1
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Artola M, Aerts JMFG, van der Marel GA, Rovira C, Codée JDC, Davies GJ, Overkleeft HS. From Mechanism-Based Retaining Glycosidase Inhibitors to Activity-Based Glycosidase Profiling. J Am Chem Soc 2024; 146:24729-24741. [PMID: 39213505 DOI: 10.1021/jacs.4c08840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Activity-based protein profiling (ABPP) is an effective technology for the identification and functional annotation of enzymes in complex biological samples. ABP designs are normally directed to an enzyme active site nucleophile, and within the field of Carbohydrate-Active Enzymes (CAZymes), ABPP has been most successful for those enzymes that feature such a residue: retaining glycosidases (GHs). Several mechanism-based covalent and irreversible retaining GH inhibitors have emerged over the past sixty years. ABP designs based on these inhibitor chemistries appeared since the turn of the millennium, and we contributed to the field by designing a suite of retaining GH ABPs modeled on the structure and mode of action of the natural product, cyclophellitol. These ABPs enable the study of both exo- and endo-acting retaining GHs in human health and disease, for instance in genetic metabolic disorders in which retaining GHs are deficient. They are also finding increasing use in the study of GHs in gut microbiota and environmental microorganisms, both in the context of drug (de)toxification in the gut and that of biomass polysaccharide processing for future sustainable energy and chemistries. This account comprises the authors' view on the history of mechanism-based retaining GH inhibitor design and discovery, on how these inhibitors served as blueprints for retaining GH ABP design, and on some current and future developments on how cyclophellitol-based ABPs may drive the discovery of retaining GHs and their inhibitors.
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Affiliation(s)
- Marta Artola
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Johannes M F G Aerts
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | | | - Carme Rovira
- Departament de Química Inorgànica I Orgànica & IQTCUB, Universitat de Barcelona, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08020, Spain
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Gideon J Davies
- Department of Chemistry, The University York, Heslington, York YO10 5DD, United Kingdom
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
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2
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Wardman JF, Withers SG. Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening. RSC Chem Biol 2024; 5:595-616. [PMID: 38966674 PMCID: PMC11221537 DOI: 10.1039/d4cb00024b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
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3
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Rossetti G, Mandelli D. How exascale computing can shape drug design: A perspective from multiscale QM/MM molecular dynamics simulations and machine learning-aided enhanced sampling algorithms. Curr Opin Struct Biol 2024; 86:102814. [PMID: 38631106 DOI: 10.1016/j.sbi.2024.102814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/11/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024]
Abstract
Molecular simulations are an essential asset in the first steps of drug design campaigns. However, the requirement of high-throughput limits applications mainly to qualitative approaches with low computational cost, but also low accuracy. Unlocking the potential of more rigorous quantum mechanical/molecular mechanics (QM/MM) models combined with molecular dynamics-based free energy techniques could have a tremendous impact. Indeed, these two relatively old techniques are emerging as promising methods in the field. This has been favored by the exponential growth of computer power and the proliferation of powerful data-driven methods. Here, we briefly review recent advances and applications, and give our perspective on the impact that QM/MM and free-energy methods combined with machine learning-aided algorithms can have on drug design.
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Affiliation(s)
- Giulia Rossetti
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany; Department of Neurology, University Hospital Aachen (UKA), RWTH Aachen University, Aachen, Germany; Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Jülich 52428, Germany. https://twitter.com/G_Rossetti_
| | - Davide Mandelli
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany.
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4
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Fujita K, Tsunomachi H, Lixia P, Maruyama S, Miyake M, Dakeshita A, Kitahara K, Tanaka K, Ito Y, Ishiwata A, Fushinobu S. Bifidobacterial GH146 β-L-arabinofuranosidase for the removal of β1,3-L-arabinofuranosides on plant glycans. Appl Microbiol Biotechnol 2024; 108:199. [PMID: 38324037 PMCID: PMC10850190 DOI: 10.1007/s00253-024-13014-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/29/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024]
Abstract
L-Arabinofuranosides with β-linkages are present in several plant molecules, such as arabinogalactan proteins (AGPs), extensin, arabinan, and rhamnogalacturonan-II. We previously characterized a β-L-arabinofuranosidase from Bifidobacterium longum subsp. longum JCM 1217, Bll1HypBA1, which was found to belong to the glycoside hydrolase (GH) family 127. This strain encodes two GH127 genes and two GH146 genes. In the present study, we characterized a GH146 β-L-arabinofuranosidase, Bll3HypBA1 (BLLJ_1848), which was found to constitute a gene cluster with AGP-degrading enzymes. This recombinant enzyme degraded AGPs and arabinan, which contain Araf-β1,3-Araf structures. In addition, the recombinant enzyme hydrolyzed oligosaccharides containing Araf-β1,3-Araf structures but not those containing Araf-β1,2-Araf and Araf-β1,5-Araf structures. The crystal structures of Bll3HypBA1 were determined at resolutions up to 1.7 Å. The monomeric structure of Bll3HypBA1 comprised a catalytic (α/α)6 barrel and two β-sandwich domains. A hairpin structure with two β-strands was observed in Bll3HypBA1, to extend from a β-sandwich domain and partially cover the active site. The active site contains a Zn2+ ion coordinated by Cys3-Glu and exhibits structural conservation of the GH127 cysteine glycosidase Bll1HypBA1. This is the first study to report on a β1,3-specific β-L-arabinofuranosidase. KEY POINTS: • β1,3-l-Arabinofuranose residues are present in arabinogalactan proteins and arabinans as a terminal sugar. • β-l-Arabinofuranosidases are widely present in intestinal bacteria. • Bll3HypBA1 is the first enzyme characterized as a β1,3-linkage-specific β-l-arabinofuranosidase.
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Affiliation(s)
- Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
| | - Hanako Tsunomachi
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Pan Lixia
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
- National Key Laboratory of Non-food Biomass Energy Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Shun Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Masayuki Miyake
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Aimi Dakeshita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kanefumi Kitahara
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8552, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-Cho, Toyonaka, Osaka, 560-0043, Japan
| | - Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
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5
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McGregor NS, de Boer C, Foucart QPO, Beenakker T, Offen WA, Codée JDC, Willems LI, Overkleeft HS, Davies GJ. A Multiplexing Activity-Based Protein-Profiling Platform for Dissection of a Native Bacterial Xyloglucan-Degrading System. ACS CENTRAL SCIENCE 2023; 9:2306-2314. [PMID: 38161374 PMCID: PMC10755729 DOI: 10.1021/acscentsci.3c00831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/26/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Bacteria and yeasts grow on biomass polysaccharides by expressing and excreting a complex array of glycoside hydrolase (GH) enzymes. Identification and annotation of such GH pools, which are valuable commodities for sustainable energy and chemistries, by conventional means (genomics, proteomics) are complicated, as primary sequence or secondary structure alignment with known active enzymes is not always predictive for new ones. Here we report a "low-tech", easy-to-use, and sensitive multiplexing activity-based protein-profiling platform to characterize the xyloglucan-degrading GH system excreted by the soil saprophyte, Cellvibrio japonicus, when grown on xyloglucan. A suite of activity-based probes bearing orthogonal fluorophores allows for the visualization of accessory exo-acting glycosidases, which are then identified using biotin-bearing probes. Substrate specificity of xyloglucanases is directly revealed by imbuing xyloglucan structural elements into bespoke activity-based probes. Our ABPP platform provides a highly useful tool to dissect xyloglucan-degrading systems from various sources and to rapidly select potentially useful ones. The observed specificity of the probes moreover bodes well for the study of other biomass polysaccharide-degrading systems, by modeling probe structures to those of desired substrates.
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Affiliation(s)
| | - Casper de Boer
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Quentin P. O. Foucart
- Department
of Chemistry, The University of York, Heslington, York YO10 5DD, United
Kingdom
| | - Thomas Beenakker
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Wendy A. Offen
- Department
of Chemistry, The University of York, Heslington, York YO10 5DD, United
Kingdom
| | - Jeroen D. C. Codée
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Lianne I. Willems
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, Heslington, York YO10 5DD, United
Kingdom
| | - Herman S. Overkleeft
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Gideon J. Davies
- Department
of Chemistry, The University of York, Heslington, York YO10 5DD, United
Kingdom
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6
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Borlandelli V, Offen W, Moroz O, Nin-Hill A, McGregor N, Binkhorst L, Ishiwata A, Armstrong Z, Artola M, Rovira C, Davies GJ, Overkleeft HS. β-l- Arabinofurano-cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes for Retaining β-l-Arabinofuranosidases. ACS Chem Biol 2023; 18:2564-2573. [PMID: 38051515 PMCID: PMC10728902 DOI: 10.1021/acschembio.3c00558] [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] [Received: 09/11/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023]
Abstract
GH127 and GH146 microorganismal retaining β-l-arabinofuranosidases, expressed by human gut microbiomes, feature an atypical catalytic domain and an unusual mechanism of action. We recently reported that both Bacteroides thetaiotaomicron BtGH146 and Bifidobacterium longum HypBA1 are inhibited by β-l-arabinofuranosyl cyclophellitol epoxide, supporting the action of a zinc-coordinated cysteine as a catalytic nucleophile, where in most retaining GH families, an aspartate or glutamate is employed. This work presents a panel of β-l-arabinofuranosyl cyclophellitol epoxides and aziridines as mechanism-based BtGH146/HypBA1 inhibitors and activity-based probes. The β-l-arabinofuranosyl cyclophellitol aziridines both inhibit and label β-l-arabinofuranosidase efficiently (however with different activities), whereas the epoxide-derived probes favor BtGH146 over HypBA1. These findings are accompanied by X-ray structural analysis of the unmodified β-l-arabinofuranosyl cyclophellitol aziridine in complex with both isozymes, which were shown to react by nucleophilic opening of the aziridine, at the pseudoanomeric carbon, by the active site cysteine nucleophile to form a stable thioether bond. Altogether, our activity-based probes may serve as chemical tools for the detection and identification of low-abundance β-l-arabinofuranosidases in complex biological samples.
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Affiliation(s)
- Valentina Borlandelli
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Wendy Offen
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Olga Moroz
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Alba Nin-Hill
- 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
| | - Nicholas McGregor
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Lars Binkhorst
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Akihiro Ishiwata
- RIKEN
Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Zachary Armstrong
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Marta Artola
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - 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
| | - Gideon J. Davies
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Herman S. Overkleeft
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
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7
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Calvelo M, Males A, Alteen MG, Willems LI, Vocadlo DJ, Davies GJ, Rovira C. Human O-GlcNAcase Uses a Preactivated Boat-skew Substrate Conformation for Catalysis. Evidence from X-ray Crystallography and QM/MM Metadynamics. ACS Catal 2023; 13:13672-13678. [PMID: 37969138 PMCID: PMC10636738 DOI: 10.1021/acscatal.3c02378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/07/2023] [Indexed: 11/17/2023]
Abstract
Human O-linked β-N-acetylglucosaminidase (hOGA) is one of the two enzymes involved in nuclear and cytoplasmic protein O-GlcNAcylation, an essential post-translational modification. The enzyme catalyzes the hydrolysis of the GlcNAc-O-(Ser/Thr) glycosidic bonds via anchimeric assistance through the 2-acetamido group of the GlcNAc sugar. However, the conformational itinerary of the GlcNAc ring during catalysis remains unclear. Here we report the crystal structure of wild type hOGA in complex with a nonhydrolyzable glycopeptide substrate and elucidate the full enzyme catalytic mechanism using QM/MM metadynamics. We show that the enzyme can bind the substrate in either a chair- or a boat-like conformation, but only the latter is catalytically competent, leading to the reaction products via 1,4B/1S3 → [4E]‡ → 4C1 and 4C1 → [4E]‡ → 1,4B/1S3 conformational itineraries for the first and second catalytic reaction steps, respectively. Our results reconcile previous experimental observations for human and bacterial OGA and will aid the development of more effective OGA inhibitors for diseases associated with impaired O-GlcNAcylation.
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Affiliation(s)
- Martín Calvelo
- Departament
de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Alexandra Males
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, United Kingdom
| | - Matthew G. Alteen
- Department
of Chemistry & Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Lianne I. Willems
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, United Kingdom
| | - David J. Vocadlo
- Department
of Chemistry & Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, United Kingdom
| | - 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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8
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Morais MAB, Nin-Hill A, Rovira C. Glycosidase mechanisms: Sugar conformations and reactivity in endo- and exo-acting enzymes. Curr Opin Chem Biol 2023; 74:102282. [PMID: 36931022 DOI: 10.1016/j.cbpa.2023.102282] [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: 11/10/2022] [Revised: 01/19/2023] [Accepted: 02/09/2023] [Indexed: 03/17/2023]
Abstract
The enzymatic breakdown of carbohydrates plays a critical role in several biological events and enables the development of sustainable processes to obtain bioproducts and biofuels. In this scenario, the design of efficient inhibitors for glycosidases that can act as drug targets and the engineering of carbohydrate-active enzymes with tailored catalytic properties is of remarkable importance. To guide rational approaches, it is necessary to elucidate enzyme molecular mechanisms, in particular understanding how the microenvironment modulates the conformational space explored by the substrate. Computer simulations, especially those based on ab initio methods, have provided a suitable atomic description of carbohydrate conformations and catalytic reactions in several glycosidase families. In this review, we will focus on how the active-site topology (pocket or cleft) and mode of cleavage (endo or exo) can affect the catalytic mechanisms adopted by glycosidases, in particular the substrate conformations along the reaction coordinate.
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Affiliation(s)
- Mariana Abrahão Bueno Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil
| | - Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
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9
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Ishiwata A, Tsunomachi H, Kameyama K, Sophon K, Nakamura M, Kitahara K, Tanaka K, Ito Y, Fujita K. Bifidobacterial GH146 β-l-Arabinofuranosidase (Bll4HypBA1) as the Last Enzyme for the Complete Removal of Oligoarabinofuranosides from Hydroxyproline-Rich Glycoproteins. Chembiochem 2023; 24:e202200637. [PMID: 36579407 DOI: 10.1002/cbic.202200637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022]
Abstract
In plant cell walls, the hydroxyproline-rich glycoproteins (HRGPs) such as extensin contain oligoarabinofuranoside linked to a hydroxyproline (Hyp) residue. The mature arabinooligosaccharide was revealed to be a tetrasaccharide (α-l-Araf-(1→3)-β-l-Araf-(1→2)-β-l-Araf-(1→2)-β-l-Araf, l-Araf4 ), whose linkages are targets of the bifidobacterial and Xanthomonas arabinooligosaccharide-degrading enzymes. The l-Araf4 motif was cleaved by GH43 α-l-arabinofuranosidase (Arafase) and converted to an l-Araf3 -linked structure. The latter is then cleaved by GH121 β-l-arabinobiosidase (HypBA2), producing β-l-Araf-(1→2)-l-Ara (β-l-arabinobiose) and mono-β-l-Araf linked to the HRGP backbone. In bifidobacteria, the β-l-arabinobiose is then hydrolyzed by GH127 β-l-Arafase (Bll1HypBA1), a mechanistically unique cysteine glycosidase. We recently identified the distantly related homologue from Xanthomonas euvesicatoria as GH146 β-l-Arafase along with paralogues from Bifidobacterium longum, one of which, Bll4HypBA1 (BLLJ_0089), can degrade l-Araf1 -Hyp in a similar way to that of GH146. As the chemical synthesis of the extensin hydrophilic motif 1 a, which possesses three distinct linkages that connect four oligoAraf residues [Hyp(l-Arafn ) (n=4, 3, 1)], was achieved previously, we precisely monitored the step-wise enzymatic cleavage of 1 a in addition to that of potato lectin. The results unequivocally revealed that this enzyme specifically degrades the Hyp(l-Araf1 ) motif.
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Affiliation(s)
- Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hanako Tsunomachi
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kyohei Kameyama
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kaeothip Sophon
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Masayuki Nakamura
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kanefumi Kitahara
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8552, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
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10
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Ishiwata A, Narita S, Kimura K, Tanaka K, Fujita K, Fushinobu S, Ito Y. Mechanism-based inhibition of GH127/146 cysteine glycosidases by stereospecifically functionalized l-arabinofuranosides. Bioorg Med Chem 2022; 75:117054. [PMID: 36334492 DOI: 10.1016/j.bmc.2022.117054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022]
Abstract
To understand the precise mechanism of the glycoside hydrolase (GH) family 127, a cysteine β-l-arabinofuranosidase (Arafase) - HypBA1 - has been isolated from Bifidobacterium longum in the human Gut microbiota, and the design and synthesis of the mechanism-based inhibitors such as l-Araf-haloacetamides have been carried out. The α-l-Araf-azide derivative was used as the monoglycosylamine equivalent to afford the l-Araf-chloroacetamides (α/β-1-Cl) as well as bromoacetamides (α/β-1-Br) in highly stereoselective manner through Staudinger reaction followed by amide formation with/without anomerization. Against HypBA1, the probes 1, especially in the case of α/β-1-Br inhibited the hydrolysis. Conformational implications of these observations are discussed in this manuscript. Additional examinations using l-Araf-azides (α/β-5) resulted in further mechanistic observations of the GH127/146 cysteine glycosidases, including the hydrolysis of β-5 as the substrate and oxidative inhibition by α-5 using the GH127 homologue.
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Affiliation(s)
- Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan.
| | - Satoru Narita
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Systems Engineering and Science, Shibaura Institute of Technology Saitama 337-8570, Japan
| | - Kenta Kimura
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Systems Engineering and Science, Shibaura Institute of Technology Saitama 337-8570, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Department of Chemical Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo 113-8647, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8647, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
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11
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Jeong WJ, Song WJ. Design and directed evolution of noncanonical β-stereoselective metalloglycosidases. Nat Commun 2022; 13:6844. [PMID: 36369431 PMCID: PMC9652281 DOI: 10.1038/s41467-022-34713-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 11/03/2022] [Indexed: 11/13/2022] Open
Abstract
Metallohydrolases are ubiquitous in nearly all subclasses of hydrolases, utilizing metal elements to activate a water molecule and facilitate its subsequent dissociation of diverse chemical bonds. However, such a catalytic role of metal ions is rarely found with glycosidases that hydrolyze the glycosidic bonds in sugars. Herein, we design metalloglycosidases by constructing a hydrolytically active Zn-binding site within a barrel-shaped outer membrane protein OmpF. Structure- and mechanism-based redesign and directed evolution have led to the emergence of Zn-dependent glycosidases with catalytic proficiency of 2.8 × 109 and high β-stereoselectivity. Biochemical characterizations suggest that the Zn-binding site constitutes a key catalytic motif along with at least one adjacent acidic residue. This work demonstrates that unprecedented metalloenzymes can be tailor-made, expanding the scope of inorganic reactivities in proteinaceous environments, resetting the structural and functional diversity of metalloenzymes, and providing the potential molecular basis of unidentified metallohydrolases and novel whole-cell biocatalysts.
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Affiliation(s)
- Woo Jae Jeong
- grid.31501.360000 0004 0470 5905Department of Chemistry, Seoul National University, Seoul, 08826 Republic of Korea
| | - Woon Ju Song
- grid.31501.360000 0004 0470 5905Department of Chemistry, Seoul National University, Seoul, 08826 Republic of Korea
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12
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Forrester TJB, Ovchinnikova OG, Li Z, Kitova EN, Nothof JT, Koizumi A, Klassen JS, Lowary TL, Whitfield C, Kimber MS. The retaining β-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step. Nat Commun 2022; 13:6277. [PMID: 36271007 PMCID: PMC9587256 DOI: 10.1038/s41467-022-33988-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
WbbB, a lipopolysaccharide O-antigen synthesis enzyme from Raoultella terrigena, contains an N-terminal glycosyltransferase domain with a highly modified architecture that adds a terminal β-Kdo (3-deoxy-D-manno-oct-2-ulosonic acid) residue to the O-antigen saccharide, with retention of stereochemistry. We show, using mass spectrometry, that WbbB forms a covalent adduct between the catalytic nucleophile, Asp232, and Kdo. We also determine X-ray structures for the CMP-β-Kdo donor complex, for Kdo-adducts with D232N and D232C WbbB variants, for a synthetic disaccharide acceptor complex, and for a ternary complex with both a Kdo-adduct and the acceptor. Together, these structures show that the enzyme-linked Asp232-Kdo adduct rotates to reposition the Kdo into a second sub-site, which then transfers Kdo to the acceptor. Retaining glycosyltransferases were thought to use only the front-side SNi substitution mechanism; here we show that retaining glycosyltransferases can also potentially use double-displacement mechanisms, but incorporating an additional catalytic subsite requires rearrangement of the protein's architecture.
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Affiliation(s)
- Taylor J. B. Forrester
- grid.34429.380000 0004 1936 8198Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1 Canada
| | - Olga G. Ovchinnikova
- grid.34429.380000 0004 1936 8198Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1 Canada
| | - Zhixiong Li
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - Elena N. Kitova
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - Jeremy T. Nothof
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - Akihiko Koizumi
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - John S. Klassen
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - Todd L. Lowary
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada ,grid.506934.d0000 0004 0633 7878Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128, Nangang, Taipei, 11529 Taiwan ,grid.19188.390000 0004 0546 0241Institute of Biochemical Sciences, National Taiwan University, Section 4, #1, Roosevelt Road, Taipei, 10617 Taiwan
| | - Chris Whitfield
- grid.34429.380000 0004 1936 8198Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1 Canada
| | - Matthew S. Kimber
- grid.34429.380000 0004 1936 8198Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1 Canada
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13
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Synthesis of naturally occurring β-l-arabinofuranosyl-l-arabinofuranoside structures towards the substrate specificity evaluation of β-l-arabinofuranosidase. Bioorg Med Chem 2022; 68:116849. [PMID: 35653870 DOI: 10.1016/j.bmc.2022.116849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/23/2022]
Abstract
Methyl β-l-arabinofuranosyl-(1 → 2)-, -(1 → 3)-, and -(1 → 5)-α-l-arabinofuranosides have been stereoselectively synthesized through 2-naphthylmethyl ether-mediated intramolecular aglycon delivery (NAP-IAD), whose β-linkages were confirmed by NMR analysis on the 3JH1-H2 coupling constant and 13C chemical shift of C1. The NAP-IAD approach was simply extended for the synthesis of trisaccharide motifs possessing β-l-arabinofuranosyl-(1 → 5)-l-arabinofuranosyl non-reducing terminal structure with the branched β-l-arabinofuranosyl-(1 → 5)-[α-l-arabinofuranosyl-(1 → 3)]-α-l-arabinofuranosyl and the liner β-l-arabinofuranosyl-(1 → 5)-β-l-arabinofuranosyl-(1 → 5)-β-l-arabinofuranosyl structures in olive arabinan and dinoflagellate polyethers, respectively. The results on the substrate specificity of a bifidobacterial β-l-arabinofuranosidase HypBA1 using the regioisomers indicated that HypBA1 could hydrolyze all three linkages however behaved clearly less active to β-(1 → 5)-linked disaccharide than other two regioisomers including the proposed natural degradation product, β-(1 → 2)-linked one from plant extracellular matrix such as extensin. On the other hand, Xanthomonas XeHypBA1 was found to hydrolyze all three disaccharides as the substrate with higher specificity to β-(1 → 2)-linkage than bifidobacterial HypBA1.
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14
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McGregor NGS, Overkleeft HS, Davies GJ. Detecting and identifying glycoside hydrolases using cyclophellitol-derived activity-based probes. Methods Enzymol 2022; 664:103-134. [PMID: 35331370 DOI: 10.1016/bs.mie.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability to detect active enzymes in a complex mixture of folded proteins (e.g., secretome, cell lysate) generally relies on observations of catalytic ability, necessitating the development of an activity assay that is compatible with the sample and selective for the enzyme(s) of interest. Deconvolution of the contributions of different enzymes to an observed catalytic ability further necessitates an often-challenging protein separation. The advent of broadly reactive activity-based probes (ABPs) for retaining glycoside hydrolases (GHs) has enabled an alternative, often complementary, assay for active GHs. Using activity-based protein profiling (ABPP) techniques, many retaining glycoside hydrolases can be separated, detected, and identified with high sensitivity and selectivity. This chapter outlines ABPP methods for the detection and identification of retaining glycoside hydrolases from microbial sources, including protein sample preparation from bacterial lysates and fungal secretomes, enzyme labeling and detection via fluorescence, and enzyme identification using affinity-based enrichment coupled to peptide sequencing following isobaric labeling.
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Affiliation(s)
- Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom.
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15
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McGregor NGS, Kuo CL, Beenakker TJM, Wong CS, Offen WA, Armstrong Z, Florea BI, Codée JDC, Overkleeft HS, Aerts JMFG, Davies GJ. Synthesis of broad-specificity activity-based probes for exo-β-mannosidases. Org Biomol Chem 2022; 20:877-886. [PMID: 35015006 PMCID: PMC8790593 DOI: 10.1039/d1ob02287c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Exo-β-mannosidases are a broad class of stereochemically retaining hydrolases that are essential for the breakdown of complex carbohydrate substrates found in all kingdoms of life. Yet the detection of exo-β-mannosidases in complex biological samples remains challenging, necessitating the development of new methodologies. Cyclophellitol and its analogues selectively label the catalytic nucleophiles of retaining glycoside hydrolases, making them valuable tool compounds. Furthermore, cyclophellitol can be readily redesigned to enable the incorporation of a detection tag, generating activity-based probes (ABPs) that can be used to detect and identify specific glycosidases in complex biological samples. Towards the development of ABPs for exo-β-mannosidases, we present a concise synthesis of β-manno-configured cyclophellitol, cyclophellitol aziridine, and N-alkyl cyclophellitol aziridines. We show that these probes covalently label exo-β-mannosidases from GH families 2, 5, and 164. Structural studies of the resulting complexes support a canonical mechanism-based mode of action in which the active site nucleophile attacks the pseudoanomeric centre to form a stable ester linkage, mimicking the glycosyl enzyme intermediate. Furthermore, we demonstrate activity-based protein profiling using an N-alkyl aziridine derivative by specifically labelling MANBA in mouse kidney tissue. Together, these results show that synthetic manno-configured cyclophellitol analogues hold promise for detecting exo-β-mannosidases in biological and biomedical research.
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Affiliation(s)
- Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK.
| | - Chi-Lin Kuo
- Department of Bio-Organic Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Thomas J M Beenakker
- Department of Bio-Organic Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Chun-Sing Wong
- Department of Bio-Organic Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Wendy A Offen
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK.
| | - Zachary Armstrong
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK.
| | - Bogdan I Florea
- Department of Bio-Organic Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Jeroen D C Codée
- Department of Bio-Organic Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Herman S Overkleeft
- Department of Bio-Organic Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK.
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16
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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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17
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Maruyama S, Sawano K, Amaki S, Suzuki T, Narita S, Kimura K, Arakawa T, Yamada C, Ito Y, Dohmae N, Fujita K, Ishiwata A, Fushinobu S. Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase. Glycobiology 2021; 32:171-180. [PMID: 34735571 DOI: 10.1093/glycob/cwab103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/16/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
β-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At the active site of HypBA1, a cysteine residue (Cys417) coordinates with a Zn2+ atom and functions as the catalytic nucleophile for the anomer-retaining hydrolytic reaction. In this study, the role of Zn2+ ion and cysteine in catalysis as well as the substrate-bound structure were studied based on biochemical and crystallographic approaches. The enzymatic activity of HypBA1 decreased after dialysis in the presence of EDTA and guanidine hydrochloride and was then recovered by the addition of Zn2+. The Michaelis complex structure was determined using a crystal of a mutant at the acid/base catalyst residue (E322Q) soaked in a solution containing the substrate p-nitrophenyl-β-l-arabinofuranoside. To investigate the covalent thioglycosyl enzyme intermediate structure, synthetic inhibitors of l-arabinofuranosyl haloacetamide derivatives with different anomer configurations were used to target the nucleophilic cysteine. In the crystal structure of HypBA1, β-configured l-arabinofuranosylamide formed a covalent link with Cys417, whereas α-configured l-arabinofuranosylamide was linked to a noncatalytic residue Cys415. Mass spectrometric analysis indicated that Cys415 was also reactive with the probe molecule. With the β-configured inhibitor, the arabinofuranoside moiety was correctly positioned at the subsite and the active site integrity was retained to successfully mimic the covalent intermediate state.
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Affiliation(s)
- Shun Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kota Sawano
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoko Amaki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takehiro Suzuki
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Satoru Narita
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Kenta Kimura
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chihaya Yamada
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yukishige Ito
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Science, Osaka University, 1-1 Machikaneyamacho, Toyonaka, Osaka 560-0043, Japan
| | - Naoshi Dohmae
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Akihiro Ishiwata
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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18
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Structure and evolution of the bifidobacterial carbohydrate metabolism proteins and enzymes. Biochem Soc Trans 2021; 49:563-578. [PMID: 33666221 PMCID: PMC8106489 DOI: 10.1042/bst20200163] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/05/2023]
Abstract
Bifidobacteria have attracted significant attention because they provide health-promoting effects in the human gut. In this review, we present a current overview of the three-dimensional structures of bifidobacterial proteins involved in carbohydrate uptake, degradation, and metabolism. As predominant early colonizers of the infant's gut, distinct bifidobacterial species are equipped with a panel of transporters and enzymes specific for human milk oligosaccharides (HMOs). Interestingly, Bifidobacterium bifidum and Bifidobacterium longum possess lacto-N-biosidases with unrelated structural folds to release the disaccharide lacto-N-biose from HMOs, suggesting the convergent evolution of this activity from different ancestral proteins. The crystal structures of enzymes that confer the degradation of glycans from the mucin glycoprotein layer provide a structural basis for the utilization of this sustainable nutrient in the gastrointestinal tract. The utilization of several plant dietary oligosaccharides has been studied in detail, and the prime importance of oligosaccharide-specific ATP-binding cassette (ABC) transporters in glycan utilisations by bifidobacteria has been revealed. The structural elements underpinning the high selectivity and roles of ABC transporter binding proteins in establishing competitive growth on preferred oligosaccharides are discussed. Distinct ABC transporters are conserved across several bifidobacterial species, e.g. those targeting arabinoxylooligosaccharide and α-1,6-galactosides/glucosides. Less prevalent transporters, e.g. targeting β-mannooligosaccharides, may contribute to the metabolic specialisation within Bifidobacterium. Some bifidobacterial species have established symbiotic relationships with humans. Structural studies of carbohydrate-utilizing systems in Bifidobacterium have revealed the interesting history of molecular coevolution with the host, as highlighted by the early selection of bifidobacteria by mucin and breast milk glycans.
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