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Dutkiewicz Z, Varrot A, Breese KJ, Stubbs KA, Nuschy L, Adduci I, Paschinger K, Wilson IBH. Bioinformatic, Enzymatic, and Structural Characterization of Trichuris suis Hexosaminidase HEX-2. Biochemistry 2024; 63:1941-1954. [PMID: 39058279 PMCID: PMC11308363 DOI: 10.1021/acs.biochem.4c00187] [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: 04/11/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
Hexosaminidases are key enzymes in glycoconjugate metabolism and occur in all kingdoms of life. Here, we have investigated the phylogeny of the GH20 glycosyl hydrolase family in nematodes and identified a β-hexosaminidase subclade present only in the Dorylaimia. We have expressed one of these, HEX-2 from Trichuris suis, a porcine parasite, and shown that it prefers an aryl β-N-acetylgalactosaminide in vitro. HEX-2 has an almost neutral pH optimum and is best inhibited by GalNAc-isofagomine. Toward N-glycan substrates, it displays a preference for the removal of GalNAc residues from LacdiNAc motifs as well as the GlcNAc attached to the α1,3-linked core mannose. Therefore, it has a broader specificity than insect fused lobe (FDL) hexosaminidases but one narrower than distant homologues from plants. Its X-ray crystal structure, the first of any subfamily 1 GH20 hexosaminidase to be determined, is closest to Streptococcus pneumoniae GH20C and the active site is predicted to be compatible with accommodating both GalNAc and GlcNAc. The new structure extends our knowledge about this large enzyme family, particularly as T. suis HEX-2 also possesses the key glutamate residue found in human hexosaminidases of either GH20 subfamily, including HEXD whose biological function remains elusive.
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Affiliation(s)
- Zuzanna Dutkiewicz
- Institut
für Biochemie, Department für Chemie, Universität für Bodenkultur, Muthgasse 18, Wien 1190, Austria
| | | | - Karen J. Breese
- School
of Molecular Sciences, University of Western
Australia, Crawley, WA 6009, Australia
| | - Keith A. Stubbs
- School
of Molecular Sciences, University of Western
Australia, Crawley, WA 6009, Australia
- ARC
Training Centre for Next-Gen Technologies in Biomedical Analysis,
School of Molecular Sciences, University
of Western Australia, Crawley, WA 6009, Australia
| | - Lena Nuschy
- Institut
für Biochemie, Department für Chemie, Universität für Bodenkultur, Muthgasse 18, Wien 1190, Austria
| | - Isabella Adduci
- Institut
für Parasitologie, Department für Pathobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Wien A-1210, Austria
| | - Katharina Paschinger
- Institut
für Biochemie, Department für Chemie, Universität für Bodenkultur, Muthgasse 18, Wien 1190, Austria
| | - Iain B. H. Wilson
- Institut
für Biochemie, Department für Chemie, Universität für Bodenkultur, Muthgasse 18, Wien 1190, Austria
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2
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Zhang Z, Dong M, Zallot R, Blackburn GM, Wang N, Wang C, Chen L, Baumann P, Wu Z, Wang Z, Fan H, Roth C, Jin Y, He Y. Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zhen Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Mochen Dong
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Rémi Zallot
- Institute of Life Sciences, Swansea University Medical School, Swansea SA2 8PP, U.K
| | - George Michael Blackburn
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, U.K
| | - Nini Wang
- Key Laboratory of Synthetic and Natural Functional Molecule, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Chengjian Wang
- Glycobiology and Glycotechnology Research Center, College of Food Science and Technology, Northwest University, Xi’an 710069, P. R. China
| | - Long Chen
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Patrick Baumann
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Zuyan Wu
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Zhongfu Wang
- Glycobiology and Glycotechnology Research Center, College of Food Science and Technology, Northwest University, Xi’an 710069, P. R. China
| | - Haiming Fan
- Key Laboratory of Synthetic and Natural Functional Molecule, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Christian Roth
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Arnimallee 22, 14195 Berlin, German
| | - Yi Jin
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Yuan He
- Key Laboratory of Synthetic and Natural Functional Molecule, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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3
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Chen X, Li M, Wang Y, Tang R, Zhang M. Biochemical characteristics and crystallographic evidence for substrate-assisted catalysis of a β-N-acetylhexosaminidase in Akkermansia muciniphila. Biochem Biophys Res Commun 2019; 517:29-35. [DOI: 10.1016/j.bbrc.2019.06.150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 06/19/2019] [Accepted: 06/27/2019] [Indexed: 02/08/2023]
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4
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Revisiting glycoside hydrolase family 20 β-N-acetyl-d-hexosaminidases: Crystal structures, physiological substrates and specific inhibitors. Biotechnol Adv 2018; 36:1127-1138. [DOI: 10.1016/j.biotechadv.2018.03.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/18/2018] [Accepted: 03/19/2018] [Indexed: 12/31/2022]
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5
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Harit VK, Ramesh NG. Amino-functionalized iminocyclitols: synthetic glycomimetics of medicinal interest. RSC Adv 2016. [DOI: 10.1039/c6ra23513a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A review on the syntheses and biological activities of unnatural glycomimetics highlighting the effect of replacement of hydroxyl groups of natural iminosugars by amino functionalities is presented.
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Affiliation(s)
- Vimal Kant Harit
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi - 110016
- India
| | - Namakkal G. Ramesh
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi - 110016
- India
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6
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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Val-Cid C, Biarnés X, Faijes M, Planas A. Structural-Functional Analysis Reveals a Specific Domain Organization in Family GH20 Hexosaminidases. PLoS One 2015; 10:e0128075. [PMID: 26024355 PMCID: PMC4449183 DOI: 10.1371/journal.pone.0128075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 04/23/2015] [Indexed: 12/20/2022] Open
Abstract
Hexosaminidases are involved in important biological processes catalyzing the hydrolysis of N-acetyl-hexosaminyl residues in glycosaminoglycans and glycoconjugates. The GH20 enzymes present diverse domain organizations for which we propose two minimal model architectures: Model A containing at least a non-catalytic GH20b domain and the catalytic one (GH20) always accompanied with an extra α-helix (GH20b-GH20-α), and Model B with only the catalytic GH20 domain. The large Bifidobacterium bifidum lacto-N-biosidase was used as a model protein to evaluate the minimal functional unit due to its interest and structural complexity. By expressing different truncated forms of this enzyme, we show that Model A architectures cannot be reduced to Model B. In particular, there are two structural requirements general to GH20 enzymes with Model A architecture. First, the non-catalytic domain GH20b at the N-terminus of the catalytic GH20 domain is required for expression and seems to stabilize it. Second, the substrate-binding cavity at the GH20 domain always involves a remote element provided by a long loop from the catalytic domain itself or, when this loop is short, by an element from another domain of the multidomain structure or from the dimeric partner. Particularly, the lacto-N-biosidase requires GH20b and the lectin-like domain at the N- and C-termini of the catalytic GH20 domain to be fully soluble and functional. The lectin domain provides this remote element to the active site. We demonstrate restoration of activity of the inactive GH20b-GH20-α construct (model A architecture) by a complementation assay with the lectin-like domain. The engineering of minimal functional units of multidomain GH20 enzymes must consider these structural requirements.
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Affiliation(s)
- Cristina Val-Cid
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
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Kulik N, Slámová K, Ettrich R, Křen V. Computational study of β-N-acetylhexosaminidase from Talaromyces flavus, a glycosidase with high substrate flexibility. BMC Bioinformatics 2015; 16:28. [PMID: 25627923 PMCID: PMC4384365 DOI: 10.1186/s12859-015-0465-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/15/2015] [Indexed: 01/17/2023] Open
Abstract
Background β-N-Acetylhexosaminidase (GH20) from the filamentous fungus Talaromyces flavus, previously identified as a prominent enzyme in the biosynthesis of modified glycosides, lacks a high resolution three-dimensional structure so far. Despite of high sequence identity to previously reported Aspergillus oryzae and Penicilluim oxalicum β-N-acetylhexosaminidases, this enzyme tolerates significantly better substrate modification. Understanding of key structural features, prediction of effective mutants and potential substrate characteristics prior to their synthesis are of general interest. Results Computational methods including homology modeling and molecular dynamics simulations were applied to shad light on the structure-activity relationship in the enzyme. Primary sequence analysis revealed some variable regions able to influence difference in substrate affinity of hexosaminidases. Moreover, docking in combination with consequent molecular dynamics simulations of C-6 modified glycosides enabled us to identify the structural features required for accommodation and processing of these bulky substrates in the active site of hexosaminidase from T. flavus. To access the reliability of predictions on basis of the reported model, all results were confronted with available experimental data that demonstrated the principal correctness of the predictions as well as the model. Conclusions The main variable regions in β-N-acetylhexosaminidases determining difference in modified substrate affinity are located close to the active site entrance and engage two loops. Differences in primary sequence and the spatial arrangement of these loops and their interplay with active site amino acids, reflected by interaction energies and dynamics, account for the different catalytic activity and substrate specificity of the various fungal and bacterial β-N-acetylhexosaminidases. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0465-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natallia Kulik
- Department of Structure and Function of Proteins, Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 37333, Nove Hrady, Czech Republic.
| | - Kristýna Slámová
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 14220, Praha 4, Czech Republic.
| | - Rüdiger Ettrich
- Department of Structure and Function of Proteins, Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 37333, Nove Hrady, Czech Republic. .,Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, 37333, Nove Hrady, Czech Republic.
| | - Vladimír Křen
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 14220, Praha 4, Czech Republic.
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9
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Ito T, Katayama T, Hattie M, Sakurama H, Wada J, Suzuki R, Ashida H, Wakagi T, Yamamoto K, Stubbs KA, Fushinobu S. Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum. J Biol Chem 2013; 288:11795-806. [PMID: 23479733 DOI: 10.1074/jbc.m112.420109] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human milk oligosaccharides contain a large variety of oligosaccharides, of which lacto-N-biose I (Gal-β1,3-GlcNAc; LNB) predominates as a major core structure. A unique metabolic pathway specific for LNB has recently been identified in the human commensal bifidobacteria. Several strains of infant gut-associated bifidobacteria possess lacto-N-biosidase, a membrane-anchored extracellular enzyme, that liberates LNB from the nonreducing end of human milk oligosaccharides and plays a key role in the metabolic pathway of these compounds. Lacto-N-biosidase belongs to the glycoside hydrolase family 20, and its reaction proceeds via a substrate-assisted catalytic mechanism. Several crystal structures of GH20 β-N-acetylhexosaminidases, which release monosaccharide GlcNAc from its substrate, have been determined, but to date, a structure of lacto-N-biosidase is unknown. Here, we have determined the first three-dimensional structures of lacto-N-biosidase from Bifidobacterium bifidum JCM1254 in complex with LNB and LNB-thiazoline (Gal-β1,3-GlcNAc-thiazoline) at 1.8-Å resolution. Lacto-N-biosidase consists of three domains, and the C-terminal domain has a unique β-trefoil-like fold. Compared with other β-N-acetylhexosaminidases, lacto-N-biosidase has a wide substrate-binding pocket with a -2 subsite specific for β-1,3-linked Gal, and the residues responsible for Gal recognition were identified. The bound ligands are recognized by extensive hydrogen bonds at all of their hydroxyls consistent with the enzyme's strict substrate specificity for the LNB moiety. The GlcNAc sugar ring of LNB is in a distorted conformation near (4)E, whereas that of LNB-thiazoline is in a (4)C1 conformation. A possible conformational pathway for the lacto-N-biosidase reaction is discussed.
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Affiliation(s)
- Tasuku Ito
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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10
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Vaaje-Kolstad G, Horn SJ, Sørlie M, Eijsink VGH. The chitinolytic machinery ofSerratia marcescens- a model system for enzymatic degradation of recalcitrant polysaccharides. FEBS J 2013; 280:3028-49. [DOI: 10.1111/febs.12181] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/30/2013] [Accepted: 02/05/2013] [Indexed: 01/13/2023]
Affiliation(s)
- Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Svein J. Horn
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Morten Sørlie
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Vincent G. H. Eijsink
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
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11
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Sumida T, Stubbs KA, Ito M, Yokoyama S. Gaining insight into the inhibition of glycoside hydrolase family 20 exo-β-N-acetylhexosaminidases using a structural approach. Org Biomol Chem 2012; 10:2607-12. [PMID: 22367352 DOI: 10.1039/c2ob06636j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
One useful methodology that has been used to give insight into how chemically synthesized inhibitors bind to enzymes and the reasons underlying their potency is crystallographic studies of inhibitor-enzyme complexes. Presented here is the X-ray structural analysis of a representative family 20 exo-β-N-acetylhexosaminidase in complex with various known classes of inhibitor of these types of enzymes, which highlights how different inhibitor classes can inhibit the same enzyme. This study will aid in the future development of inhibitors of not only exo-β-N-acetylhexosaminidases but also other types of glycoside hydrolases.
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Affiliation(s)
- Tomomi Sumida
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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12
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Wang Y, Liu T, Yang Q, Li Z, Qian X. A Modeling Study for Structure Features of β-N-acetyl-D-hexosaminidase from Ostrinia furnacalis and its Novel Inhibitor Allosamidin: Species Selectivity and Multi-Target Characteristics. Chem Biol Drug Des 2012; 79:572-82. [DOI: 10.1111/j.1747-0285.2011.01301.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Vaněk O, Brynda J, Hofbauerová K, Kukačka Z, Pachl P, Bezouška K, Řezáčová P. Crystallization and diffraction analysis of β-N-acetylhexosaminidase from Aspergillus oryzae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:498-503. [PMID: 21505251 PMCID: PMC3080160 DOI: 10.1107/s1744309111004945] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 02/09/2011] [Indexed: 11/10/2022]
Abstract
Fungal β-N-acetylhexosaminidases are enzymes that are used in the chemoenzymatic synthesis of biologically interesting oligosaccharides. The enzyme from Aspergillus oryzae was produced and purified from its natural source and crystallized using the hanging-drop vapour-diffusion method. Diffraction data from two crystal forms (primitive monoclinic and primitive tetragonal) were collected to resolutions of 3.2 and 2.4 Å, respectively. Electrophoretic and quantitative N-terminal protein-sequencing analyses confirmed that the crystals are formed by a complete biologically active enzyme consisting of a glycosylated catalytic unit and a noncovalently attached propeptide.
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Affiliation(s)
- Ondřej Vaněk
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12840 Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Kateřina Hofbauerová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12840 Prague, Czech Republic
| | - Petr Pachl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Karel Bezouška
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12840 Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
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Stütz AE, Wrodnigg TM. Imino sugars and glycosyl hydrolases: historical context, current aspects, emerging trends. Adv Carbohydr Chem Biochem 2011; 66:187-298. [PMID: 22123190 DOI: 10.1016/b978-0-12-385518-3.00004-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Forty years of discoveries and research on imino sugars, which are carbohydrate analogues having a basic nitrogen atom instead of oxygen in the sugar ring and, acting as potent glycosidase inhibitors, have made considerable impact on our contemporary understanding of glycosidases. Imino sugars have helped to elucidate the catalytic machinery of glycosidases and have refined our methods and concepts of utilizing them. A number of new aspects have emerged for employing imino sugars as pharmaceutical compounds, based on their profound effects on metabolic activities in which glycosidases are involved. From the digestion of starch to the fight against viral infections, from research into malignant diseases to potential improvements in hereditary storage disorders, glycosidase action and inhibition are essential issues. This account aims at combining general developments with a focus on some niches where imino sugars have become useful tools for glycochemistry and glycobiology.
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Affiliation(s)
- Arnold E Stütz
- Institut für Organische Chemie, Technische Universität Graz, Austria
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15
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Usuki H, Yamamoto Y, Kumagai Y, Nitoda T, Kanzaki H, Hatanaka T. MS/MS fragmentation-guided search of TMG-chitooligomycins and their structure–activity relationship in specific β-N-acetylglucosaminidase inhibition. Org Biomol Chem 2011; 9:2943-51. [DOI: 10.1039/c0ob01090a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Slámová K, Bojarová P, Petrásková L, Křen V. β-N-Acetylhexosaminidase: What's in a name…? Biotechnol Adv 2010; 28:682-93. [DOI: 10.1016/j.biotechadv.2010.04.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 04/17/2010] [Accepted: 04/24/2010] [Indexed: 01/28/2023]
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17
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Lammerts van Bueren A, Popat SD, Lin CH, Davies GJ. Structural and Thermodynamic Analyses of α-L-Fucosidase Inhibitors. Chembiochem 2010; 11:1971-4. [DOI: 10.1002/cbic.201000339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Martinez-Fleites C, Korczynska JE, Davies GJ, Cope MJ, Turkenburg JP, Taylor EJ. The crystal structure of a family GH25 lysozyme from Bacillus anthracis implies a neighboring-group catalytic mechanism with retention of anomeric configuration. Carbohydr Res 2009; 344:1753-7. [PMID: 19595298 DOI: 10.1016/j.carres.2009.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 05/27/2009] [Accepted: 06/01/2009] [Indexed: 11/30/2022]
Abstract
Lysozymes are found in many of the sequence-based families of glycoside hydrolases (www.cazy.org) where they show considerable structural and mechanistic diversity. Lysozymes from glycoside hydrolase family GH25 adopt a (alpha/beta)(5)(beta)(3)-barrel-like fold with a proposal in the literature that these enzymes act with inversion of anomeric configuration; the lack of a suitable substrate, however, means that no group has successfully demonstrated the configuration of the product. Here we report the 3-D structure of the GH25 enzyme from Bacillus anthracis at 1.4A resolution. We show that the active center is extremely similar to those from glycoside hydrolase families GH18, GH20, GH56, GH84, and GH85 implying that, in the absence of evidence to the contrary, GH25 enzymes also act with net retention of anomeric configuration using the neighboring-group catalytic mechanism that is common to this 'super-family' of enzymes.
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Affiliation(s)
- Carlos Martinez-Fleites
- Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5YW, United Kingdom
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19
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GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation. Biochem J 2009; 420:221-7. [PMID: 19275764 PMCID: PMC2691177 DOI: 10.1042/bj20090110] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
O-GlcNAcylation is an essential, dynamic and inducible post-translational glycosylation of cytosolic proteins in metazoa and can show interplay with protein phosphorylation. Inhibition of OGA (O-GlcNAcase), the enzyme that removes O-GlcNAc from O-GlcNAcylated proteins, is a useful strategy to probe the role of this modification in a range of cellular processes. In the present study, we report the rational design and evaluation of GlcNAcstatins, a family of potent, competitive and selective inhibitors of human OGA. Kinetic experiments with recombinant human OGA reveal that the GlcNAcstatins are the most potent human OGA inhibitors reported to date, inhibiting the enzyme in the sub-nanomolar to nanomolar range. Modification of the GlcNAcstatin N-acetyl group leads to up to 160-fold selectivity against the human lysosomal hexosaminidases which employ a similar substrate-assisted catalytic mechanism. Mutagenesis studies in a bacterial OGA, guided by the structure of a GlcNAcstatin complex, provides insight into the role of conserved residues in the human OGA active site. GlcNAcstatins are cell-permeant and, at low nanomolar concentrations, effectively modulate intracellular O-GlcNAc levels through inhibition of OGA, in a range of human cell lines. Thus these compounds are potent selective tools to study the cell biology of O-GlcNAc.
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Steiner AJ, Schitter G, Stütz AE, Wrodnigg TM, Tarling CA, Withers SG, Mahuran DJ, Tropak MB. 2-Acetamino-1,2-dideoxynojirimycin-lysine hybrids as hexosaminidase inhibitors. TETRAHEDRON, ASYMMETRY 2009; 20:832-835. [PMID: 22328804 PMCID: PMC3276585 DOI: 10.1016/j.tetasy.2009.02.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cyclisation by double reductive amination of 2-acetamino-2-deoxy-D-xylo-hexos-5-ulose with N-2 protected L-lysine derivatives provided 2-acetamino-1,2-dideoxynojirimycin derivatives without any observable epimer formation at C-5. Modifications on the lysine moiety gave access to lipophilic derivatives that exhibited improved hexosaminidase inhibitory activities.
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Affiliation(s)
- Andreas J. Steiner
- Glycogroup, Institut für Organische Chemie, Technische Universität Graz, Stremayrgasse 16, A-8010 Graz, Austria
| | - Georg Schitter
- Glycogroup, Institut für Organische Chemie, Technische Universität Graz, Stremayrgasse 16, A-8010 Graz, Austria
| | - Arnold E. Stütz
- Glycogroup, Institut für Organische Chemie, Technische Universität Graz, Stremayrgasse 16, A-8010 Graz, Austria
| | - Tanja M. Wrodnigg
- Glycogroup, Institut für Organische Chemie, Technische Universität Graz, Stremayrgasse 16, A-8010 Graz, Austria
| | - Chris A. Tarling
- Chemistry Department, University of British Columbia, 300-6174 University Boulevard, Vancouver, BC, Canada V6T 1Z3
| | - Stephen G. Withers
- Chemistry Department, University of British Columbia, 300-6174 University Boulevard, Vancouver, BC, Canada V6T 1Z3
| | - Don J. Mahuran
- Department of Laboratory Medicine and Pathobiology, Sick Kids Hospital, 555 University Avenue, University of Toronto, Ont., Canada M5G 1X8
| | - Michael B. Tropak
- Department of Laboratory Medicine and Pathobiology, Sick Kids Hospital, 555 University Avenue, University of Toronto, Ont., Canada M5G 1X8
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21
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Hurtado-Guerrero R, Dorfmueller HC, van Aalten DMF. Molecular mechanisms of O-GlcNAcylation. Curr Opin Struct Biol 2008; 18:551-7. [DOI: 10.1016/j.sbi.2008.09.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2008] [Revised: 09/08/2008] [Accepted: 09/15/2008] [Indexed: 11/29/2022]
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22
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Hill AD, Reilly PJ. A Gibbs free energy correlation for automated docking of carbohydrates. J Comput Chem 2008; 29:1131-41. [PMID: 18074341 DOI: 10.1002/jcc.20873] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thermodynamic information can be inferred from static atomic configurations. To model the thermodynamics of carbohydrate binding to proteins accurately, a large binding data set has been assembled from the literature. The data set contains information from 262 unique protein-carbohydrate crystal structures for which experimental binding information is known. Hydrogen atoms were added to the structures and training conformations were generated with the automated docking program AutoDock 3.06, resulting in a training set of 225,920 all-atom conformations. In all, 288 formulations of the AutoDock 3.0 free energy model were trained against the data set, testing each of four alternate methods of computing the van der Waals, solvation, and hydrogen-bonding energetic components. The van der Waals parameters from AutoDock 1 produced the lowest errors, and an entropic model derived from statistical mechanics produced the only models with five physically and statistically significant coefficients. Eight models predict the Gibbs free energy of binding with an error of less than 40% of the error of any similar models previously published.
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Affiliation(s)
- Anthony D Hill
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
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23
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N-Acetylhexosaminidase inhibitory properties of C-1 homologated GlcNAc- and GalNAc-thiazolines. Bioorg Med Chem Lett 2008; 18:2944-7. [DOI: 10.1016/j.bmcl.2008.03.067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Accepted: 03/24/2008] [Indexed: 11/17/2022]
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24
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Ettrich R, Kopecký V, Hofbauerová K, Baumruk V, Novák P, Pompach P, Man P, Plíhal O, Kutý M, Kulik N, Sklenář J, Ryšlavá H, Křen V, Bezouška K. Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies. BMC STRUCTURAL BIOLOGY 2007; 7:32. [PMID: 17509134 PMCID: PMC1885261 DOI: 10.1186/1472-6807-7-32] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 05/17/2007] [Indexed: 11/29/2022]
Abstract
Background Fungal β-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal β-N-acetylhexosaminidase. The fungal β-N-acetylhexosaminidases are robust enzymes commonly used in chemoenzymatic syntheses of oligosaccharides. The enzyme from Aspergillus oryzae was purified and its sequence was determined. Results The complete primary structure of the fungal β-N-acetylhexosaminidase from Aspergillus oryzae CCF1066 was used to construct molecular models of the catalytic subunit of the enzyme, the enzyme dimer, and the N-glycosylated dimer. Experimental data were obtained from infrared and Raman spectroscopy, and biochemical studies of the native and deglycosylated enzyme, and are in good agreement with the models. Enzyme deglycosylated under native conditions displays identical kinetic parameters but is significantly less stable in acidic conditions, consistent with model predictions. The molecular model of the deglycosylated enzyme was solvated and a molecular dynamics simulation was run over 20 ns. The molecular model is able to bind the natural substrate – chitobiose with a stable value of binding energy during the molecular dynamics simulation. Conclusion Whereas the intracellular bacterial β-N-acetylhexosaminidases are monomeric, the extracellular secreted enzymes of fungi and humans occur as dimers. Dimerization of the fungal β-N-acetylhexosaminidase appears to be a reversible process that is strictly pH dependent. Oligosaccharide moieties may also participate in the dimerization process that might represent a unique feature of the exclusively extracellular enzymes. Deglycosylation had only limited effect on enzyme activity, but it significantly affected enzyme stability in acidic conditions. Dimerization and N-glycosylation are the enzyme's strategy for catalytic subunit stabilization. The disulfide bridge that connects Cys448 with Cys483 stabilizes a hinge region in a flexible loop close to the active site, which is an exclusive feature of the fungal enzymes, neither present in bacterial nor mammalian structures. This loop may play the role of a substrate binding site lid, anchored by a disulphide bridge that prevents the substrate binding site from being influenced by the flexible motion of the loop.
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Affiliation(s)
- Rüdiger Ettrich
- Laboratory of High Performance Computing, Institute of Systems Biology and Ecology of the Academy of Sciences of the Czech Republic and Institute of Physical Biology of USB, Zámek136, CZ-37333 Nové Hrady, Czech Republic
| | - Vladimír Kopecký
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu5, CZ-12116 Prague2, Czech Republic
| | - Kateřina Hofbauerová
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu5, CZ-12116 Prague2, Czech Republic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská1083, CZ-14220 Prague4, Czech Republic
| | - Vladimír Baumruk
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu5, CZ-12116 Prague2, Czech Republic
| | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská1083, CZ-14220 Prague4, Czech Republic
| | - Petr Pompach
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská1083, CZ-14220 Prague4, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Albertov2030, CZ-12840 Prague2, Czech Republic
| | - Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská1083, CZ-14220 Prague4, Czech Republic
| | - Ondřej Plíhal
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská1083, CZ-14220 Prague4, Czech Republic
| | - Michal Kutý
- Laboratory of High Performance Computing, Institute of Systems Biology and Ecology of the Academy of Sciences of the Czech Republic and Institute of Physical Biology of USB, Zámek136, CZ-37333 Nové Hrady, Czech Republic
| | - Natallia Kulik
- Laboratory of High Performance Computing, Institute of Systems Biology and Ecology of the Academy of Sciences of the Czech Republic and Institute of Physical Biology of USB, Zámek136, CZ-37333 Nové Hrady, Czech Republic
| | - Jan Sklenář
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská1083, CZ-14220 Prague4, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Albertov2030, CZ-12840 Prague2, Czech Republic
| | - Helena Ryšlavá
- Department of Biochemistry, Faculty of Science, Charles University, Albertov2030, CZ-12840 Prague2, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská1083, CZ-14220 Prague4, Czech Republic
| | - Karel Bezouška
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská1083, CZ-14220 Prague4, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Albertov2030, CZ-12840 Prague2, Czech Republic
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25
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Mayer C, Vocadlo DJ, Mah M, Rupitz K, Stoll D, Warren RAJ, Withers SG. Characterization of a beta-N-acetylhexosaminidase and a beta-N-acetylglucosaminidase/beta-glucosidase from Cellulomonas fimi. FEBS J 2006; 273:2929-41. [PMID: 16762038 DOI: 10.1111/j.1742-4658.2006.05308.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The gram-positive soil bacterium Cellulomonas fimi is shown to produce at least two intracellular beta-N-acetylglucosaminidases, a family 20 beta-N-acetylhexosaminidase (Hex20), and a novel family 3-beta-N-acetylglucosaminidase/beta-glucosidase (Nag3), through screening of a genomic expression library, cloning of genes and analysis of their sequences. Nag3 exhibits broad substrate specificity for substituents at the C2 position of the glycone: kcat/Km values at 25 degrees C were 0.066 s(-1) x mM(-1) and 0.076 s(-1) x mM(-1) for 4'-nitrophenyl beta-N-acetyl-D-glucosaminide and 4'-nitrophenyl beta-D-glucoside, respectively. The first glycosidase with this broad specificity to be described, Nag3, suggests an interesting evolutionary link between beta-N-acetylglucosaminidases and beta-glucosidases of family 3. Reaction by a double-displacement mechanism was confirmed for Nag3 through the identification of a glycosyl-enzyme species trapped with the slow substrate 2',4'-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside. Hex20 requires the acetamido group at C2 of the substrate, being unable to cleave beta-glucosides, since its mechanism involves an oxazolinium ion intermediate. However, it is broad in its specificity for the D-glucosyl/D-galactosyl configuration of the glycone: Km and kcat values were 53 microM and 482.3 s(-1) for 4'-nitrophenyl beta-N-acetyl-D-glucosaminide and 66 microM and 129.1 s(-1) for 4'-nitrophenyl beta-N-acetyl-D-galactosaminide.
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Affiliation(s)
- Christoph Mayer
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
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26
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Rao FV, Dorfmueller HC, Villa F, Allwood M, Eggleston IM, van Aalten DMF. Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis. EMBO J 2006; 25:1569-78. [PMID: 16541109 PMCID: PMC1440316 DOI: 10.1038/sj.emboj.7601026] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Accepted: 02/08/2006] [Indexed: 11/08/2022] Open
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) modification of specific serines/threonines on intracellular proteins in higher eukaryotes has been shown to directly regulate important processes such as the cell cycle, insulin sensitivity and transcription. The structure, molecular mechanisms of catalysis, protein substrate recognition/specificity of the eukaryotic O-GlcNAc transferase and hydrolase are largely unknown. Here we describe the crystal structure, enzymology and in vitro activity on human substrates of Clostridium perfringens NagJ, a close homologue of human O-GlcNAcase (OGA), representing the first family 84 glycoside hydrolase structure. The structure reveals a deep active site pocket highly conserved with the human enzyme, compatible with binding of O-GlcNAcylated peptides. Together with mutagenesis data, the structure supports a variant of the substrate-assisted catalytic mechanism, involving two aspartic acids and an unusually positioned tyrosine. Insights into recognition of substrate come from a complex with the transition state mimic O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (Ki=5.4 nM). Strikingly, the enzyme is inhibited by the pseudosubstrate peptide Ala-Cys(-S-GlcNAc)-Ala, and has OGA activity against O-GlcNAcylated human proteins, suggesting that the enzyme is a suitable model for further studies into the function of human OGA.
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Affiliation(s)
- Francesco V Rao
- Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Helge C Dorfmueller
- Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Fabrizio Villa
- Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
- MRC Protein Phosphorylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matthew Allwood
- Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ian M Eggleston
- Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Daan M F van Aalten
- Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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27
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Greimel P, Häusler H, Lundt I, Rupitz K, Stütz AE, Tarling CA, Withers SG, Wrodnigg TM. Fluorescent glycosidase inhibiting 1,5-dideoxy-1,5-iminoalditols. Bioorg Med Chem Lett 2006; 16:2067-70. [PMID: 16481162 DOI: 10.1016/j.bmcl.2006.01.095] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 01/17/2006] [Accepted: 01/18/2006] [Indexed: 10/25/2022]
Abstract
1,5-Dideoxy-1,5-iminoalditols of various configurations as well as isofagomine were N-alkylated with non-polar straight chain spacer-arms by a set of simple standard procedures. The spacer-arms' terminal functional groups, primary amines, were employed to introduce fluorescent tags such as dansyl and dapoxyl moieties. Resulting derivatives in the D-xylo, D-gluco, D-galacto as well as GlcNAc series showed distinctly improved glycosidase inhibitory activities compared to parent compounds and are designed to be useful analytical tools.
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Affiliation(s)
- Peter Greimel
- Glycogroup, Institut für Organische Chemie, Technische Universität Graz, Stremayrgasse 16, A-8010 Graz, Austria
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28
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Taylor EJ, Goyal A, Guerreiro CIPD, Prates JAM, Money VA, Ferry N, Morland C, Planas A, Macdonald JA, Stick RV, Gilbert HJ, Fontes CMGA, Davies GJ. How Family 26 Glycoside Hydrolases Orchestrate Catalysis on Different Polysaccharides. J Biol Chem 2005; 280:32761-7. [PMID: 15987675 DOI: 10.1074/jbc.m506580200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One of the most intriguing features of the 90 glycoside hydrolase families (GHs) is the range of specificities displayed by different members of the same family, whereas the catalytic apparatus and mechanism are often invariant. Family GH26 predominantly comprises beta-1,4 mannanases; however, a bifunctional Clostridium thermocellum GH26 member (hereafter CtLic26A) displays a markedly different specificity. We show that CtLic26A is a lichenase, specific for mixed (Glcbeta1,4Glcbeta1,4Glcbeta1,3)n oligo- and polysaccharides, and displays no activity on manno-configured substrates or beta-1,4-linked homopolymers of glucose or xylose. The three-dimensional structure of the native form of CtLic26A has been solved at 1.50-A resolution, revealing a characteristic (beta/alpha)8 barrel with Glu-109 and Glu-222 acting as the catalytic acid/base and nucleophile in a double-displacement mechanism. The complex with the competitive inhibitor, Glc-beta-1,3-isofagomine (Ki 1 microm), at 1.60 A sheds light on substrate recognition in the -2 and -1 subsites and illuminates why the enzyme is specific for lichenan-based substrates. Hydrolysis of beta-mannosides by GH26 members is thought to proceed through transition states in the B2,5 (boat) conformation in which structural distinction of glucosides versus mannosides reflects not the configuration at C2 but the recognition of the pseudoaxial O3 of the B2,5 conformation. We suggest a different conformational itinerary for the GH26 enzymes active on gluco-configured substrates.
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Affiliation(s)
- Edward J Taylor
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, United Kingdom
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29
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Jiang YL, Cao C, Stivers JT, Song F, Ichikawa Y. The merits of bipartite transition-state mimics for inhibition of uracil DNA glycosylase. Bioorg Chem 2005; 32:244-62. [PMID: 15210339 DOI: 10.1016/j.bioorg.2004.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Indexed: 10/26/2022]
Abstract
The glycosidic bond hydrolysis reaction of the enzyme uracil DNA glycosylase (UDG) occurs by a two-step mechanism involving complete bond breakage to the uracil anion leaving group in the first step, formation of a discrete glycosyl cation-uracil anion intermediate, followed by water attack in a second transition-state leading to the enzyme-bound products of uracil and abasic DNA. We have synthesized and determined the binding affinities of unimolecular mimics of the substrate and first transition-state (TS1) in which the uracil base is covalently attached to the sugar, and in addition, bimolecular mimics of the second addition transition state (TS2) in which the base and sugar are detached. We find that the bipartite mimics of TS2 are superior to the TS1 mimics. These results indicate that bipartite TS2 inhibitors could be useful for inhibition of glycosylases that proceed by stepwise reaction mechanisms.
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Affiliation(s)
- Yu Lin Jiang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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30
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Mark BL, Mahuran DJ, Cherney MM, Zhao D, Knapp S, James MNG. Crystal structure of human beta-hexosaminidase B: understanding the molecular basis of Sandhoff and Tay-Sachs disease. J Mol Biol 2003; 327:1093-109. [PMID: 12662933 PMCID: PMC2910754 DOI: 10.1016/s0022-2836(03)00216-x] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In humans, two major beta-hexosaminidase isoenzymes exist: Hex A and Hex B. Hex A is a heterodimer of subunits alpha and beta (60% identity), whereas Hex B is a homodimer of beta-subunits. Interest in human beta-hexosaminidase stems from its association with Tay-Sachs and Sandhoff disease; these are prototypical lysosomal storage disorders resulting from the abnormal accumulation of G(M2)-ganglioside (G(M2)). Hex A degrades G(M2) by removing a terminal N-acetyl-D-galactosamine (beta-GalNAc) residue, and this activity requires the G(M2)-activator, a protein which solubilizes the ganglioside for presentation to Hex A. We present here the crystal structure of human Hex B, alone (2.4A) and in complex with the mechanistic inhibitors GalNAc-isofagomine (2.2A) or NAG-thiazoline (2.5A). From these, and the known X-ray structure of the G(M2)-activator, we have modeled Hex A in complex with the activator and ganglioside. Together, our crystallographic and modeling data demonstrate how alpha and beta-subunits dimerize to form either Hex A or Hex B, how these isoenzymes hydrolyze diverse substrates, and how many documented point mutations cause Sandhoff disease (beta-subunit mutations) and Tay-Sachs disease (alpha-subunit mutations).
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Affiliation(s)
- Brian L. Mark
- Canadian Institutes of Heath Research Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alt.,Canada T6G 2H7
| | - Don J. Mahuran
- The Research Institute, The Hospital for Sick Children, 555 University Ave, Toronto Ont., Canada M5G1X8
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ont., Canada M5G1L6
| | - Maia M. Cherney
- Canadian Institutes of Heath Research Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alt.,Canada T6G 2H7
| | - Dalian Zhao
- Department of Chemistry, Rutgers University, New Brunswick, NJ 08903, USA
| | - Spencer Knapp
- Department of Chemistry, Rutgers University, New Brunswick, NJ 08903, USA
| | - Michael N. G. James
- Canadian Institutes of Heath Research Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alt.,Canada T6G 2H7
- Corresponding author:
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31
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Williams SJ, Mark BL, Vocadlo DJ, James MNG, Withers SG. Aspartate 313 in the Streptomyces plicatus hexosaminidase plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state. J Biol Chem 2002; 277:40055-65. [PMID: 12171933 DOI: 10.1074/jbc.m206481200] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SpHex, a retaining family 20 glycosidase from Streptomyces plicatus, catalyzes the hydrolysis of N-acetyl-beta-hexosaminides. Accumulating evidence suggests that the hydrolytic mechanism involves substrate-assisted catalysis wherein the 2-acetamido substituent acts as a nucleophile to form an oxazolinium ion intermediate. The role of a conserved aspartate residue (D313) in the active site of SpHex was investigated through kinetic and structural analyses of two variant enzymes, D313A and D313N. Three-dimensional structures of the wild-type and variant enzymes in product complexes with N-acetyl-d-glucosamine revealed substantial differences. In the D313A variant the 2-acetamido group was found in two conformations of which only one is able to aid in catalysis through anchimeric assistance. The mutation D313N results in a steric clash in the active site between Asn-313 and the 2-acetamido group preventing the 2-acetamido group from providing anchimeric assistance, consistent with the large reduction in catalytic efficiency and the insensitivity of this variant to chemical rescue. By comparison, the D313A mutation results in a shift in a shift in the pH optimum and a modest decrease in activity that can be rescued by using azide as an exogenous nucleophile. These structural and kinetic data provide evidence that Asp-313 stabilizes the transition states flanking the oxazoline intermediate and also assists to correctly orient the 2-acetamido group for catalysis. Based on analogous conserved residues in the family 18 chitinases and family 56 hyaluronidases, the roles played by the Asp-313 residue is likely general for all hexosaminidases using a mechanism involving substrate-assisted catalysis.
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Affiliation(s)
- Spencer J Williams
- Protein Engineering Network Centres of Excellence of Canada and the Department of Chemistry, University of British Columbia, Vancouver, V6T 1Z1 Canada
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32
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Abstract
The three-dimensional structure of glycosidases and of their complexes and the study of transition-state mimics reveal structural details that correlate with mechanism. Of particular interest are the transition-state conformations harnessed by individual enzymes and the substrate distortion observed in enzyme-ligand complexes. 3D-structure in synergy with transition-state mimicry opens the way for mechanistic interpretation of enzyme inhibition and for the development of therapeutic agents.
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Affiliation(s)
- Andrea Vasella
- Laboratorium für Organische Chemie, ETH Hönggerberg, HCI H317, CH-8093 Zürich, Switzerland
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Abstract
Configuration retaining glycosidases catalyse the hydrolysis of glycosidic bonds via a double displacement mechanism, typically involving two key active site carboxyl groups (Glu or Asp). One of the enzymic carboxyl groups functions as a general acidbase catalyst, the other acts as a nucleophile. Alternatively, configuration-retaining hexosaminidases from the sequence-related glycosidase families 18, 20, and 56 lack a suitably positioned enzymic nucleophile; instead, they use the carbonyl oxygen atom of the neighbouring C2-acetamido group of the substrate. The carbonyl oxygen atom of the 2-acetamido group provides anchimeric assistance to the enzyme catalyzed reaction by acting as an intramolecular nucleophile, attacking the anomeric center and forming a cyclized oxazolinium ion intermediate that is stereochemically equivalent to the glycosylenzyme intermediate formed in the "normal" double displacement mechanism. Although there is little sequence similarity between families 18, 20, and 56 hexosaminidases, X-ray crystallographic studies demonstrate that they have evolved similar catalytic domains and active site architectures that are designed to distort the bound substrate so that the C2-acetamido group can become appropriately positioned to participate in catalysis. The substrate distortion allows for a substrate-assisted catalytic reaction that displays all the general characteristics of the classic double-displacement mechanism including the formation of a covalent intermediate.Key words: glycoside hydrolase, hexosaminidase, glycosidase, substrate-assisted catalysis, anchimeric assistance.
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Nidetzky B, Eis C. Alpha-retaining glucosyl transfer catalysed by trehalose phosphorylase from Schizophyllum commune: mechanistic evidence obtained from steady-state kinetic studies with substrate analogues and inhibitors. Biochem J 2001; 360:727-36. [PMID: 11736665 PMCID: PMC1222278 DOI: 10.1042/0264-6021:3600727] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fungal trehalose phosphorylase is classified as a family 4 glucosyltransferase that catalyses the reversible phosphorolysis of alpha,alpha-trehalose with net retention of anomeric configuration. Glucosyl transfer to and from phosphate takes place by the partly rate-limiting interconversion of ternary enzyme-substrate complexes formed from binary enzyme-phosphate and enzyme-alpha-d-glucopyranosyl phosphate adducts respectively. To advance a model of the chemical mechanism of trehalose phosphorylase, we performed a steady-state kinetic study with the purified enzyme from the basidiomycete fungus Schizophyllum commune by using alternative substrates, inhibitors and combinations thereof in pairs as specific probes of substrate-binding recognition and transition-state structure. Orthovanadate is a competitive inhibitor against phosphate and alpha-d-glucopyranosyl phosphate, and binds 3 x 10(4)-fold tighter (K(i) approximately 1 microM) than phosphate. Structural alterations of d-glucose at C-2 and O-5 are tolerated by the enzyme at subsite +1. They lead to parallel effects of approximately the same magnitude (slope=1.14; r(2)=0.98) on the reciprocal catalytic efficiency for reverse glucosyl transfer [log (K(m)/k(cat))] and the apparent affinity of orthovanadate determined in the presence of the respective glucosyl acceptor (log K(i)). An adduct of orthovanadate and the nucleophile/leaving group bound at subsite +1 is therefore the true inhibitor and displays partial transition state analogy. Isofagomine binds to subsite -1 in the enzyme-phosphate complex with a dissociation constant of 56 microM and inhibits trehalose phosphorylase at least 20-fold better than 1-deoxynojirimycin. The specificity of the reversible azasugars inhibitors would be explained if a positive charge developed on C-1 rather than O-5 in the proposed glucosyl cation-like transition state of the reaction. The results are discussed in the context of alpha-retaining glucosyltransferase mechanisms that occur with and without a beta-glucosyl enzyme intermediate.
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Affiliation(s)
- B Nidetzky
- Institute of Food Technology, University of Agricultural Sciences Vienna (BOKU), Muthgasse 18, A-1190 Vienna, Austria.
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