic invasive mycosis since they are necessary for fungal cell wall remodeling. This study presents the design of new chitinase inhibitors from a known hydrolysis intermediate. Firstly, a bioinformatic analysis of Aspergillus fumigatus chitinase B1 (AfChiB1) and chitotriosidase (CHIT1) by length and conservation was done to obtain consensus sequences, and molecular homology models of fungi and human chitinases were built to determine their structural differences. We explored the octahydroisoindolone scaffold as a potential new antifungal series by means of its structural and electronic features. Therefore, we evaluated several synthesis-safe octahydroisoindolone derivatives by molecular docking and evaluated their AfChiB1 interaction profile. Additionally, compounds with the best interaction profile (1–5) were docked within the CHIT1 catalytic site to evaluate their selectivity over AfChiB1. Furthermore, we considered the interaction energy (MolDock score) and a lipophilic parameter (aLogP) for the selection of the best candidates. Based on these descriptors, we constructed a mathematical model for the IC50 prediction of our candidates (60–200 μM), using experimental known inhibitors of AfChiB1. As a final step, ADME characteristics were obtained for all the candidates, showing that 5 is our best designed hit, which possesses the best pharmacodynamic and pharmacokinetic character.
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4
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Mészáros Z, Nekvasilová P, Bojarová P, Křen V, Slámová K. Reprint of: Advanced glycosidases as ingenious biosynthetic instruments. Biotechnol Adv 2021; 51:107820. [PMID: 34462167 DOI: 10.1016/j.biotechadv.2021.107820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 11/27/2022]
Abstract
Until recently, glycosidases, naturally hydrolyzing carbohydrate-active enzymes, have found few synthetic applications in industry, being primarily used for cleaving unwanted carbohydrates. With the establishment of glycosynthase and transglycosidase technology by genetic engineering, the view of glycosidases as industrial biotechnology tools has started to change. Their easy production, affordability, robustness, and substrate versatility, added to the possibility of controlling undesired side hydrolysis by enzyme engineering, have made glycosidases competitive synthetic tools. Current promising applications of engineered glycosidases include the production of well-defined chitooligomers, precious galactooligosaccharides or specialty chemicals such as glycosylated flavonoids. Other synthetic pathways leading to human milk oligosaccharides or remodeled antibodies are on the horizon. This work provides an overview of the synthetic achievements to date for glycosidases, emphasizing the latest trends and outlining possible developments in the field.
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Affiliation(s)
- Zuzana Mészáros
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 1903/3, CZ-16628 Praha 6, Czech Republic
| | - Pavlína Nekvasilová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, CZ-12843, Praha 2, Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Kristýna Slámová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic.
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5
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Teze D, Zhao J, Wiemann M, Kazi ZGA, Lupo R, Zeuner B, Vuillemin M, Rønne ME, Carlström G, Duus JØ, Sanejouand YH, O'Donohue MJ, Nordberg Karlsson E, Fauré R, Stålbrand H, Svensson B. Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases. Chemistry 2021; 27:10323-10334. [PMID: 33914359 DOI: 10.1002/chem.202100110] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here, a straightforward strategy that involves rational rapid in silico analysis of protein sequences is described. The method pinpoints 6-12 single-mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d/l-, α/β-pyranosides or furanosides, and exo or endo action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.
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Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Jiao Zhao
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Mathias Wiemann
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Zubaida G A Kazi
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Rossana Lupo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Birgitte Zeuner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Marlène Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Mette E Rønne
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Göran Carlström
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Jens Ø Duus
- Department of Chemistry, Technical University of Denmark, Kemitorvet, bulding 207, DK-2800, Kongens Lyngby, Denmark
| | - Yves-Henri Sanejouand
- UFIP, UMR 6286, Université de Nantes, CNRS, 2, chemin de la Houssiniere, Nantes, France
| | - Michael J O'Donohue
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | | | - Régis Fauré
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Henrik Stålbrand
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
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6
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Mendoza F, Masgrau L. Computational modeling of carbohydrate processing enzymes reactions. Curr Opin Chem Biol 2021; 61:203-213. [PMID: 33812143 DOI: 10.1016/j.cbpa.2021.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 12/14/2022]
Abstract
Carbohydrate processing enzymes are of biocatalytic interest. Glycoside hydrolases and the recently discovered lytic polysaccharide monooxygenase for their use in biomass degradation to obtain biofuels or valued chemical entities. Glycosyltransferases or engineered glycosidases and phosphorylases for the synthesis of carbohydrates and glycosylated products. Quantum mechanics-molecular mechanics (QM/MM) methods are highly contributing to establish their different chemical reaction mechanisms. Other computational methods are also used to study enzyme conformational changes, ligand pathways, and processivity, e.g. for processive glycosidases like cellobiohydrolases. There is still a long road to travel to fully understand the role of conformational dynamics in enzyme activity and also to disclose the variety of reaction mechanisms these enzymes employ. Additionally, computational tools for enzyme engineering are beginning to be applied to evaluate substrate specificity or aid in the design of new biocatalysts with increased thermostability or tailored activity, a growing field where molecular modeling is finding its way.
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Affiliation(s)
- Fernanda Mendoza
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Talcahuano, 4260000, Chile
| | - Laura Masgrau
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Institut de Biotecnología i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018, Barcelona, Spain.
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7
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Mészáros Z, Nekvasilová P, Bojarová P, Křen V, Slámová K. Advanced glycosidases as ingenious biosynthetic instruments. Biotechnol Adv 2021; 49:107733. [PMID: 33781890 DOI: 10.1016/j.biotechadv.2021.107733] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 12/22/2022]
Abstract
Until recently, glycosidases, naturally hydrolyzing carbohydrate-active enzymes, have found few synthetic applications in industry, being primarily used for cleaving unwanted carbohydrates. With the establishment of glycosynthase and transglycosidase technology by genetic engineering, the view of glycosidases as industrial biotechnology tools has started to change. Their easy production, affordability, robustness, and substrate versatility, added to the possibility of controlling undesired side hydrolysis by enzyme engineering, have made glycosidases competitive synthetic tools. Current promising applications of engineered glycosidases include the production of well-defined chitooligomers, precious galactooligosaccharides or specialty chemicals such as glycosylated flavonoids. Other synthetic pathways leading to human milk oligosaccharides or remodeled antibodies are on the horizon. This work provides an overview of the synthetic achievements to date for glycosidases, emphasizing the latest trends and outlining possible developments in the field.
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Affiliation(s)
- Zuzana Mészáros
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 1903/3, CZ-16628 Praha 6, Czech Republic
| | - Pavlína Nekvasilová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, CZ-12843, Praha 2, Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Kristýna Slámová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic.
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Morais MAB, Coines J, Domingues MN, Pirolla RAS, Tonoli CCC, Santos CR, Correa JBL, Gozzo FC, Rovira C, Murakami MT. Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations. Nat Commun 2021; 12:367. [PMID: 33446650 PMCID: PMC7809346 DOI: 10.1038/s41467-020-20620-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.
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Affiliation(s)
- Mariana A B Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Celisa C C Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Camila R Santos
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Jessica B L Correa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Fabio C Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, 13083-970, Brazil
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil.
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9
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Du JJ, Klontz EH, Guerin ME, Trastoy B, Sundberg EJ. Structural insights into the mechanisms and specificities of IgG-active endoglycosidases. Glycobiology 2020; 30:268-279. [PMID: 31172182 DOI: 10.1093/glycob/cwz042] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/22/2019] [Accepted: 06/02/2019] [Indexed: 11/12/2022] Open
Abstract
The conserved N-glycan on Asn297 of immunoglobulin G (IgG) has significant impacts on antibody effector functions, and is a frequent target for antibody engineering. Chemoenzymatic synthesis has emerged as a strategy for producing antibodies with homogenous glycosylation and improved effector functions. Central to this strategy is the use of enzymes with activity on the Asn297 glycan. EndoS and EndoS2, produced by Streptococcus pyogenes, are endoglycosidases with remarkable specificity for Asn297 glycosylation, making them ideal tools for chemoenzymatic synthesis. Although both enzymes are specific for IgG, EndoS2 recognizes a wider range of glycans than EndoS. Recent progress has been made in understanding the structural basis for their activities on antibodies. In this review, we examine the molecular mechanism of glycosidic bond cleavage by these enzymes and how specific point mutations convert them into glycosynthases. We also discuss the structural basis for differences in the glycan repertoire that IgG-active endoglycosidases recognize, which focuses on the structure of the loops within the glycoside hydrolase (GH) domain. Finally, we discuss the important contributions of carbohydrate binding modules (CBMs) to endoglycosidase activity, and how CBMs work in concert with GH domains to produce optimal activity on IgG.
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Affiliation(s)
- Jonathan J Du
- Institute of Human Virology 725 W Lombard Street, Baltimore, MD 21201, USA
| | - Erik H Klontz
- Institute of Human Virology 725 W Lombard Street, Baltimore, MD 21201, USA.,Department of Microbiology & Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street HSF-I Suite 380, Baltimore, MD 21201, USA.,Program in Molecular Microbiology & Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, HSF-I Suite 380, Baltimore, MD 21201, USA
| | - Marcelo E Guerin
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, María Díaz Haroko Kalea, 3, 48013 Bilbo, Bizkaia, Spain
| | - Beatriz Trastoy
- Program in Molecular Microbiology & Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, HSF-I Suite 380, Baltimore, MD 21201, USA
| | - Eric J Sundberg
- Institute of Human Virology 725 W Lombard Street, Baltimore, MD 21201, USA.,Department of Microbiology & Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street HSF-I Suite 380, Baltimore, MD 21201, USA.,Department of Medicine, University of Maryland School of Medicine, 655 W Baltimore St, Baltimore, MD 21201, USA
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10
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Glycoside hydrolase family 18 chitinases: The known and the unknown. Biotechnol Adv 2020; 43:107553. [DOI: 10.1016/j.biotechadv.2020.107553] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/09/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
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11
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Alsina C, Sancho-Vaello E, Aranda-Martínez A, Faijes M, Planas A. Auxiliary active site mutations enhance the glycosynthase activity of a GH18 chitinase for polymerization of chitooligosaccharides. Carbohydr Polym 2020; 252:117121. [PMID: 33183587 DOI: 10.1016/j.carbpol.2020.117121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/14/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
Depolymerization of chitin results in chitooligosaccharides (COS) that induce immunostimulatory effects and disease protective responses and have many potential applications in agriculture and medicine. Isolation of bioactive COS with degree of polymerization (DP) larger than six from chitin hydrolyzates is hampered by their water insolubility. Enzymatic synthesis by exploiting the transglycosylation activity of GH18 chitinases offers a potential strategy to access oligomers in the range of bioactive DPs. We engineered SpChiD chitinase as a glycosynthase by mutation of the assisting residue of the catalytic triad in the substrate-assisted mechanism for polymerization of an oxazoline substrate (DP5ox). The insoluble polymer containing DP10 was partially hydrolyzed due to the significant residual hydrolase activity of the mutant enzyme. Combined mutations that strongly reduce the hydrolytic activity, in which the original catalytic triad only retains the essential acid/base residue, together with neighboring mutations in the -1/+1 subsites region, render glycosynthase-like chitinases able to produce chitin oligomers with DP10 as major product in good yields.
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Affiliation(s)
- Cristina Alsina
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Barcelona, Spain
| | - Enea Sancho-Vaello
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Barcelona, Spain
| | | | - Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Barcelona, Spain.
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12
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Alonso-Gil S. Mimicking the transition state of reactions of glycoside hydrolases: Updating the conformational space of the oxocarbenium cation. J Carbohydr Chem 2020. [DOI: 10.1080/07328303.2020.1766481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Santiago Alonso-Gil
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague 8, Czech Republic
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13
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Sobala L, Speciale G, Zhu S, Raich L, Sannikova N, Thompson AJ, Hakki Z, Lu D, Shamsi Kazem Abadi S, Lewis AR, Rojas-Cervellera V, Bernardo-Seisdedos G, Zhang Y, Millet O, Jiménez-Barbero J, Bennet AJ, Sollogoub M, Rovira C, Davies GJ, Williams SJ. An Epoxide Intermediate in Glycosidase Catalysis. ACS CENTRAL SCIENCE 2020; 6:760-770. [PMID: 32490192 PMCID: PMC7256955 DOI: 10.1021/acscentsci.0c00111] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Indexed: 05/18/2023]
Abstract
Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational, and kinetic evidence for neighboring-group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99 endo-α-1,2-mannanases. We present a series of crystallographic snapshots of key species along the reaction coordinate: a Michaelis complex with a tetrasaccharide substrate; complexes with intermediate mimics, a sugar-shaped cyclitol β-1,2-aziridine and β-1,2-epoxide; and a product complex. The 1,2-epoxide intermediate mimic displayed hydrolytic and transfer reactivity analogous to that expected for the 1,2-anhydro sugar intermediate supporting its catalytic equivalence. Quantum mechanics/molecular mechanics modeling of the reaction coordinate predicted a reaction pathway through a 1,2-anhydro sugar via a transition state in an unusual flattened, envelope (E 3) conformation. Kinetic isotope effects (k cat/K M) for anomeric-2H and anomeric-13C support an oxocarbenium ion-like transition state, and that for C2-18O (1.052 ± 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism.
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Affiliation(s)
- Lukasz
F. Sobala
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gaetano Speciale
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sha Zhu
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Lluís Raich
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Natalia Sannikova
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J. Thompson
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Zalihe Hakki
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dan Lu
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Saeideh Shamsi Kazem Abadi
- Department
of Biochemistry and Molecular Biology, Simon
Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew R. Lewis
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Víctor Rojas-Cervellera
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Ganeko Bernardo-Seisdedos
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Yongmin Zhang
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Oscar Millet
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Jesús Jiménez-Barbero
- Ikerbasque,
Basque Foundation for Science, Marıá Dıáz de Haro 3, 48013 Bilbao, Spain
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Andrew J. Bennet
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Biochemistry and Molecular Biology, Simon
Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
- E-mail:
| | - Matthieu Sollogoub
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
- E-mail:
| | - Carme Rovira
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
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), Pg. Lluís Companys
23, 08010 Barcelona, Spain
- E-mail:
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- E-mail:
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
- E-mail:
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14
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Abstract
β-N-acetylhexosaminidases (EC 3.2.1.52) are retaining hydrolases of glycoside hydrolase family 20 (GH20). These enzymes catalyze hydrolysis of terminal, non-reducing N-acetylhexosamine residues, notably N-acetylglucosamine or N-acetylgalactosamine, in N-acetyl-β-D-hexosaminides. In nature, bacterial β-N-acetylhexosaminidases are mainly involved in cell wall peptidoglycan synthesis, analogously, fungal β-N-acetylhexosaminidases act on cell wall chitin. The enzymes work via a distinct substrate-assisted mechanism that utilizes the 2-acetamido group as nucleophile. Curiously, the β-N-acetylhexosaminidases possess an inherent trans-glycosylation ability which is potentially useful for biocatalytic synthesis of functional carbohydrates, including biomimetic synthesis of human milk oligosaccharides and other glycan-functionalized compounds. In this review, we summarize the reaction engineering approaches (donor substrate activation, additives, and reaction conditions) that have proven useful for enhancing trans-glycosylation activity of GH20 β-N-acetylhexosaminidases. We provide comprehensive overviews of reported synthesis reactions with GH20 enzymes, including tables that list the specific enzyme used, donor and acceptor substrates, reaction conditions, and details of the products and yields obtained. We also describe the active site traits and mutations that appear to favor trans-glycosylation activity of GH20 β-N-acetylhexosaminidases. Finally, we discuss novel protein engineering strategies and suggest potential “hotspots” for mutations to promote trans-glycosylation activity in GH20 for efficient synthesis of specific functional carbohydrates and other glyco-engineered products.
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15
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Teze D, Coines J, Raich L, Kalichuk V, Solleux C, Tellier C, André-Miral C, Svensson B, Rovira C. A Single Point Mutation Converts GH84 O-GlcNAc Hydrolases into Phosphorylases: Experimental and Theoretical Evidence. J Am Chem Soc 2020; 142:2120-2124. [DOI: 10.1021/jacs.9b09655] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 224, DK-2800 Kongens Lyngby, Denmark
- UFIP, CNRS, Université de Nantes, 44300 Nantes, France
| | - Joan Coines
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Lluís Raich
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | | | | | | | | | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 224, DK-2800 Kongens Lyngby, Denmark
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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16
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Rovira C, Males A, Davies GJ, Williams SJ. Mannosidase mechanism: at the intersection of conformation and catalysis. Curr Opin Struct Biol 2019; 62:79-92. [PMID: 31891872 DOI: 10.1016/j.sbi.2019.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/06/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Mannosidases are a diverse group of enzymes that are important in the biological processing of mannose-containing polysaccharides and complex glycoconjugates. They are found in 12 of the >160 sequence-based glycosidase families. We discuss evidence that nature has evolved a small set of common mechanisms that unite almost all of these mannosidase families. Broadly, mannosidases (and the closely related rhamnosidases) perform catalysis through just two conformations of the oxocarbenium ion-like transition state: a B2,5 (or enantiomeric 2,5B) boat and a 3H4 half-chair. This extends to a new family (GT108) of GDPMan-dependent β-1,2-mannosyltransferases/phosphorylases that perform mannosyl transfer through a boat conformation as well as some mannosidases that are metalloenzymes and require divalent cations for catalysis. Yet, among this commonality lies diversity. New evidence shows that one unique family (GH99) of mannosidases use an unusual mechanism involving anchimeric assistance via a 1,2-anhydro sugar (epoxide) intermediate.
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Affiliation(s)
- Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & 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), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Alexandra Males
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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17
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Coines J, Raich L, Rovira C. Modeling catalytic reaction mechanisms in glycoside hydrolases. Curr Opin Chem Biol 2019; 53:183-191. [PMID: 31731209 DOI: 10.1016/j.cbpa.2019.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 01/21/2023]
Abstract
Modeling catalysis in carbohydrate-active enzymes is a daunting challenge because of the high flexibility and diversity of both enzymes and carbohydrates. Glycoside hydrolases (GHs) are an illustrative example, where conformational changes and subtle interactions have been shown to be critical for catalysis. GHs have pivotal roles in industry (e.g. biofuel or detergent production) and biomedicine (e.g. targets for cancer and diabetes), and thus, a huge effort is devoted to unveil their molecular mechanisms. Besides experimental techniques, computational methods have served to provide an in-depth understanding of GH mechanisms, capturing complex reaction coordinates and the conformational itineraries that substrates follow during the whole catalytic pathway, providing a framework that ultimately may assist the engineering of these enzymes and the design of new inhibitors.
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Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain
| | - Lluís Raich
- Departament de Química Inorgànica I Orgànica (secció 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 Inorgànica I Orgànica (secció 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, 08010 Barcelona, Spain.
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18
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Alsina C, Faijes M, Planas A. Glycosynthase-type GH18 mutant chitinases at the assisting catalytic residue for polymerization of chitooligosaccharides. Carbohydr Res 2019; 478:1-9. [PMID: 31005672 DOI: 10.1016/j.carres.2019.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/15/2019] [Accepted: 04/10/2019] [Indexed: 11/16/2022]
Abstract
Chitooligosaccharides (COS), the depolymerization products of chitin, have many potential applications in agriculture and medicine since they induce immunostimulating effects and disease protective responses. Most of their biological activities require degrees of polymerization (DP) larger than the tetrasaccharide, but structurally well-defined COS with DP larger than six are difficult to produce due to their high insolubility and complex isolation from chitin hydrolysates. Enzymatic synthesis by exploiting the transglycosylation activity of chitinases offers a potential strategy for the assembly of oligomers in the range of bioactive DPs. We here explore the glycosynthase-like activity of six GH18 chitinases from bacterial and archaeal origin by mutating the catalytic assisting residue in the substrate-assisted mechanism of this enzyme family. The alanine mutants at the assisting residue have a significant, but not essential, effect on the hydrolase activity. We studied the ability of the alanine mutants at the assisting residue to catalyze the polymerization of an oxazoline derivative as donor substrate, selecting the oxazoline of pentaacetylchitopentaose (DP5ox) with the aim of obtaining larger oligomers/polymers that, being insoluble, might be resistant to further reactions by the hydrolytically compromised mutant enzymes. For all the enzymes, insoluble polymeric material was obtained, with DP10 as major component, but other COS with different DPs were also obtained, limiting the practical application to produce oligomers/polymers with a defined DP. The balance between the residual hydrolase activity of the mutant enzymes and the solubility/precipitation kinetics still lead to hydrolysis and/or transglycosylation reactions on the newly formed products. From the selected enzymes, the Thermococcus kodakaraensis ChiA D1022A mutant gave the best results, with the formation of insoluble polymers in 45% yield (w/w) and containing about 55% of the target DP10 product.
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Affiliation(s)
- Cristina Alsina
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull Via Augusta 390, 08017, Barcelona, Spain
| | - Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull Via Augusta 390, 08017, Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull Via Augusta 390, 08017, Barcelona, Spain.
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19
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Klontz EH, Trastoy B, Deredge D, Fields JK, Li C, Orwenyo J, Marina A, Beadenkopf R, Günther S, Flores J, Wintrode PL, Wang LX, Guerin ME, Sundberg EJ. Molecular Basis of Broad Spectrum N-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2. ACS CENTRAL SCIENCE 2019; 5:524-538. [PMID: 30937380 PMCID: PMC6439443 DOI: 10.1021/acscentsci.8b00917] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 06/02/2023]
Abstract
Immunoglobulin G (IgG) glycosylation critically modulates antibody effector functions. Streptococcus pyogenes secretes a unique endo-β-N-acetylglucosaminidase, EndoS2, which deglycosylates the conserved N-linked glycan at Asn297 on IgG Fc to eliminate its effector functions and evade the immune system. EndoS2 and specific point mutants have been used to chemoenzymatically synthesize antibodies with customizable glycosylation for gain of functions. EndoS2 is useful in these schemes because it accommodates a broad range of N-glycans, including high-mannose, complex, and hybrid types; however, its mechanism of substrate recognition is poorly understood. We present crystal structures of EndoS2 alone and bound to complex and high-mannose glycans; the broad N-glycan specificity is governed by critical loops that shape the binding site of EndoS2. Furthermore, hydrolytic experiments, domain-swap chimeras, and hydrogen-deuterium exchange mass spectrometry reveal the importance of the carbohydrate-binding module in the mechanism of IgG recognition by EndoS2, providing insights into engineering enzymes to catalyze customizable glycosylation reactions.
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Affiliation(s)
- Erik H. Klontz
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Beatriz Trastoy
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Daniel Deredge
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - James K. Fields
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Chao Li
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Jared Orwenyo
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Alberto Marina
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Robert Beadenkopf
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Sebastian Günther
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Photon
Science, Deutsches Elektronen-Synchrotron, Hamburg 22607, Germany
| | - Jair Flores
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Patrick L. Wintrode
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Lai-Xi Wang
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Marcelo E. Guerin
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48013 Bilbao, Spain
| | - Eric J. Sundberg
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Department
of Medicine, University of Maryland School
of Medicine, Baltimore, Maryland 21201, United States
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20
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Iino T, Sakurai M, Furuta T. A novel ring-shaped reaction pathway with interconvertible intermediates in chitinase A as revealed by QM/MM simulation combined with a one-dimensional projection technique. Phys Chem Chem Phys 2019; 21:24956-24966. [DOI: 10.1039/c9cp05163e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient sampling achieved by the use of a one-dimensional projection technique reveals the catalytic mechanism of chitinase A from Serratia marcescens.
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Affiliation(s)
- Tsubasa Iino
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Yokohama
- Japan
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21
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Brockerman JA, Okon M, Withers SG, McIntosh LP. The pK a values of the catalytic residues in the retaining glycoside hydrolase T26H mutant of T4 lysozyme. Protein Sci 2018; 28:620-632. [PMID: 30537432 DOI: 10.1002/pro.3562] [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: 10/23/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/24/2022]
Abstract
T4 phage lysozyme (T4L) is an enzyme that cleaves bacterial cell wall peptidoglycan. Remarkably, the single substitution of the active site Thr26 to a His (T26H) converts T4L from an inverting to a retaining glycoside hydrolase with transglycosylase activity. It has been proposed that T26H-T4L follows a double displacement mechanism with His26 serving as a nucleophile to form a covalent glycosyl-enzyme intermediate (Kuroki et al., PNAS 1999; 96:8949-8954). To gain further insights into this or alternative mechanisms, we used NMR spectroscopy to measure the acid dissociation constants (pKa values) and/or define the ionization states of the Asp, Glu, His, and Arg residues in the T4L mutant. Most notably, the pKa value of the putative nucleophile His26 is 6.8 ± 0.1, whereas that of the general acid Glu11 is 4.7 ± 0.1. If the proposed mechanism holds true, then T26H-T4L follows a reverse protonation pathway in which only a minor population of the free enzyme is in its catalytically competent ionization state with His26 deprotonated and Glu11 protonated. Our studies also confirm that all arginines in T26H-T4L, including the active site Arg145, are positively charged under neutral pH conditions. BRIEF STATEMENT: The replacement of a single amino acid changes T4 lysozyme from an inverting to a retaining glycoside hydrolase. Using NMR spectroscopy, we measured the pKa values of the ionizable residues in the active site of this mutant enzyme. Along with previously reported data, these results provide important constraints for understanding the catalytic mechanisms by which the wild-type and mutant form of T4 lysozyme cleave bacterial peptidoglycan.
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Affiliation(s)
- Jacob A Brockerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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