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Litschko C, Di Domenico V, Schulze J, Li S, Ovchinnikova OG, Voskuilen T, Bethe A, Cifuente JO, Marina A, Budde I, Mast TA, Sulewska M, Berger M, Buettner FFR, Lowary TL, Whitfield C, Codée JDC, Schubert M, Guerin ME, Fiebig T. Transition transferases prime bacterial capsule polymerization. Nat Chem Biol 2024:10.1038/s41589-024-01664-8. [PMID: 38951648 DOI: 10.1038/s41589-024-01664-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/04/2024] [Indexed: 07/03/2024]
Abstract
Capsules are long-chain carbohydrate polymers that envelop the surfaces of many bacteria, protecting them from host immune responses. Capsule biosynthesis enzymes are potential drug targets and valuable biotechnological tools for generating vaccine antigens. Despite their importance, it remains unknown how structurally variable capsule polymers of Gram-negative pathogens are linked to the conserved glycolipid anchoring these virulence factors to the bacterial membrane. Using Actinobacillus pleuropneumoniae as an example, we demonstrate that CpsA and CpsC generate a poly(glycerol-3-phosphate) linker to connect the glycolipid with capsules containing poly(galactosylglycerol-phosphate) backbones. We reconstruct the entire capsule biosynthesis pathway in A. pleuropneumoniae serotypes 3 and 7, solve the X-ray crystal structure of the capsule polymerase CpsD, identify its tetratricopeptide repeat domain as essential for elongating poly(glycerol-3-phosphate) and show that CpsA and CpsC stimulate CpsD to produce longer polymers. We identify the CpsA and CpsC product as a wall teichoic acid homolog, demonstrating similarity between the biosynthesis of Gram-positive wall teichoic acid and Gram-negative capsules.
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Affiliation(s)
- Christa Litschko
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Valerio Di Domenico
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona, Spanish National Research Council, Barcelona Science Park, Tower R, Barcelona, Spain
| | - Julia Schulze
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Sizhe Li
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Olga G Ovchinnikova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Thijs Voskuilen
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Andrea Bethe
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Javier O Cifuente
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Bizkaia Technology Park, Derio, Spain
| | - Alberto Marina
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Bizkaia Technology Park, Derio, Spain
| | - Insa Budde
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Tim A Mast
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Małgorzata Sulewska
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Monika Berger
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
- Proteomics, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain.
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona, Spanish National Research Council, Barcelona Science Park, Tower R, Barcelona, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Bizkaia Technology Park, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - Timm Fiebig
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
- German Center for Infection Research, Partner Site Hannover-Braunschweig, Hannover, Germany.
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2
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Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
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Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
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3
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Abstract
Glycosyltransferases (GTs) attach sugar molecules to a broad range of acceptors, generating a remarkable amount of structural diversity in biological systems. GTs are classified as either "retaining" or "inverting" enzymes. Most retaining GTs typically use an SNi mechanism. In a recent article in the JBC, Doyle et al. demonstrate a covalent intermediate in the dual-module KpsC GT (GT107) supporting a double displacement mechanism.
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Affiliation(s)
- Marcelo E Guerin
- Department of Structural and Molecular Biology, Structural Glycobiology Laboratory, Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Catalonia, Spain.
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4
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Paparella A, Cahill SM, Aboulache BL, Schramm VL. Clostridioides difficile TcdB Toxin Glucosylates Rho GTPase by an S Ni Mechanism and Ion Pair Transition State. ACS Chem Biol 2022; 17:2507-2518. [PMID: 36038138 PMCID: PMC9486934 DOI: 10.1021/acschembio.2c00408] [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: 01/19/2023]
Abstract
Toxins TcdA and TcdB from Clostridioides difficile glucosylate human colon Rho GTPases. TcdA and TcdB glucosylation of RhoGTPases results in cytoskeletal changes, causing cell rounding and loss of intestinal integrity. Clostridial toxins TcdA and TcdB are proposed to catalyze glucosylation of Rho GTPases with retention of stereochemistry from UDP-glucose. We used kinetic isotope effects to analyze the mechanisms and transition-state structures of the glucohydrolase and glucosyltransferase activities of TcdB. TcdB catalyzes Rho GTPase glucosylation with retention of stereochemistry, while hydrolysis of UDP-glucose by TcdB causes inversion of stereochemistry. Kinetic analysis revealed TcdB glucosylation via the formation of a ternary complex with no intermediate, supporting an SNi mechanism with nucleophilic attack and leaving group departure occurring on the same face of the glucose ring. Kinetic isotope effects combined with quantum mechanical calculations revealed that the transition states of both glucohydrolase and glucosyltransferase activities of TcdB are highly dissociative. Specifically, the TcdB glucosyltransferase reaction proceeds via an SNi mechanism with the formation of a distinct oxocarbenium phosphate ion pair transition state where the glycosidic bond to the UDP leaving group breaks prior to attack of the threonine nucleophile from Rho GTPase.
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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Kaur H, Singh R, Rishikant. Synthesis, Molecular Docking, and Antitubercular Evaluation of Triazole–Chalcone Conjugates. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s107042802204008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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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
![]()
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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8
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Julian JD, Zabotina OA. Xyloglucan Biosynthesis: From Genes to Proteins and Their Functions. FRONTIERS IN PLANT SCIENCE 2022; 13:920494. [PMID: 35720558 PMCID: PMC9201394 DOI: 10.3389/fpls.2022.920494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/13/2022] [Indexed: 05/12/2023]
Abstract
The plant's recalcitrant cell wall is composed of numerous polysaccharides, including cellulose, hemicellulose, and pectin. The most abundant hemicellulose in dicot cell walls is xyloglucan, which consists of a β-(1- > 4) glucan backbone with α-(1- > 6) xylosylation producing an XXGG or XXXG pattern. Xylose residues of xyloglucan are branched further with different patterns of arabinose, fucose, galactose, and acetylation that varies between species. Although xyloglucan research in other species lag behind Arabidopsis thaliana, significant advances have been made into the agriculturally relevant species Oryza sativa and Solanum lycopersicum, which can be considered model organisms for XXGG type xyloglucan. In this review, we will present what is currently known about xyloglucan biosynthesis in A. thaliana, O. sativa, and S. lycopersicum and discuss the recent advances in the characterization of the glycosyltransferases involved in this complex process and their organization in the Golgi.
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Affiliation(s)
- Jordan D Julian
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Olga A Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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9
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Ferreira P, Fernandes PA, Ramos MJ. THE CATALYTIC MECHANISM OF THE RETAINING GLYCOSYLTRANSFERASE MANNOSYLGLYCERATE SYNTHASE. Chemistry 2021; 27:13998-14006. [PMID: 34355437 DOI: 10.1002/chem.202101724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Indexed: 11/07/2022]
Abstract
To protect their intracellular proteins, extremophile microorganisms synthesize molecules called compatible solutes. These molecules are the result of the attachment of a small negatively charged molecule to a sugar molecule. It has been found that these molecules, not only protect the microorganism against osmotic stress, as initially thought, but also against other extreme conditions. The observation that these molecules can confer protection against extreme conditions to isolated enzymes from different organisms made them an exciting prospect for potential biotechnological applications. One of the most widespread compatible solute in hyperthermophile organisms is the molecule 2-O-α-D-mannosyl-D-glycerate (MG). In addition to confer protection to proteins against extreme conditions, MG was found to prevent Alzheimer's β-amyloid aggregation and reduce α-synuclein fibril formation in Parkinson's disease. In this work we studied, using computational methods, the catalytic mechanism of the synthesis of MG by the enzyme mannosylglycerate synthase (MGS) from the thermophilic bacteria Rhodothermus marinus . MGS is a promiscuous enzyme, accepting a variety of sugar donors and acceptors. This feature can be used to synthesize other molecules with potential biotechnological applications beyond MG. The unravelling of the catalytic mechanism with atomistic resolution and the associated free energies and electrostatic profiles of the stationary states obtained in the present work will help future investigations to full explore the potential of MGS.
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Affiliation(s)
- Pedro Ferreira
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro A Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria J Ramos
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
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10
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Mendoza F, Jaña GA. The inverting mechanism of the metal ion-independent LanGT2: the first step to understand the glycosylation of natural product antibiotic precursors through QM/MM simulations. Org Biomol Chem 2021; 19:5888-5898. [PMID: 34132308 DOI: 10.1039/d1ob00544h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Glycosyltransferases (GTs) from the GT1 family are responsible for the glycosylation of various important organic structures such as terpenes, steroids and peptide antibiotics, making it one of the most intensely studied families of GTs. The target of our study, LanGT2, is a member of the GT1 family that uses an inverting mechanism for transferring olivose from TDP-olivose, the donor substrate, to the natural product tetrangulol (Tet), the precursor of the antibiotic landomycin A. X-ray crystallography in conjunction with mutagenesis experiments has revealed the catalytic significance of 3 amino acids (Ser10, Ser219 and Asp137), suggesting Asp137 as the base catalyst. In the absence of X-ray structures that include the acceptor substrate Tet, in silico experiments and MD simulations that have modeled ternary complexes propose that Asp137 could recruit a water molecule to facilitate the nucleophilic activation of Tet, since the distance between Asp137 and the nucleophile is too long to directly deprotonate the nucleophilic moiety. So far, there is no computational evidence regarding the precise mechanism by which LanGT2 catalyzes the transfer of olivose, which raises questions such as: is a water-assisted mechanism possible? and how does this metal ion-independent GT stabilize the growing negative charge of the diphosphate leaving group? In this work, the QM/MM approach was used to unravel the catalytic mechanism of LanGT2, and to identify the role of crucial catalytic amino acids at a molecular level. Our calculations show that the minimum energy path (MEP) describes an SN2-like mechanism, identifying an oxocarbenium ion-like TS in which the olivosyl moiety adopts a 4H3 conformation. Interactions established between the diphosphate group of TDP and Ser10, Ser219, Arg220 and His283 are key to stabilize the development of charge on the leaving group. Our work also suggests that a water-mediated proton transfer mechanism is feasible, in which the water molecule is key to stabilize the phenolate ion-like nucleophile in the TS. This is the first computational insight into the inverting mechanism of an antibiotic natural product GT, and its implications may serve to guide the design of new biocatalysts for natural product glycodiversification.
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Affiliation(s)
- Fernanda Mendoza
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile.
| | - Gonzalo A Jaña
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile.
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11
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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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12
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Zabotina OA, Zhang N, Weerts R. Polysaccharide Biosynthesis: Glycosyltransferases and Their Complexes. FRONTIERS IN PLANT SCIENCE 2021; 12:625307. [PMID: 33679837 PMCID: PMC7933479 DOI: 10.3389/fpls.2021.625307] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/14/2021] [Indexed: 05/04/2023]
Abstract
Glycosyltransferases (GTs) are enzymes that catalyze reactions attaching an activated sugar to an acceptor substrate, which may be a polysaccharide, peptide, lipid, or small molecule. In the past decade, notable progress has been made in revealing and cloning genes encoding polysaccharide-synthesizing GTs. However, the vast majority of GTs remain structurally and functionally uncharacterized. The mechanism by which they are organized in the Golgi membrane, where they synthesize complex, highly branched polysaccharide structures with high efficiency and fidelity, is also mostly unknown. This review will focus on current knowledge about plant polysaccharide-synthesizing GTs, specifically focusing on protein-protein interactions and the formation of multiprotein complexes.
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13
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Mikkola S. Nucleotide Sugars in Chemistry and Biology. Molecules 2020; 25:E5755. [PMID: 33291296 PMCID: PMC7729866 DOI: 10.3390/molecules25235755] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleotide sugars have essential roles in every living creature. They are the building blocks of the biosynthesis of carbohydrates and their conjugates. They are involved in processes that are targets for drug development, and their analogs are potential inhibitors of these processes. Drug development requires efficient methods for the synthesis of oligosaccharides and nucleotide sugar building blocks as well as of modified structures as potential inhibitors. It requires also understanding the details of biological and chemical processes as well as the reactivity and reactions under different conditions. This article addresses all these issues by giving a broad overview on nucleotide sugars in biological and chemical reactions. As the background for the topic, glycosylation reactions in mammalian and bacterial cells are briefly discussed. In the following sections, structures and biosynthetic routes for nucleotide sugars, as well as the mechanisms of action of nucleotide sugar-utilizing enzymes, are discussed. Chemical topics include the reactivity and chemical synthesis methods. Finally, the enzymatic in vitro synthesis of nucleotide sugars and the utilization of enzyme cascades in the synthesis of nucleotide sugars and oligosaccharides are briefly discussed.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, 20014 Turku, Finland
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14
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Kóňa J. How inverting β-1,4-galactosyltransferase-1 can quench a high charge of the by-product UDP 3- in catalysis: a QM/MM study of enzymatic reaction with native and UDP-5' thio galactose substrates. Org Biomol Chem 2020; 18:7585-7596. [PMID: 32945815 DOI: 10.1039/d0ob01490g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
The catalysis of inverting glycosyltransferases consists of several biophysical and biochemical processes during which the transfer of a sugar residue from the purine phosphate donor substrate to an acceptor substrate occurs with stereo-inversion of the anomeric C1 center at a product. During catalysis a highly charged phosphate by-product (UDP3-) is formed and a mechanism of how the enzyme stabilizes it back to the UDP2- form is not known. Using methods of molecular modeling (hybrid DFT-QM/MM calculations) we proposed and validated a catalytic mechanism of bovine inverting β-1,4-galactosyltransferase-1 (β4Gal-T1) with native (UDP-galactose) and thio donor substrates (UDP-5' thio galactose). We focused on three aspects of the mechanism not yet investigated: (i) the formation of an oxocarbenium ion intermediate, which was only found for the retaining glycosyltransferases for the time being; (ii) the mechanism of stabilization of a highly charged phosphate by-product (UDP3-) back to its standard in vivo form (UDP2-); (iii) explanation for why in experimental measurements the rate of catalysis with the thio donor substrate is only 8% of the rate of that with the natural substrate. To understand the differences in the interaction patterns between the complexes enzyme : UDP-Gal and enzyme : UDP-5S-Gal, fragmented molecular orbital (FMO) decomposition energy analysis was carried out at the DFT level.
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Affiliation(s)
- J Kóňa
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovak Republic.
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15
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Rodrigo-Unzueta A, Ghirardello M, Urresti S, Delso I, Giganti D, Anso I, Trastoy B, Comino N, Tersa M, D'Angelo C, Cifuente JO, Marina A, Liebau J, Mäler L, Chenal A, Albesa-Jové D, Merino P, Guerin ME. Dissecting the Structural and Chemical Determinants of the "Open-to-Closed" Motion in the Mannosyltransferase PimA from Mycobacteria. Biochemistry 2020; 59:2934-2945. [PMID: 32786405 DOI: 10.1021/acs.biochem.0c00376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The phosphatidyl-myo-inositol mannosyltransferase A (PimA) is an essential peripheral membrane glycosyltransferase that initiates the biosynthetic pathway of phosphatidyl-myo-inositol mannosides (PIMs), key structural elements and virulence factors of Mycobacterium tuberculosis. PimA undergoes functionally important conformational changes, including (i) α-helix-to-β-strand and β-strand-to-α-helix transitions and (ii) an "open-to-closed" motion between the two Rossmann-fold domains, a conformational change that is necessary to generate a catalytically competent active site. In previous work, we established that GDP-Man and GDP stabilize the enzyme and facilitate the switch to a more compact active state. To determine the structural contribution of the mannose ring in such an activation mechanism, we analyzed a series of chemical derivatives, including mannose phosphate (Man-P) and mannose pyrophosphate-ribose (Man-PP-RIB), and additional GDP derivatives, such as pyrophosphate ribose (PP-RIB) and GMP, by the combined use of X-ray crystallography, limited proteolysis, circular dichroism, isothermal titration calorimetry, and small angle X-ray scattering methods. Although the β-phosphate is present, we found that the mannose ring, covalently attached to neither phosphate (Man-P) nor PP-RIB (Man-PP-RIB), does promote the switch to the active compact form of the enzyme. Therefore, the nucleotide moiety of GDP-Man, and not the sugar ring, facilitates the "open-to-closed" motion, with the β-phosphate group providing the high-affinity binding to PimA. Altogether, the experimental data contribute to a better understanding of the structural determinants involved in the "open-to-closed" motion not only observed in PimA but also visualized and/or predicted in other glycosyltransfeases. In addition, the experimental data might prove to be useful for the discovery and/or development of PimA and/or glycosyltransferase inhibitors.
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Affiliation(s)
- Ane Rodrigo-Unzueta
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
| | - Mattia Ghirardello
- Department of Synthesis and Structure of Biomolecules, Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH), University of Zaragoza-CSIC, 50009 Zaragoza, Spain
| | - Saioa Urresti
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
| | - Ignacio Delso
- Department of Synthesis and Structure of Biomolecules, Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH), University of Zaragoza-CSIC, 50009 Zaragoza, Spain
| | - David Giganti
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Unité de Microbiologie Structurale (CNRS URA 2185), Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Itxaso Anso
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Beatriz Trastoy
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Natalia Comino
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Montse Tersa
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Cecilia D'Angelo
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Javier O Cifuente
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Alberto Marina
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden.,Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Alexandre Chenal
- Unité de Biochimie des Interactions Macromoléculaires (CNRS UMR 3528), Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - David Albesa-Jové
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Pedro Merino
- Glycobiology Unit, Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain
| | - Marcelo E Guerin
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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16
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Yan L, Liu Y. The Retaining Mechanism of Xylose Transfer Catalyzed by Xyloside α-1,3-Xylosyltransferase (XXYLT1): a Quantum Mechanics/Molecular Mechanics Study. J Chem Inf Model 2020; 60:1585-1594. [PMID: 32105482 DOI: 10.1021/acs.jcim.9b00976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycosyltransferases (GTs) are a ubiquitous group of enzymes that catalyze the synthesis of glycosidic bonds. In this work, we focused on the retained reaction catalyzed by xyloside α-1,3-xylosyltransferase (XXYLT1) from Mus musculus. Our calculations revealed that the xylose transfer reaction follows the SNi-like mechanism, which involves a short-lived oxocarbenium-phosphate ion-pair intermediate (IP). The previously obtained crystal structure of the UDP-Xyl ternary Michaelis reaction complex was found to be an inactive form. Accordingly, the β-phosphate oxygen O3B of the donor should first undergo a conformational change to reach an active state where the donor forms a strong hydrogen bond with the acceptor, facilitating the departure of the phosphate group. Our calculations also revealed that two predicated transition states for the sugar-phosphate bond cleavage and glycosidic bond formation are structurally similar to the short-lived intermediate, which contains a three-member ring formed by the β-phosphate oxygen, the hydroxyl oxygen in the acceptor, and the anomeric carbon. It can be considered as a typical characteristic of the SNi-like mechanism. In addition, a nearby polar residue, Q330, is responsible for stabilizing the short-lived intermediate by electrostatic interactions. Thus, the Q330A mutant can abolish the activity of XXYLT1. In addition, using UDP-glucose as the donor, our calculations revealed that glucose transfer would correspond to a higher energy barrier owing to the steric repulsion between the glucosyl moiety and the nearby residue L327, indicating the requirement of active site architecture for glucose transfer. These findings not only explain the experimental observations but also are meaningful for clarifying the mechanism of GTs.
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Affiliation(s)
- Lijuan Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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17
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Emerging structural insights into glycosyltransferase-mediated synthesis of glycans. Nat Chem Biol 2019; 15:853-864. [PMID: 31427814 DOI: 10.1038/s41589-019-0350-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/17/2019] [Indexed: 12/27/2022]
Abstract
Glycans linked to proteins and lipids play key roles in biology; thus, accurate replication of cellular glycans is crucial for maintaining function following cell division. The fact that glycans are not copied from genomic templates suggests that fidelity is provided by the catalytic templates of glycosyltransferases that accurately add sugars to specific locations on growing oligosaccharides. To form new glycosidic bonds, glycosyltransferases bind acceptor substrates and orient a specific hydroxyl group, frequently one of many, for attack of the donor sugar anomeric carbon. Several recent crystal structures of glycosyltransferases with bound acceptor substrates reveal that these enzymes have common core structures that function as scaffolds upon which variable loops are inserted to confer substrate specificity and correctly orient the nucleophilic hydroxyl group. The varied approaches for acceptor binding site assembly suggest an ongoing evolution of these loop regions provides templates for assembly of the diverse glycan structures observed in biology.
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18
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Structural basis of glycogen metabolism in bacteria. Biochem J 2019; 476:2059-2092. [PMID: 31366571 DOI: 10.1042/bcj20170558] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 01/25/2023]
Abstract
The evolution of metabolic pathways is a major force behind natural selection. In the spotlight of such process lies the structural evolution of the enzymatic machinery responsible for the central energy metabolism. Specifically, glycogen metabolism has emerged to allow organisms to save available environmental surplus of carbon and energy, using dedicated glucose polymers as a storage compartment that can be mobilized at future demand. The origins of such adaptive advantage rely on the acquisition of an enzymatic system for the biosynthesis and degradation of glycogen, along with mechanisms to balance the assembly and disassembly rate of this polysaccharide, in order to store and recover glucose according to cell energy needs. The first step in the classical bacterial glycogen biosynthetic pathway is carried out by the adenosine 5'-diphosphate (ADP)-glucose pyrophosphorylase. This allosteric enzyme synthesizes ADP-glucose and acts as a point of regulation. The second step is carried out by the glycogen synthase, an enzyme that generates linear α-(1→4)-linked glucose chains, whereas the third step catalyzed by the branching enzyme produces α-(1→6)-linked glucan branches in the polymer. Two enzymes facilitate glycogen degradation: glycogen phosphorylase, which functions as an α-(1→4)-depolymerizing enzyme, and the debranching enzyme that catalyzes the removal of α-(1→6)-linked ramifications. In this work, we rationalize the structural basis of glycogen metabolism in bacteria to the light of the current knowledge. We describe and discuss the remarkable progress made in the understanding of the molecular mechanisms of substrate recognition and product release, allosteric regulation and catalysis of all those enzymes.
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19
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Romero-Téllez S, Lluch JM, González-Lafont À, Masgrau L. Comparing Hydrolysis and Transglycosylation Reactions Catalyzed by Thermus thermophilus β-Glycosidase. A Combined MD and QM/MM Study. Front Chem 2019; 7:200. [PMID: 31024890 PMCID: PMC6467970 DOI: 10.3389/fchem.2019.00200] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/15/2019] [Indexed: 01/26/2023] Open
Abstract
The synthesis of oligosaccharides and other carbohydrate derivatives is of relevance for the advancement of glycosciences both at the fundamental and applied level. For many years, glycosyl hydrolases (GHs) have been explored to catalyze the synthesis of glycosidic bonds. In particular, retaining GHs can catalyze a transglycosylation (T) reaction that competes with hydrolysis (H). This has been done either employing controlled conditions in wild type GHs or by engineering new mutants. The goal, which is to increase the T/H ratio, has been achieved with moderate success in several cases despite the fact that the molecular basis for T/H modulation are unclear. Here we have used QM(DFT)/MM calculations to compare the glycosylation, hydrolysis and transglycosylation steps catalyzed by wild type Thermus thermophilus β-glycosidase (family GH1), a retaining glycosyl hydrolase for which a transglycosylation yield of 36% has been determined experimentally. The three transition states have a strong oxocarbenium character and ring conformations between 4H3 and 4E. The atomic charges at the transition states for hydrolysis and transglycosylation are very similar, except for the more negative charge of the oxygen atom of water when compared to that of the acceptor Glc. The glycosylation transition state has a stronger SN2 character than the deglycosylation ones and the proton transfer is less advanced. At the QM(PBE0/TZVP)/MM level, the TS for transglycosylation has shorter O4GLC-C1FUC (forming bond) distance and longer OE2GLU338-C1FUC (breaking) distance than the hydrolysis one, although the HACC proton is closer to the Glu164 base in the hydrolysis TS. The QM(SCC-DFTB)/MM free energy maxima show the inverted situation, although the hydrolysis TS presents significant structural fluctuations. The 3-OHGLC group of the acceptor Glc (transglycosylation) and WAT432 (neighbor water in hydrolysis) are identified to stabilize the oxocarbenium transition states through interaction with O5FUC and O4FUC. The analysis of interaction suggests that perturbing the Glu392-Fuc interaction could increase the T/H ratio, either by direct mutation of this residue or indirectly as reported experimentally in the Asn390I and Phe401S cases. The molecular understanding of similarities and differences between hydrolysis and transglycosylation steps may be of help in the design of new biocatalysts for glycan synthesis.
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Affiliation(s)
- Sonia Romero-Téllez
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Masgrau
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
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20
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Albesa-Jové D, Cifuente JO, Trastoy B, Guerin ME. Quick-soaking of crystals reveals unprecedented insights into the catalytic mechanism of glycosyltransferases. Methods Enzymol 2019; 621:261-279. [PMID: 31128783 DOI: 10.1016/bs.mie.2019.02.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glycosyltransferases (GTs) catalyze the transfer of a sugar moiety from nucleotide-sugar or lipid-phospho-sugar donors to a wide range of acceptor substrates, generating a remarkable amount of structural diversity in biological systems. Glycosyl transfer reactions can proceed with either inversion or retention of the anomeric configuration with respect to the sugar donor substrate. In this chapter, we discuss the application of a quick soaking method of substrates and products into protein crystals to visualize native ternary complexes of retaining glycosyltransferases. The crystal structures provide different snapshots of the catalytic cycle, including the Michaelis complex. During this sequence of events, we visualize how the enzyme guides the substrates into the reaction center where the glycosyl transfer reaction takes place, and unveil the mechanism of product release, involving multiple conformational changes not only in the substrates and products but also in the enzyme. The methodology described here provides unprecedented insights into the catalytic mechanism of glycosyltransferases at the molecular level, and can be applied to the study a myriad of enzymatic mediated reactions.
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Affiliation(s)
- David Albesa-Jové
- Structural Biology Unit, CIC bioGUNE, Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | | | - Marcelo E Guerin
- Structural Biology Unit, CIC bioGUNE, Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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21
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Albesa-Jové D, Sainz-Polo MÁ, Marina A, Guerin ME. Structural Snapshots of α-1,3-Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David Albesa-Jové
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - M. Ángela Sainz-Polo
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - Alberto Marina
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - Marcelo E. Guerin
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
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22
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Albesa-Jové D, Sainz-Polo MÁ, Marina A, Guerin ME. Structural Snapshots of α-1,3-Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases. Angew Chem Int Ed Engl 2017; 56:14853-14857. [DOI: 10.1002/anie.201707922] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/19/2017] [Indexed: 11/11/2022]
Affiliation(s)
- David Albesa-Jové
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - M. Ángela Sainz-Polo
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - Alberto Marina
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - Marcelo E. Guerin
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
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23
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Albesa-Jové D, Romero-García J, Sancho-Vaello E, Contreras FX, Rodrigo-Unzueta A, Comino N, Carreras-González A, Arrasate P, Urresti S, Biarnés X, Planas A, Guerin ME. Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS. Structure 2017. [PMID: 28625787 DOI: 10.1016/j.str.2017.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Glycosyltransferases (GTs) play a central role in nature. They catalyze the transfer of a sugar moiety to a broad range of acceptor substrates. GTs are highly selective enzymes, allowing the recognition of subtle structural differences in the sequences and stereochemistry of their sugar and acceptor substrates. We report here a series of structural snapshots of the reaction center of the retaining glucosyl-3-phosphoglycerate synthase (GpgS). During this sequence of events, we visualize how the enzyme guides the substrates into the reaction center where the glycosyl transfer reaction takes place, and unveil the mechanism of product release, involving multiple conformational changes not only in the substrates/products but also in the enzyme. The structural data are further complemented by metadynamics free-energy calculations, revealing how the equilibrium of loop conformations is modulated along these itineraries. The information reported here represent an important contribution for the understanding of GT enzymes at the molecular level.
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Affiliation(s)
- David Albesa-Jové
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48080 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Javier Romero-García
- Laboratory of Biochemistry, Bioengineering Department, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona 08017, Spain
| | - Enea Sancho-Vaello
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
| | - F-Xabier Contreras
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48080 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Ane Rodrigo-Unzueta
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
| | - Natalia Comino
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48080 Bilbao, Spain
| | - Ana Carreras-González
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain
| | - Pedro Arrasate
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
| | - Saioa Urresti
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Bioengineering Department, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona 08017, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Bioengineering Department, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona 08017, Spain
| | - Marcelo E Guerin
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48080 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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24
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Sladek V, Tvaroška I. First-Principles Interaction Analysis Assessment of the Manganese Cation in the Catalytic Activity of Glycosyltransferases. J Phys Chem B 2017; 121:6148-6162. [DOI: 10.1021/acs.jpcb.7b03714] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Vladimir Sladek
- Institute
of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
- Department
of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Tokyo 171-8501, Japan
| | - Igor Tvaroška
- Institute
of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
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25
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A front-face 'SNi synthase' engineered from a retaining 'double-SN2' hydrolase. Nat Chem Biol 2017; 13:874-881. [DOI: 10.1038/nchembio.2394] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 03/08/2017] [Indexed: 01/13/2023]
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26
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Blanco Capurro JI, Hopkins CW, Pierdominici Sottile G, González Lebrero MC, Roitberg AE, Marti MA. Theoretical Insights into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis. J Phys Chem B 2017; 121:471-478. [PMID: 27935720 DOI: 10.1021/acs.jpcb.6b10130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding enzymatic reactions with atomic resolution has proven in recent years to be of tremendous interest for biochemical research, and thus, the use of QM/MM methods for the study of reaction mechanisms is experiencing a continuous growth. Glycosyltransferases (GTs) catalyze the formation of glycosidic bonds, and are important for many biotechnological purposes, including drug targeting. Their reaction product may result with only one of the two possible stereochemical outcomes for the reacting anomeric center, and therefore, they are classified as either inverting or retaining GTs. While the inverting GT reaction mechanism has been widely studied, the retaining GT mechanism has always been controversial and several questions remain open to this day. In this work, we take advantage of our recent GPU implementation of a pure QM(DFT-PBE)/MM approach to explore the reaction and inhibition mechanism of MshA, a key retaining GT responsible for the first step of mycothiol biosynthesis, a low weight thiol compound found in pathogens like Mycobacterium tuberculosis that is essential for its survival under oxidative stress conditions. Our results show that the reaction proceeds via a front-side SNi-like concerted reaction mechanism (DNAN in IUPAC nomenclature) and has a 17.5 kcal/mol free energy barrier, which is in remarkable agreement with experimental data. Detailed analysis shows that the key reaction step is the diphosphate leaving group dissociation, leading to an oxocarbenium-ion-like transition state. In contrast, fluorinated substrate analogues increase the reaction barrier significantly, rendering the enzyme effectively inactive. Detailed analysis of the electronic structure along the reaction suggests that this particular inhibition mechanism is associated with fluorine's high electronegative nature, which hinders phosphate release and proper stabilization of the transition state.
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Affiliation(s)
- Juan I Blanco Capurro
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| | - Chad W Hopkins
- Department of Physics, University of Florida , Gainesville, Florida 32611, United States
| | - Gustavo Pierdominici Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, Bernal B1876BXD, Argentina
| | - Mariano C González Lebrero
- Departamento de Quimica Inorgánica, Anlı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.,Insituto de Quimica Inorgánica, Materiales Ambiente y Energı́a (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
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Mendoza F, Lluch JM, Masgrau L. Computational insights into active site shaping for substrate specificity and reaction regioselectivity in the EXTL2 retaining glycosyltransferase. Org Biomol Chem 2017; 15:9095-9107. [DOI: 10.1039/c7ob01937h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
QM(DFT)/MM calculations and molecular dynamics simulations on wild-type retaining α1,4-N-acetylhexosaminyltransferase (EXTL2) and Arg293Ala, Asp246Ala, Arg293Ala/Asp246Ala and Asp246Glu mutants are used to understand the role of these two residues.
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Affiliation(s)
- Fernanda Mendoza
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Sede Concepción
- Talcahuano
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
- 08193 Bellaterra (Cerdanyola del Vallès)
- Barcelona
- Spain
| | - Laura Masgrau
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
- 08193 Bellaterra (Cerdanyola del Vallès)
- Barcelona
- Spain
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Nunes-Costa D, Maranha A, Costa M, Alarico S, Empadinhas N. Glucosylglycerate metabolism, bioversatility and mycobacterial survival. Glycobiology 2016; 27:213-227. [DOI: 10.1093/glycob/cww132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/14/2016] [Indexed: 12/17/2022] Open
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Structural basis of phosphatidyl-myo-inositol mannosides biosynthesis in mycobacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1355-1367. [PMID: 27826050 DOI: 10.1016/j.bbalip.2016.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/29/2016] [Accepted: 11/02/2016] [Indexed: 11/22/2022]
Abstract
Phosphatidyl-myo-inositol mannosides (PIMs) are glycolipids of unique chemical structure found in the inner and outer membranes of the cell envelope of all Mycobacterium species. The PIM family of glycolipids comprises phosphatidyl-myo-inositol mono-, di-, tri-, tetra-, penta-, and hexamannosides with different degrees of acylation. PIMs are considered not only essential structural components of the cell envelope but also the precursors of lipomannan and lipoarabinomannan, two major lipoglycans implicated in host-pathogen interactions. Since the description of the complete chemical structure of PIMs, major efforts have been committed to defining the molecular bases of its biosynthetic pathway. The structural characterization of the integral membrane phosphatidyl-myo-inositol phosphate synthase (PIPS), and that of three enzymes working at the protein-membrane interface, the phosphatidyl-myo-inositol mannosyltransferases A and B, and the acyltransferase PatA, established the basis of the early steps of the PIM pathway at the molecular level. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Abstract
The catalytic mechanism of retaining glycosyltransferases (ret-GTs) remains a controversial issue in glycobiology. By analogy to the well-established mechanism of retaining glycosidases, it was first suggested that ret-GTs follow a double-displacement mechanism. However, only family 6 GTs exhibit a putative nucleophile protein residue properly located in the active site to participate in catalysis, prompting some authors to suggest an unusual single-displacement mechanism [named as front-face or SNi (substitution nucleophilic internal)-like]. This mechanism has now received strong support, from both experiment and theory, for several GT families except family 6, for which a double-displacement reaction is predicted. In the last few years, we have uncovered the molecular mechanisms of several retaining GTs by means of quantum mechanics/molecular mechanics (QM/MM) metadynamics simulations, which we overview in the present work.
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31
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Albesa-Jové D, Guerin ME. The conformational plasticity of glycosyltransferases. Curr Opin Struct Biol 2016; 40:23-32. [DOI: 10.1016/j.sbi.2016.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/23/2016] [Accepted: 07/08/2016] [Indexed: 12/22/2022]
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32
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Ghirardello M, de Las Rivas M, Lacetera A, Delso I, Lira-Navarrete E, Tejero T, Martín-Santamaría S, Hurtado-Guerrero R, Merino P. Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates. Chemistry 2016; 22:7215-24. [PMID: 27071848 DOI: 10.1002/chem.201600467] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 12/11/2022]
Abstract
The Leloir donors are nucleotide sugars essential for a variety of glycosyltransferases (GTs) involved in the transfer of a carbohydrate to an acceptor substrate, typically a protein or an oligosaccharide. A series of less-polar nucleotide sugar analogues derived from uridine have been prepared by replacing one phosphate unit with an alkyl chain. The methodology is based on the radical hydrophosphonylation of alkenes, which allows coupling of allyl glycosyl compounds with a phosphate unit suitable for conjugation to uridine. Two of these compounds, the GalNAc and galactose derivatives, were further tested on a model GT, such as GalNAc-T2 (an important GT widely distributed in human tissues), to probe that both compounds bound in the medium-high micromolar range. The crystal structure of GalNAc-T2 with the galactose derivative traps the enzyme in an inactive form; this suggests that compounds only containing the β-phosphate could be efficient ligands for the enzyme. Computational studies with GalNAc-T2 corroborate these findings and provide further insights into the mechanism of the catalytic cycle of this family of enzymes.
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Affiliation(s)
- Mattia Ghirardello
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain
| | - Matilde de Las Rivas
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Alessandra Lacetera
- Departamento de Biología Físico-Química, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Ignacio Delso
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain
- Servicio de Resonancia Magnética Nuclear, Centro de Química y Materiales de Aragón (CEQMA), Universidad de Zaragoza, CSIC, Campus San Francisco, 50009, Zaragoza, Spain
| | - Erandi Lira-Navarrete
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain
| | - Tomás Tejero
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain
| | - Sonsoles Martín-Santamaría
- Departamento de Biología Físico-Química, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain.
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009, Zaragoza, Spain.
- Fundación ARAID, 50018, Zaragoza, Spain.
- Instituto de Investigaciones Sanitarias de Aragón (IIS-A), Zaragoza, 50009, Spain.
| | - Pedro Merino
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain.
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Mendoza F, Gómez H, Lluch JM, Masgrau L. α1,4-N-Acetylhexosaminyltransferase EXTL2: The Missing Link for Understanding Glycosidic Bond Biosynthesis with Retention of Configuration. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Fernanda Mendoza
- Institut
de Biotecnologia i de Biomedicina (IBB) and ‡Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Hansel Gómez
- Institut
de Biotecnologia i de Biomedicina (IBB) and ‡Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - José M. Lluch
- Institut
de Biotecnologia i de Biomedicina (IBB) and ‡Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Laura Masgrau
- Institut
de Biotecnologia i de Biomedicina (IBB) and ‡Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
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34
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Recent structural and mechanistic insights into protein O-GalNAc glycosylation. Biochem Soc Trans 2016; 44:61-7. [DOI: 10.1042/bst20150178] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein O-GalNAcylation is an abundant post-translational modification and predicted to occur in over 80% of the proteins passing through the Golgi apparatus. This modification is driven by 20 polypeptide GaINAc (N-acetylgalactosamine)-transferases (GalNAc-Ts), which are unique in that they possess both catalytic and lectin domains. The peptide substrate specificities of GalNAc-Ts are still poorly defined and our understanding of the sequence and structural features that direct O-glycosylation of proteins is limited. Part of this may be attributed to the complex regulation by coordinated action of multiple GalNAc-T isoforms, and part of this may also be attributed to the two functional domains of GalNAc-Ts that both seems to be involved in directing the substrate specificities. Recent studies have resulted in 3D structures of GalNAc-Ts and determination of the reaction mechanism of this family of enzymes. Key advances include the trapping of binary/ternary complexes in combination with computational simulations and AFM/small-SAXS experiments, which have allowed for the dissection of the reaction coordinates and the mechanism by which the lectin domains modulate the glycosylation. These studies not only broaden our knowledge of the modes-of-action of this family of enzymes but also open up potential avenues for the rational design of effective and selective inhibitors of O-glycosylation.
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