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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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Sekiya H, Nonaka Y, Kamitori S, Miyaji T, Tamai E. X-ray structure and mutagenesis analyses of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain. Biochem Biophys Res Commun 2024; 715:149957. [PMID: 38688057 DOI: 10.1016/j.bbrc.2024.149957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Clostridioides difficile endolysin (Ecd09610) consists of an unknown domain at its N terminus, followed by two catalytic domains, a glucosaminidase domain and endopeptidase domain. X-ray structure and mutagenesis analyses of the Ecd09610 catalytic domain with glucosaminidase activity (Ecd09610CD53) were performed. Ecd09610CD53 was found to possess an α-bundle-like structure with nine helices, which is well conserved among GH73 family enzymes. The mutagenesis analysis based on X-ray structures showed that Glu405 and Asn470 were essential for enzymatic activity. Ecd09610CD53 may adopt a neighboring-group mechanism for a catalytic reaction in which Glu405 acted as an acid/base catalyst and Asn470 helped to stabilize the oxazolinium ion intermediate. Structural comparisons with the newly identified Clostridium perfringens autolysin catalytic domain (AcpCD) in the P1 form and a zymography analysis demonstrated that AcpCD was 15-fold more active than Ecd09610CD53. The strength of the glucosaminidase activity of the GH73 family appears to be dependent on the depth of the substrate-binding groove.
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Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Yasuhiro Nonaka
- Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Shigehiro Kamitori
- Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan; Research Facility Center for Science & Technology, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Tomomi Miyaji
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan.
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3
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Moreno Prieto ES, Fjermedal S, Siebenhaar S, Vuillemin M, Holck J, Vincentelli R, Gippert GP, Wilkens C, Morth JP, Henrissat B. Characterization and structural study of a novel β-N-acetylgalactosaminidase from Niabella aurantiaca. FEBS J 2024; 291:1439-1456. [PMID: 38129294 DOI: 10.1111/febs.17042] [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: 08/31/2023] [Revised: 11/06/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
We report here the identification, characterization and three-dimensional (3D) structure determination of NaNga, a newly identified β-N-acetylgalactosaminidase from the Gram-negative soil bacterium Niabella aurantiaca DSM 17617. When recombinantly expressed in Escherichia coli, the enzyme selectively cleaved 4-nitrophenyl-N-acetyl-β-d-galactosamine (pNP-β-d-GalpNAc). The X-ray crystal structure of the protein was refined to 2.5 Å and consists of an N-terminal β-sandwich domain and a (β/α)8 barrel catalytic domain. Despite a mere 22% sequence identity, the 3D structure of NaNga is similar to those previously determined for family GH123 members, suggesting it also employs the same substrate-assisted catalytic mechanism. Inhibition by N-acetyl-galactosamine thiazoline (GalNAc-thiazoline) supports the suggested mechanism. A phylogenetic analysis of its proximal sequence space shows significant clustering of unknown sequences around NaNga with sufficient divergence with previously identified GH123 members to subdivide this family into distinct subfamilies. Although the actual biological substrate of our enzyme remains unknown, examination of the active site pocket suggests that it may be a β-N-acetylgalactosaminide substituted by a monosaccharide at O-3. Analysis of the genomic context suggests, in turn, that this substituted β-N-acetylgalactosaminide may be appended to a d-arabinan from an environmental Actinomycete.
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Affiliation(s)
| | - Sune Fjermedal
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Suzana Siebenhaar
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marlène Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, France
| | - Garry P Gippert
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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4
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Moran CL, Debowski A, Vrielink A, Stubbs K, Sarkar-Tyson M. N-acetyl-β-hexosaminidase activity is important for chitooligosaccharide metabolism and biofilm formation in Burkholderia pseudomallei. Environ Microbiol 2024; 26:e16571. [PMID: 38178319 DOI: 10.1111/1462-2920.16571] [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: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Burkholderia pseudomallei is a saprophytic Gram-negative bacillus that can cause the disease melioidosis. Although B. pseudomallei is a recognised member of terrestrial soil microbiomes, little is known about its contribution to the saprophytic degradation of polysaccharides within its niche. For example, while chitin is predicted to be abundant within terrestrial soils the chitinolytic capacity of B. pseudomallei is yet to be defined. This study identifies and characterises a putative glycoside hydrolase, bpsl0500, which is expressed by B. pseudomallei K96243. Recombinant BPSL0500 was found to exhibit activity against substrate analogues and GlcNAc disaccharides relevant to chitinolytic N-acetyl-β-d-hexosaminidases. In B. pseudomallei, bpsl0500 was found to be essential for both N-acetyl-β-d-hexosaminidase activity and chitooligosaccharide metabolism. Furthermore, bpsl0500 was also observed to significantly affect biofilm deposition. These observations led to the identification of BPSL0500 activity against model disaccharide linkages that are present in biofilm exopolysaccharides, a feature that has not yet been described for chitinolytic enzymes. The results in this study indicate that chitinolytic N-acetyl-β-d-hexosaminidases like bpsl0500 may facilitate biofilm disruption as well as chitin assimilation, providing dual functionality for saprophytic bacteria such as B. pseudomallei within the competitive soil microbiome.
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Affiliation(s)
- Clare L Moran
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Aleksandra Debowski
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
| | - Keith Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, University of Western Australia, Crawley, Australia
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
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5
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Oh H, Koo J, An SY, Hong SH, Suh JY, Bae E. Structural and functional investigation of GajB protein in Gabija anti-phage defense. Nucleic Acids Res 2023; 51:11941-11951. [PMID: 37897358 PMCID: PMC10681800 DOI: 10.1093/nar/gkad951] [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: 06/01/2023] [Revised: 09/13/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria and archaea. To fend off invading phages, the hosts have evolved a variety of anti-phage defense mechanisms. Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB. GajA has been characterized experimentally as a sequence-specific DNA endonuclease. Although GajB was previously predicted to be a UvrD-like helicase, its function is unclear. Here, we report the results of structural and functional analyses of GajB. The crystal structure of GajB revealed a UvrD-like domain architecture, including two RecA-like core and two accessory subdomains. However, local structural elements that are important for the helicase function of UvrD are not conserved in GajB. In functional assays, GajB did not unwind or bind various types of DNA substrates. We demonstrated that GajB interacts with GajA to form a heterooctameric Gabija complex, but GajB did not exhibit helicase activity when bound to GajA. These results advance our understanding of the molecular mechanism underlying Gabija anti-phage defense and highlight the role of GajB as a component of a multi-subunit antiviral complex in bacteria.
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Affiliation(s)
- Hyejin Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - So Young An
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sung-Hyun Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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6
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Bains RK, Nasseri SA, Liu F, Wardman JF, Rahfeld P, Withers SG. Characterization of a new family of 6-sulfo-N-acetylglucosaminidases. J Biol Chem 2023; 299:105214. [PMID: 37660924 PMCID: PMC10570127 DOI: 10.1016/j.jbc.2023.105214] [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: 06/15/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
Sulfation is widespread in nature and plays an important role in modulating biological function. Among the strategies developed by microbes to access sulfated oligosaccharides as a nutrient source is the production of 6-sulfoGlcNAcases to selectively release 6-sulfoGlcNAc from target oligosaccharides. Thus far, all 6-sulfoGlcNAcases identified have belonged to the large GH20 family of β-hexosaminidases. Ηere, we identify and characterize a new, highly specific non-GH20 6-sulfoGlcNAcase from Streptococcus pneumoniae TIGR4, Sp_0475 with a greater than 110,000-fold preference toward N-acetyl-β-D-glucosamine-6-sulfate substrates over the nonsulfated version. Sp_0475 shares distant sequence homology with enzymes of GH20 and with the newly formed GH163 family. However, the sequence similarity between them is sufficiently low that Sp_0475 has been assigned as the founding member of a new glycoside hydrolase family, GH185. By combining results from site-directed mutagenesis with mechanistic studies and bioinformatics we provide insight into the substrate specificity, mechanism, and key active site residues of Sp_0475. Enzymes of the GH185 family follow a substrate-assisted mechanism, consistent with their distant homology to the GH20 family, but the catalytic residues involved are quite different. Taken together, our results highlight in more detail how microbes can degrade sulfated oligosaccharides for nutrients.
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Affiliation(s)
- Rajneesh K Bains
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Seyed A Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Liu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jacob F Wardman
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Rahfeld
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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7
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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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8
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A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem. Nat Chem Biol 2023; 19:778-789. [PMID: 36864192 DOI: 10.1038/s41589-023-01272-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 01/25/2023] [Indexed: 03/04/2023]
Abstract
Mucinolytic bacteria modulate host-microbiota symbiosis and dysbiosis through their ability to degrade mucin O-glycans. However, how and to what extent bacterial enzymes are involved in the breakdown process remains poorly understood. Here we focus on a glycoside hydrolase family 20 sulfoglycosidase (BbhII) from Bifidobacterium bifidum, which releases N-acetylglucosamine-6-sulfate from sulfated mucins. Glycomic analysis showed that, in addition to sulfatases, sulfoglycosidases are involved in mucin O-glycan breakdown in vivo and that the released N-acetylglucosamine-6-sulfate potentially affects gut microbial metabolism, both of which were also supported by a metagenomic data mining analysis. Enzymatic and structural analysis of BbhII reveals the architecture underlying its specificity and the presence of a GlcNAc-6S-specific carbohydrate-binding module (CBM) 32 with a distinct sugar recognition mode that B. bifidum takes advantage of to degrade mucin O-glycans. Comparative analysis of the genomes of prominent mucinolytic bacteria also highlights a CBM-dependent O-glycan breakdown strategy used by B. bifidum.
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Phengsakun G, Boonyarit B, Rungrotmongkol T, Suginta W. Structure-based virtual screening for potent inhibitors of GH-20 β-N-acetylglucosaminidase: classical and machine learning scoring functions, and molecular dynamics simulations. Comput Biol Chem 2023; 104:107856. [PMID: 37003097 DOI: 10.1016/j.compbiolchem.2023.107856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
GH-20 β-N-acetylglucosaminidases (GlcNAcases) are promising targets in the development of antimicrobial agents against Vibrio infections in humans and aquatic animals. In this study, we set up structure-based virtual screening to identify potential GH-20 GlcNAcase inhibitors from the Reaxys commercial database, using VhGlcNAcase from V. campbellii type strain ATCC® BAA 1116 as the protein target and Redoxal as the reference ligand. Using ChemPLP and RF-Score-VS machine learning scoring functions, eight lead compounds were identified and further evaluated for protein interaction preference and pharmacological properties. Protein-ligand analysis demonstrated that all selected compounds interacted exclusively at subsite - 1 with five hydrophobic residues W487, W505, W546, W582 and V544 at site S1, and with two polar residues, D437 and E438, at site 3. For subsite + 1, the most common residues were R274 and E584 at site 2 and I397 and Q398 at site 4. Based on the data obtained from binding free energy changes (ΔG°binding), pharmacological property analysis and molecular dynamic simulations, two ChemPLP compounds, 338175 and 1146525, and one RF-Score-VS compound, 337447, were considered as the likely lead compounds. The most promising compound, 1146525, could serve as a scaffold for the future design of novel antimicrobial agents against Vibrio infections.
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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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11
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Li CC, Yi H, Wang YM, Tang XY, Zhu YB, Song YJ, Zhao NL, Huang Q, Mou XY, Luo GH, Liu TG, Yang GL, Zeng YJ, Wang LJ, Tang H, Fan G, Bao R. Nucleotide binding as an allosteric regulatory mechanism for Akkermansia muciniphila β- N-acetylhexosaminidase Am2136. Gut Microbes 2022; 14:2143221. [PMID: 36394293 PMCID: PMC9673926 DOI: 10.1080/19490976.2022.2143221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
β-N-acetylhexosaminidases (EC3.2.1.52), which belong to the glycosyl hydrolase family GH20, are important enzymes for oligosaccharides modification. Numerous microbial β-N-acetylhexosaminidases have been investigated for applications in biology, biomedicine and biotechnology. Akkermansia muciniphila is an anaerobic intestinal commensal bacterium which possesses specific β-N-acetylhexosaminidases for gut mucosal layer colonization and mucin degradation. In this study, we assessed the in vitro mucin glycan cleavage activity of the A. muciniphila β-N-acetylhexosaminidase Am2136 and demonstrated its ability that hydrolyzing the β-linkages joining N-acetylglucosamine to a wide variety of aglycone residues, which indicated that Am2136 may be a generalist β-N-acetylhexosaminidase. Structural and enzyme activity assay experiments allowed us to probe the essential function of the inter-domain interactions in β23-β33. Importantly, we revealed that the hydrolysis activity of Am2136 was enhanced by nucleotides. We further speculated that this activation mechanism might be associated with the conformational motions between domain III and IV. To our knowledge, this is the first report of nucleotide effector regulated β-N-acetylhexosaminidase, to reveal its novel biological functions. These findings contribute to understanding the distinct properties within the GH20 family and lay a certain foundation to develop controllable glycan hydrolyzing catalysts.Abbreviations: OD600 - optical cell densities at 600 nm; LB - Luria-Bertani; IPTG - isopropyl β-D-1-thiogalactopyranoside; PMSF - phenylmethanesulfonyl fluoride; rmsd - root mean square deviation; GlcNAc - N-acetyl-β-D-glucosamine; GalNAc - N-acetyl-β-D-galactosamine; Gal - galactose.
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Affiliation(s)
- Chang-Cheng Li
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Huan Yi
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yan-Mei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu, China
| | - Xin-Yue Tang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Yi-Bo Zhu
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ying-Jie Song
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ning-Lin Zhao
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Qin Huang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Xing-Yu Mou
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Gui-Hua Luo
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Tong-Gen Liu
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Gang-Long Yang
- School of Biotechnology, Jiangnan University, Chengdu, China
| | - Yu-Jiao Zeng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Li-Jie Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hong Tang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China,Hong Tang Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University. Chengdu. China
| | - Gang Fan
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China,Gang Fan State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine. Chengdu. China
| | - Rui Bao
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China,CONTACT Rui Bao
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12
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Mészáros Z, Petrásková L, Kulik N, Pelantová H, Bojarová P, Křen V, Slámová K. Hypertransglycosylating Variants of the GH20 β‐
N
‐Acetylhexosaminidase for the Synthesis of Chitooligomers. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Zuzana Mészáros
- Laboratory of Biotransformation Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 Prague 4 CZ 14220 Czech Republic
- Department of Biochemistry University of Chemistry and Technology Prague Technická 6 Prague 6 CZ 16000 Czech Republic
| | - Lucie Petrásková
- Laboratory of Biotransformation Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 Prague 4 CZ 14220 Czech Republic
| | - Natalia Kulik
- Laboratory of Structural Biology and Bioinformatics Institute of Microbiology of the Czech Academy of Sciences Zámek 136 Nové Hrady CZ 37333 Czech Republic
| | - Helena Pelantová
- Laboratory of Molecular Structure Characterization Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 Prague 4 CZ 14220 Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 Prague 4 CZ 14220 Czech Republic
| | - Vladimír Křen
- Laboratory of Biotransformation Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 Prague 4 CZ 14220 Czech Republic
| | - Kristýna Slámová
- Laboratory of Biotransformation Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 Prague 4 CZ 14220 Czech Republic
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13
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Cuxart I, Coines J, Esquivias O, Faijes M, Planas A, Biarnés X, Rovira C. Enzymatic Hydrolysis of Human Milk Oligosaccharides. The Molecular Mechanism of Bifidobacterium Bifidum Lacto- N-biosidase. ACS Catal 2022; 12:4737-4743. [PMID: 35465242 PMCID: PMC9016705 DOI: 10.1021/acscatal.2c00309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/26/2022] [Indexed: 12/22/2022]
Abstract
![]()
Bifidobacterium
bifidum lacto-N-biosidase (LnbB)
is a critical enzyme for the degradation
of human milk oligosaccharides in the gut microbiota of breast-fed
infants. Guided by recent crystal structures, we unveil its molecular
mechanism of catalysis using QM/MM metadynamics. We show that the
oligosaccharide substrate follows 1S3/1,4B → [4E]‡ → 4C1/4H5 and 4C1/4H5 → [4E/4H5]‡ → 1,4B conformational itineraries for the two
successive reaction steps, with reaction free energy barriers in agreement
with experiments. The simulations also identify a critical histidine
(His263) that switches between two orientations to modulate the pKa of the acid/base residue, facilitating catalysis.
The reaction intermediate of LnbB is best depicted as an oxazolinium
ion, with a minor population of neutral oxazoline. The present study
sheds light on the processing of oligosaccharides of the early life
microbiota and will be useful for the engineering of LnbB and similar
glycosidases for biocatalysis.
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Affiliation(s)
- Irene Cuxart
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Oriol Esquivias
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08020 Barcelona, Spain
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14
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Mechanism of cooperative N-glycan processing by the multi-modular endoglycosidase EndoE. Nat Commun 2022; 13:1137. [PMID: 35241669 PMCID: PMC8894350 DOI: 10.1038/s41467-022-28722-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/04/2022] [Indexed: 11/29/2022] Open
Abstract
Bacteria produce a remarkably diverse range of glycoside hydrolases to metabolize glycans from the environment as a primary source of nutrients, and to promote the colonization and infection of a host. Here we focus on EndoE, a multi-modular glycoside hydrolase secreted by Enterococcus faecalis, one of the leading causes of healthcare-associated infections. We provide X-ray crystal structures of EndoE, which show an architecture composed of four domains, including GH18 and GH20 glycoside hydrolases connected by two consecutive three α-helical bundles. We determine that the GH20 domain is an exo-β-1,2-N-acetylglucosaminidase, whereas the GH18 domain is an endo-β-1,4-N-acetylglucosaminidase that exclusively processes the central core of complex-type or high-mannose-type N-glycans. Both glycoside hydrolase domains act in a concerted manner to process diverse N-glycans on glycoproteins, including therapeutic IgG antibodies. EndoE combines two enzyme domains with distinct functions and glycan specificities to play a dual role in glycan metabolism and immune evasion. EndoE is a multi-domain glycoside hydrolase of the human pathogen Enterococcus faecalis. Here, the authors present crystal structures of EndoE and provide biochemical insights into the molecular basis of EndoE’s substrate specificity and catalytic mechanism.
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15
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Singh RP, Niharika J, Kondepudi KK, Bishnoi M, Tingirikari JMR. Recent understanding of human milk oligosaccharides in establishing infant gut microbiome and roles in immune system. Food Res Int 2022; 151:110884. [PMID: 34980411 DOI: 10.1016/j.foodres.2021.110884] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 11/19/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022]
Abstract
Human milk oligosaccharides (HMOs) are complex sugars with distinctive structural diversity present in breast milk. HMOs have various functional roles to play in infant development starting from establishing the gut microbiome and immune system to take it up to the mature phase. It has been a major energy source for human gut microbes that confer positive benefits on infant health by directly interacting through intestinal cells and generating short-chain fatty acids. It has recently become evident that each species of Bifidobacterium and other genera which are resident of the infant gut employ distinct molecular mechanisms to capture and digest diverse structural HMOs to avoid competition among themselves and successfully maintain gut homeostasis. HMOs also directly modulate gut immune responses and can decoy receptors of pathogenic bacteria and viruses, inhibiting their binding on intestinal cells, thus preventing the emergence of a disease. This review provides a critical understanding of how different gut bacteria capture and utilize selective sugars from the HMO pool and how different structural HMOs protect infants from infectious diseases.
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Affiliation(s)
- Ravindra Pal Singh
- Laboratory of Gut Glycobiology, Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Punjab 140306, India.
| | - Jayashree Niharika
- Laboratory of Gut Glycobiology, Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Punjab 140306, India
| | - Kanthi Kiran Kondepudi
- Healthy Gut Research Group, Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Punjab 140306, India
| | - Mahendra Bishnoi
- Healthy Gut Research Group, Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Punjab 140306, India
| | - Jagan Mohan Rao Tingirikari
- Department of Biotechnology, National Institute of Technology Andhra Pradesh, Tadepalligudem, Andhra Pradesh 534101, India
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16
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Bouquet J, Auberger N, Ashmus R, King D, Bordes A, Fontelle N, Nakagawa S, Madden Z, Proceviat C, Kato A, Désiré J, Vocadlo DJ, Blériot Y. Structural variation of the 3-acetamido-4,5,6-trihydroxyazepane iminosugar through epimerization and C-alkylation leads to low micromolar HexAB and NagZ inhibitors. Org Biomol Chem 2021; 20:619-629. [PMID: 34940771 DOI: 10.1039/d1ob02280f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis of seven-membered iminosugars derived from a 3S-acetamido-4R,5R,6S-trihydroxyazepane scaffold and their evaluation as inhibitors of functionally related exo-N-acetylhexosaminidases including human O-GlcNAcase (OGA), human lysosomal β-hexosaminidase (HexAB), and Escherichia coli NagZ. Capitalizing on the flexibility of azepanes and the active site tolerances of hexosaminidases, we explore the effects of epimerization of stereocenters at C-3, C-5 and C-6 and C-alkylation at the C-2 or C-7 positions. Accordingly, epimerization at C-6 (L-ido) and at C-5 (D-galacto) led to selective HexAB inhibitors whereas introduction of a propyl group at C-7 on the C-3 epimer furnished a potent NagZ inhibitor.
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Affiliation(s)
- J Bouquet
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - N Auberger
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - R Ashmus
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - D King
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - A Bordes
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - N Fontelle
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - S Nakagawa
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Z Madden
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - C Proceviat
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - A Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - J Désiré
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - D J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - Y Blériot
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
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17
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Désiré J, Foucart Q, Poveda A, Gourlaouen G, Shimadate Y, Kise M, Proceviat C, Ashmus R, Vocadlo DJ, Jiménez-Barbero J, Kato A, Blériot Y. Synthesis, conformational analysis and glycosidase inhibition of bicyclic nojirimycin C-glycosides based on an octahydrofuro[3,2-b]pyridine motif. Carbohydr Res 2021; 511:108491. [PMID: 34953389 DOI: 10.1016/j.carres.2021.108491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 12/13/2022]
Abstract
A set of bicyclic iminosugar C-glycosides, based on an octahydrofuro[3,2-b]pyridine motif, has been synthesized from a C-allyl iminosugar exploiting a debenzylative iodocycloetherification and an iodine nucleophilic displacement as the key steps. The halogen allowed the introduction of a range of aglycon moieties of different sizes bearing several functionalities such as alcohol, amine, amide and triazole. In these carbohydrate mimics the fused THF ring forces the piperidine to adopt a flattened 4C1 conformation according to NMR and DFT calculations studies. In their deprotected form, these bicycles were assayed on a panel of 23 glycosidases. The iminosugars displaying hydrophobic aglycon moieties proved to be superior glycosidase inhibitors, leading to a low micromolar inhibition of human lysosome β-glucosidase (compound 11; IC50 = 2.7 μM) and rice α-glucosidase (compound 10; IC50 = 7.7 μM). Finally, the loose structural analogy of these derivatives with Thiamet G, a potent OGA bicyclic inhibitor, was illustrated by the weak OGA inhibitory activity (Ki = 140 μM) of iminosugar 5.
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Affiliation(s)
- Jérôme Désiré
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "Synthèse Organique", Groupe Glycochimie, 4 rue Michel Brunet, 86073, Poitiers Cedex 9, France.
| | - Quentin Foucart
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "Synthèse Organique", Groupe Glycochimie, 4 rue Michel Brunet, 86073, Poitiers Cedex 9, France
| | - Ana Poveda
- CIC bioGUNE, Parque technologico de Bizkaia, Edif. 801A-1°, Derio-Bizkaia 48160, and Ikerbasque, Basque Foundation for Science, Maria Lopez de Haro 3, 48013, Bilbao, Spain
| | - Gurvan Gourlaouen
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "Synthèse Organique", Groupe Glycochimie, 4 rue Michel Brunet, 86073, Poitiers Cedex 9, France
| | - Yuna Shimadate
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Maki Kise
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Cameron Proceviat
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5S 1P6
| | - Roger Ashmus
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5S 1P6
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5S 1P6
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Parque technologico de Bizkaia, Edif. 801A-1°, Derio-Bizkaia 48160, and Ikerbasque, Basque Foundation for Science, Maria Lopez de Haro 3, 48013, Bilbao, Spain
| | - Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.
| | - Yves Blériot
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "Synthèse Organique", Groupe Glycochimie, 4 rue Michel Brunet, 86073, Poitiers Cedex 9, France.
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18
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Improvement of the Transglycosylation Efficiency of a Lacto-N-Biosidase from Bifidobacterium bifidum by Protein Engineering. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112311493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The lacto-N-biosidase LnbB from Bifidobacterium bifidum JCM 1254 was engineered to improve its negligible transglycosylation efficiency with the purpose of enzymatically synthesizing lacto-N-tetraose (LNT; Gal-β1,3-GlcNAc-β1,3-Gal-β1,4-Glc) in one enzymatic step. LNT is a prebiotic human milk oligosaccharide in itself and constitutes the structural core of a range of more complex human milk oligosaccharides as well. Thirteen different LnbB variants were expressed and screened for transglycosylation activity by monitoring transglycosylation product formation using lacto-N-biose 1,2-oxazoline as donor substrate and lactose as acceptor substrate. LNT was the major reaction product, yet careful reaction analysis revealed the formation of three additional LNT isomers, which we identified to have a β1,2-linkage, a β1,6-linkage, and a 1,1-linkage, respectively, between lacto-N-biose (Gal-β1,3-GlcNAc) and lactose. Considering both maximal transglycosylation yield and regioselectivity as well as minimal product hydrolysis, the best variant was LnbB W394H, closely followed by W465H and Y419N. A high transglycosylation yield was also obtained with W394F, yet the substitution of W394 and W465 of the subsite −1 hydrophobic platform in the enzyme with His dramatically impaired the undesirable product hydrolysis as compared to substitution with Phe; the effect was most pronounced for W465. Using p-nitrophenyl-β-lacto-N-bioside as donor substrate manifested W394 as an important target position. The optimization of the substrate concentrations confirmed that high initial substrate concentration and high acceptor-to-donor ratio both favor transglycosylation.
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19
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Multifunctional fluorescent probes for high-throughput characterization of hexosaminidase enzyme activity. Bioorg Chem 2021; 119:105532. [PMID: 34883361 DOI: 10.1016/j.bioorg.2021.105532] [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: 08/25/2021] [Revised: 10/29/2021] [Accepted: 11/25/2021] [Indexed: 12/28/2022]
Abstract
Microbial polysaccharides composed of N-acetylglucosamine (GlcNAc), such as chitin, peptidoglycan and poly-β-(1 → 6)-GlcNAc (dPNAG), play a critical role in maintaining cell integrity or in facilitating biofilm formation in numerous fungal and bacterial pathogens. Glycosyl hydrolase enzymes that catalyze the degradation of these β-GlcNAc containing polysaccharides play important roles in normal microbial cell physiology and can also be exploited as biocatalysts with applications as anti-fungal, anti-bacterial, or biofilm dispersal agents. Assays to rapidly detect and characterize the activity of such glycosyl hydrolase enzymes can facilitate their development as biocatalyst, however, currently available probes such as 4-methylumbelliferyl-β-GlcNAc (4MU-GlcNAc) are not universally accepted as substrates, and their fluorescent signal is sensitive to changes in pH. Here, we present the development of a new multifunctional fluorescent substrate analog for the detection and characterization of hexosaminidase enzyme activity containing a 7-amino-4-methyl coumarin (AMC) carbamate aglycone. This probe is widely tolerated as a substrate for exo-acting β-hexosaminidase, family 19 endo-chitinase, and the dPNAG hydrolase enzyme Dispersin B (DspB) and enables detection of hexosaminidase enzyme activity via either single wavelength fluorescent measurements or ratiometric fluorescent detection. We demonstrate the utility of this probe to screen for recombinant DspB activity in Escherichia coli cell lysates, and for the development of a high-throughput assay to screen for DspB inhibitors.
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20
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Mészáros Z, Nekvasilová P, Bojarová P, Křen V, Slámová K. Reprint of: Advanced glycosidases as ingenious biosynthetic instruments. Biotechnol Adv 2021; 51:107820. [PMID: 34462167 DOI: 10.1016/j.biotechadv.2021.107820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 11/27/2022]
Abstract
Until recently, glycosidases, naturally hydrolyzing carbohydrate-active enzymes, have found few synthetic applications in industry, being primarily used for cleaving unwanted carbohydrates. With the establishment of glycosynthase and transglycosidase technology by genetic engineering, the view of glycosidases as industrial biotechnology tools has started to change. Their easy production, affordability, robustness, and substrate versatility, added to the possibility of controlling undesired side hydrolysis by enzyme engineering, have made glycosidases competitive synthetic tools. Current promising applications of engineered glycosidases include the production of well-defined chitooligomers, precious galactooligosaccharides or specialty chemicals such as glycosylated flavonoids. Other synthetic pathways leading to human milk oligosaccharides or remodeled antibodies are on the horizon. This work provides an overview of the synthetic achievements to date for glycosidases, emphasizing the latest trends and outlining possible developments in the field.
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Affiliation(s)
- Zuzana Mészáros
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 1903/3, CZ-16628 Praha 6, Czech Republic
| | - Pavlína Nekvasilová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, CZ-12843, Praha 2, Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Kristýna Slámová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic.
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21
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Nanomolar inhibition of human OGA by 2-acetamido-2-deoxy-d-glucono-1,5-lactone semicarbazone derivatives. Eur J Med Chem 2021; 223:113649. [PMID: 34186233 DOI: 10.1016/j.ejmech.2021.113649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 12/25/2022]
Abstract
O-GlcNAcylation is a dynamic post-translational modification mediated by O-linked β-N-acetylglucosamine transferase (OGT) and O-GlcNAc hydrolase (OGA), that adds or removes a single β-N-acetylglucosamine (GlcNAc) moiety to or from serine/threonine residues of nucleocytosolic and mitochondrial proteins, respectively. The perturbed homeostasis of O-GlcNAc cycling results in several pathological conditions. Human OGA is a promising therapeutic target in diseases where aberrantly low levels of O-GlcNAc are experienced, such as tauopathy in Alzheimer's disease. A new class of potent OGA inhibitors, 2-acetamido-2-deoxy-d-glucono-1,5-lactone (thio)semicarbazones, have been identified. Eight inhibitors were designed and synthesized in five steps starting from d-glucosamine and with 15-55% overall yields. A heterologous OGA expression protocol with strain selection and isolation has been optimized that resulted in stable, active and full length human OGA (hOGA) isomorph. Thermal denaturation kinetics of hOGA revealed environmental factors affecting hOGA stability. From kinetics experiments, the synthesized compounds proved to be efficient competitive inhibitors of hOGA with Ki-s in the range of ∼30-250 nM and moderate selectivity with respect to lysosomal β-hexosaminidases. In silico studies consisting of Prime protein-ligand refinements, QM/MM optimizations and QM/MM-PBSA binding free energy calculations revealed the factors governing the observed potencies, and led to design of the most potent analogue 2-acetamido-2-deoxy-d-glucono-1,5-lactone 4-(2-naphthyl)-semicarbazone 6g (Ki = 36 nM). The protocol employed has applications in future structure based inhibitor design targeting OGA.
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22
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Meekrathok P, Bürger M, Porfetye AT, Kumsaoad S, Aunkham A, Vetter IR, Suginta W. Structural basis of chitin utilization by a GH20 β-N-acetylglucosaminidase from Vibrio campbellii strain ATCC BAA-1116. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:674-689. [PMID: 33950022 PMCID: PMC8098473 DOI: 10.1107/s2059798321002771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/15/2021] [Indexed: 12/03/2022]
Abstract
Crystal structures of a GH20 β-N-acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization. Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β-N-acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA-1116. Crystal structures of wild-type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N-terminal carbohydrate-binding domain linked to a small α+β domain and a C-terminal (β/α)8 catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).
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Affiliation(s)
- Piyanat Meekrathok
- Biochemistry-Electrochemistry Research Unit, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Marco Bürger
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Arthur T Porfetye
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Sawitree Kumsaoad
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Payupnai, Wangchan, Rayong 21210, Thailand
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Payupnai, Wangchan, Rayong 21210, Thailand
| | - Ingrid R Vetter
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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23
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Mészáros Z, Nekvasilová P, Bojarová P, Křen V, Slámová K. Advanced glycosidases as ingenious biosynthetic instruments. Biotechnol Adv 2021; 49:107733. [PMID: 33781890 DOI: 10.1016/j.biotechadv.2021.107733] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 12/22/2022]
Abstract
Until recently, glycosidases, naturally hydrolyzing carbohydrate-active enzymes, have found few synthetic applications in industry, being primarily used for cleaving unwanted carbohydrates. With the establishment of glycosynthase and transglycosidase technology by genetic engineering, the view of glycosidases as industrial biotechnology tools has started to change. Their easy production, affordability, robustness, and substrate versatility, added to the possibility of controlling undesired side hydrolysis by enzyme engineering, have made glycosidases competitive synthetic tools. Current promising applications of engineered glycosidases include the production of well-defined chitooligomers, precious galactooligosaccharides or specialty chemicals such as glycosylated flavonoids. Other synthetic pathways leading to human milk oligosaccharides or remodeled antibodies are on the horizon. This work provides an overview of the synthetic achievements to date for glycosidases, emphasizing the latest trends and outlining possible developments in the field.
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Affiliation(s)
- Zuzana Mészáros
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 1903/3, CZ-16628 Praha 6, Czech Republic
| | - Pavlína Nekvasilová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, CZ-12843, Praha 2, Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Kristýna Slámová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic.
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24
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Castejón-Vilatersana M, Faijes M, Planas A. Transglycosylation Activity of Engineered Bifidobacterium Lacto- N-Biosidase Mutants at Donor Subsites for Lacto- N-Tetraose Synthesis. Int J Mol Sci 2021; 22:3230. [PMID: 33810098 PMCID: PMC8004761 DOI: 10.3390/ijms22063230] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/14/2021] [Accepted: 03/19/2021] [Indexed: 01/11/2023] Open
Abstract
The health benefits of human milk oligosaccharides (HMOs) make them attractive targets as supplements for infant formula milks. However, HMO synthesis is still challenging and only two HMOs have been marketed. Engineering glycoside hydrolases into transglycosylases may provide biocatalytic routes to the synthesis of complex oligosaccharides. Lacto-N-biosidase from Bifidobacterium bifidum (LnbB) is a GH20 enzyme present in the gut microbiota of breast-fed infants that hydrolyzes lacto-N-tetraose (LNT), the core structure of the most abundant type I HMOs. Here we report a mutational study in the donor subsites of the substrate binding cleft with the aim of reducing hydrolytic activity and conferring transglycosylation activity for the synthesis of LNT from p-nitrophenyl β-lacto-N-bioside and lactose. As compared with the wt enzyme with negligible transglycosylation activity, mutants with residual hydrolase activity within 0.05% to 1.6% of the wild-type enzyme result in transglycosylating enzymes with LNT yields in the range of 10-30%. Mutations of Trp394, located in subsite -1 next to the catalytic residues, have a large impact on the transglycosylation/hydrolysis ratio, with W394F being the best mutant as a biocatalyst producing LNT at 32% yield. It is the first reported transglycosylating LnbB enzyme variant, amenable to further engineering for practical enzymatic synthesis of LNT.
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Affiliation(s)
| | - Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017 Barcelona, Spain;
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017 Barcelona, Spain;
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25
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Monge EC, Gardner JG. Efficient chito-oligosaccharide utilization requires two TonB-dependent transporters and one hexosaminidase in Cellvibrio japonicus. Mol Microbiol 2021; 116:366-380. [PMID: 33735458 DOI: 10.1111/mmi.14717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/13/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
Chitin utilization by microbes plays a significant role in biosphere carbon and nitrogen cycling, and studying the microbial approaches used to degrade chitin will facilitate our understanding of bacterial strategies to degrade a broad range of recalcitrant polysaccharides. The early stages of chitin depolymerization by the bacterium Cellvibrio japonicus have been characterized and are dependent on one chitin-specific lytic polysaccharide monooxygenase and nonredundant glycoside hydrolases from the family GH18 to generate chito-oligosaccharides for entry into metabolism. Here, we describe the mechanisms for the latter stages of chitin utilization by C. japonicus with an emphasis on the fate of chito-oligosaccharides. Our systems biology approach combined transcriptomics and bacterial genetics using ecologically relevant substrates to determine the essential mechanisms for chito-oligosaccharide transport and catabolism in C. japonicus. Using RNAseq analysis we found a coordinated expression of genes that encode polysaccharide-degrading enzymes. Mutational analysis determined that the hex20B gene product, predicted to encode a hexosaminidase, was required for efficient utilization of chito-oligosaccharides. Furthermore, two gene loci (CJA_0353 and CJA_1157), which encode putative TonB-dependent transporters, were also essential for chito-oligosaccharides utilization. This study further develops our model of C. japonicus chitin metabolism and may be predictive for other environmentally or industrially important bacteria.
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Affiliation(s)
- Estela C Monge
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
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26
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Katoh T, Yamamoto K. Innovative Preparation of Biopharmaceuticals Using Transglycosylation Activity of Microbial Endoglycosidases. J Appl Glycosci (1999) 2021; 68:1-9. [PMID: 34354540 PMCID: PMC8113915 DOI: 10.5458/jag.jag.jag-2020_0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/16/2020] [Indexed: 12/02/2022] Open
Abstract
Most functional biopharmaceuticals such as antibodies are glycoproteins carrying N-linked oligosaccharides (N-glycans). In animal cells, these glycans are generally expressed as heterogeneous glycoforms that are difficult to separate into a pure form. The structure of these glycans directly affects several biological aspects of the glycoproteins, especially binding affinity. Therefore, the preparation of glycoproteins with well-defined and homogeneous glycoforms is necessary for functional studies and improved efficacy, particularly for biopharmaceuticals. This review describes the recent remarkable progress in the development and production of biopharmaceutical glycan-modified antibodies, through the use of glycan remodeling using microbial endoglycosidases and sophisticated glycoengineering techniques utilizing microbial enzymatic reaction mechanisms.
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Affiliation(s)
| | - Kenji Yamamoto
- 2 Center for Innovative and Joint Research, Wakayama University
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27
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McGregor NGS, Coines J, Borlandelli V, Amaki S, Artola M, Nin‐Hill A, Linzel D, Yamada C, Arakawa T, Ishiwata A, Ito Y, Marel GA, Codée JDC, Fushinobu S, Overkleeft HS, Rovira C, Davies GJ. Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent β‐
l‐
Arabinofuranosidase Inhibitor. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Nicholas G. S. McGregor
- York Structural Biology Laboratory Department of Chemistry The University of York Heslington York YO10 5DD UK
| | - Joan Coines
- 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
| | - Valentina Borlandelli
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Satoko Amaki
- Department of Biotechnology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Marta Artola
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - 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
| | - Daniël Linzel
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Chihaya Yamada
- Department of Biotechnology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Takatoshi Arakawa
- Department of Biotechnology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Akihiro Ishiwata
- Synthetic Cellular Chemistry Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Graduate School of Science Osaka University Toyonaka Osaka 560-0043 Japan
| | - Gijsbert A. Marel
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Shinya Fushinobu
- Department of Biotechnology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2300 RA 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
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 23 08020 Barcelona Spain
| | - Gideon J. Davies
- York Structural Biology Laboratory Department of Chemistry The University of York Heslington York YO10 5DD UK
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28
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McGregor NGS, Coines J, Borlandelli V, Amaki S, Artola M, Nin-Hill A, Linzel D, Yamada C, Arakawa T, Ishiwata A, Ito Y, van der Marel GA, Codée JDC, Fushinobu S, Overkleeft HS, Rovira C, Davies GJ. Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent β-l-Arabinofuranosidase Inhibitor. Angew Chem Int Ed Engl 2021; 60:5754-5758. [PMID: 33528085 DOI: 10.1002/anie.202013920] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/30/2020] [Indexed: 11/08/2022]
Abstract
The recent discovery of zinc-dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys)3 (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on a Zn-coordinated cysteine nucleophile and passing through a thioglycosyl enzyme intermediate, remains controversial. This is primarily due to the expected stability of the intermediate C-S bond. To facilitate the study of this atypical mechanism, we report the synthesis of a cyclophellitol-derived β-l-arabinofuranosidase inhibitor, hypothesised to react with the catalytic nucleophile to form a non-hydrolysable adduct analogous to the mechanistic covalent intermediate. This β-l-arabinofuranosidase inhibitor reacts exclusively with the proposed cysteine thiol catalytic nucleophiles of representatives of GH families 127 and 146. X-ray crystal structures determined for the resulting adducts enable MD and QM/MM simulations, which provide insight into the mechanism of thioglycosyl enzyme intermediate breakdown. Leveraging the unique chemistry of cyclophellitol derivatives, the structures and simulations presented here support the assignment of a zinc-coordinated cysteine as the catalytic nucleophile and illuminate the finely tuned energetics of this remarkable metalloenzyme clan.
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Affiliation(s)
- Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK
| | - Joan Coines
- 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
| | - Valentina Borlandelli
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300, RA, Leiden, The Netherlands
| | - Satoko Amaki
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300, RA, Leiden, The Netherlands
| | - 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
| | - Daniël Linzel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300, RA, Leiden, The Netherlands
| | - Chihaya Yamada
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Akihiro Ishiwata
- Synthetic Cellular Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300, RA, Leiden, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300, RA, Leiden, The Netherlands
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300, RA, 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.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08020, Barcelona, Spain
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK
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29
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Breslawec AP, Wang S, Li C, Poulin MB. Anionic amino acids support hydrolysis of poly-β-(1,6)-N-acetylglucosamine exopolysaccharides by the biofilm dispersing glycosidase Dispersin B. J Biol Chem 2020; 296:100203. [PMID: 33334876 PMCID: PMC7949127 DOI: 10.1074/jbc.ra120.015524] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/14/2022] Open
Abstract
The exopolysaccharide poly-β-(1→6)-N-acetylglucosamine (PNAG) is a major structural determinant of bacterial biofilms responsible for persistent and nosocomial infections. The enzymatic dispersal of biofilms by PNAG-hydrolyzing glycosidase enzymes, such as Dispersin B (DspB), is a possible approach to treat biofilm-dependent bacterial infections. The cationic charge resulting from partial de-N-acetylation of native PNAG is critical for PNAG-dependent biofilm formation. We recently demonstrated that DspB has increased catalytic activity on de-N-acetylated PNAG oligosaccharides, but the molecular basis for this increased activity is not known. Here, we analyze the role of anionic amino acids surrounding the catalytic pocket of DspB in PNAG substrate recognition and hydrolysis using a combination of site-directed mutagenesis, activity measurements using synthetic PNAG oligosaccharide analogs, and in vitro biofilm dispersal assays. The results of these studies support a model in which bound PNAG is weakly associated with a shallow anionic groove on the DspB protein surface with recognition driven by interactions with the -1 GlcNAc residue in the catalytic pocket. An increased rate of hydrolysis for cationic PNAG was driven, in part, by interaction with D147 on the anionic surface. Moreover, we identified that a DspB mutant with improved hydrolysis of fully acetylated PNAG oligosaccharides correlates with improved in vitro dispersal of PNAG-dependent Staphylococcus epidermidis biofilms. These results provide insight into the mechanism of substrate recognition by DspB and suggest a method to improve DspB biofilm dispersal activity by mutation of the amino acids within the anionic binding surface.
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Affiliation(s)
- Alexandra P Breslawec
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Shaochi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Crystal Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Myles B Poulin
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA.
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30
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Nekvasilová P, Kulik N, Rychlá N, Pelantová H, Petrásková L, Bosáková Z, Cvačka J, Slámová K, Křen V, Bojarová P. How Site‐Directed Mutagenesis Boosted Selectivity of a Promiscuous Enzyme. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Pavlína Nekvasilová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
- Department of Genetics and Microbiology Faculty of Science Charles University Viničná 5 CZ-12843 Praha 2 Czech Republic
- Department of Analytical Chemistry Faculty of Science Charles University Hlavova 2030/8. CZ-12843 Praha 2 Czech Republic
| | - Natalia Kulik
- Center for Nanobiology and Structural Biology Institute of Microbiology Czech Academy of Sciences Zámek 136 CZ-37333 Nové Hrady Czech Republic
| | - Nikola Rychlá
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
- Department of Health Care Disciplines and Population Protection Faculty of Biomedical Engineering Czech Technical University in Prague Nám. Sítná 3105 CZ-27201 Kladno Czech Republic
| | - Helena Pelantová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Lucie Petrásková
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Zuzana Bosáková
- Department of Analytical Chemistry Faculty of Science Charles University Hlavova 2030/8. CZ-12843 Praha 2 Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nám. 2 CZ-16610 Praha 6 Czech Republic
| | - Kristýna Slámová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Vladimír Křen
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
- Department of Health Care Disciplines and Population Protection Faculty of Biomedical Engineering Czech Technical University in Prague Nám. Sítná 3105 CZ-27201 Kladno Czech Republic
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31
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Wang S, Breslawec AP, Li C, Poulin MB. A Colorimetric Assay to Enable High-Throughput Identification of Biofilm Exopolysaccharide-Hydrolyzing Enzymes. Chemistry 2020; 26:10719-10723. [PMID: 32589289 DOI: 10.1002/chem.202002475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/25/2020] [Indexed: 11/06/2022]
Abstract
Glycosidase enzymes that hydrolyze the biofilm exopolysaccharide poly-β-(1→6)-N-acetylglucosamine (PNAG) are critical tools to study biofilm and potential therapeutic biofilm dispersal agents. Function-driven metagenomic screening is a powerful approach for the discovery of new glycosidase but requires sensitive assays capable of distinguishing between the desired enzyme and functionally related enzymes. Herein, we report the synthesis of a colorimetric PNAG disaccharide analogue whose hydrolysis by PNAG glycosidases results in production of para-nitroaniline that can be continuously monitored at 410 nm. The assay is specific for enzymes capable of hydrolyzing PNAG and not related β-hexosaminidase enzymes with alternative glycosidic linkage specificities. This analogue enabled development of a continuous colorimetric assay for detection of PNAG hydrolyzing enzyme activity in crude E. coli cell lysates and suggests that this disaccharide probe will be critical for establishing the functional screening of metagenomic DNA libraries.
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Affiliation(s)
- Shaochi Wang
- Department of Chemistry and Biochemistry, University of Maryland College Park, 8051 Regents Drive, College Park, MD 20742, USA
| | - Alexandra P Breslawec
- Department of Chemistry and Biochemistry, University of Maryland College Park, 8051 Regents Drive, College Park, MD 20742, USA
| | - Crystal Li
- Department of Chemistry and Biochemistry, University of Maryland College Park, 8051 Regents Drive, College Park, MD 20742, USA
| | - Myles B Poulin
- Department of Chemistry and Biochemistry, University of Maryland College Park, 8051 Regents Drive, College Park, MD 20742, USA
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32
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Xu W, Yang W, Wang Y, Wang M, Zhang M. Structural and biochemical analyses of β-N-acetylhexosaminidase Am0868 from Akkermansia muciniphila involved in mucin degradation. Biochem Biophys Res Commun 2020; 529:876-881. [PMID: 32819592 DOI: 10.1016/j.bbrc.2020.06.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 12/30/2022]
Abstract
β-N-acetylhexosaminidases from the gut microbes are found to be capable of cleaving the specific glycoside linkages in the process of mucin degradation that has relevance for human health. However, features of the enzyme used in regulating the sugar-degrading capacities of Akkermansia muciniphila have not been well defined. Here we reported the crystal structure of a novel β-N-acetylhexosaminidase from Akkermansia muciniphila (Am0868), which displayed a typical (β/α) 8 barrel fold with a GlcNAc bound to the active center. Crystallographic and subsequent mutagenic analyses confirmed that Asp326 and Glu327 are the key catalytic residues of Am0868. Furthermore, Am0868 exhibited high specificity to β-GlcNAc supporting the substrate-assisted catalytic mechanism. Am0868 was also active in a broad pH and temperature range but inhibited strongly by metal ions Zn2+ and Cu2+. Collectively, these results indicate that Am0868 has the potential for mucin hydrolysis under some severe conditions, which highlight the superiority of A. muciniphila surviving in gut.
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Affiliation(s)
- Wenjuan Xu
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, 230601, China
| | - Wenyi Yang
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, 230601, China
| | - Yongzhong Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, 230601, China
| | - Mingzhu Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, 230601, China; Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China.
| | - Min Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, 230601, China.
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33
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Elbatrawy AA, Kim EJ, Nam G. O‐GlcNAcase: Emerging Mechanism, Substrate Recognition and Small‐Molecule Inhibitors. ChemMedChem 2020; 15:1244-1257. [DOI: 10.1002/cmdc.202000077] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/22/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Ahmed A. Elbatrawy
- Center for Neuro-Medicine Brain Science Institute Korea Institutes of Science and Technology Seoul 02792 (Republic of Korea
- Division of Bio-Med KIST school Korea University of Science and Technology (UST) Gajungro 217 Youseong-gu Daejeon (Republic of Korea
| | - Eun Ju Kim
- Daegu University Department of Science Education-Chemistry Gyeongsan-si, Gyeongsangbuk-do Gyeongbuk 38453 (Republic of Korea
| | - Ghilsoo Nam
- Center for Neuro-Medicine Brain Science Institute Korea Institutes of Science and Technology Seoul 02792 (Republic of Korea
- Division of Bio-Med KIST school Korea University of Science and Technology (UST) Gajungro 217 Youseong-gu Daejeon (Republic of Korea
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34
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Kapešová J, Petrásková L, Kulik N, Straková Z, Bojarová P, Markošová K, Rebroš M, Křen V, Slámová K. Transglycosidase activity of glycosynthase-type mutants of a fungal GH20 β-N-acetylhexosaminidase. Int J Biol Macromol 2020; 161:1206-1215. [PMID: 32522540 DOI: 10.1016/j.ijbiomac.2020.05.273] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/29/2020] [Accepted: 05/20/2020] [Indexed: 02/07/2023]
Abstract
β-N-Acetylhexosaminidases (CAZy GH20, EC 3.2.1.52) are exo-glycosidases specific for cleaving N-acetylglucosamine and N-acetylgalactosamine moieties of various substrates. The β-N-acetylhexosaminidase from the filamentous fungus Talaromyces flavus (TfHex), a model enzyme in this study, has a broad substrate flexibility and outstanding synthetic ability. We have designed and characterized seven glycosynthase-type variants of TfHex mutated at the catalytic aspartate residue that stabilizes the oxazoline reaction intermediate. Most of the obtained enzyme variants lost the majority of their original hydrolytic activity towards the standard substrate p-nitrophenyl 2-acetamido-2-deoxy-β-D-glucopyranoside (pNP-β-GlcNAc); moreover, the mutants were not active with the proposed glycosynthase donor 2-acetamido-2-deoxy-d-glucopyranosyl-α-fluoride (GlcNAc-α-F) either as would be expected in a glycosynthase. Importantly, the mutant enzymes instead retained a strong transglycosylation activity towards the standard substrate pNP-β-GlcNAc. In summary, five out of seven prepared TfHex variants bearing mutation at the catalytic Asp370 residue acted as efficient transglycosidases, which makes them excellent tools for the synthesis of chitooligosaccharides, with the advantage of processing an inexpensive, stable and commercially available pNP-β-GlcNAc.
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Affiliation(s)
- Jana Kapešová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 4 CZ 14220, Czech Republic
| | - Lucie Petrásková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 4 CZ 14220, Czech Republic
| | - Natalia Kulik
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, Nové Hrady, CZ 37333, Czech Republic
| | - Zuzana Straková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 4 CZ 14220, Czech Republic.; Department of Biochemistry, University of Chemistry and Technology Prague, Technická 6, Prague 6, CZ 16000, Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 4 CZ 14220, Czech Republic
| | - Kristína Markošová
- Institute of Biotechnology, Slovak University of Technology, Radlinského 9, Bratislava, SK 81237, Slovakia
| | - Martin Rebroš
- Institute of Biotechnology, Slovak University of Technology, Radlinského 9, Bratislava, SK 81237, Slovakia
| | - Vladimír Křen
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 4 CZ 14220, Czech Republic
| | - Kristýna Slámová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 4 CZ 14220, Czech Republic..
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35
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Ka D, Oh H, Park E, Kim JH, Bae E. Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD + degradation. Nat Commun 2020; 11:2816. [PMID: 32499527 PMCID: PMC7272460 DOI: 10.1038/s41467-020-16703-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/18/2020] [Indexed: 01/08/2023] Open
Abstract
The intense arms race between bacteria and phages has led to the development of diverse antiphage defense systems in bacteria. Unlike well-known restriction-modification and CRISPR-Cas systems, recently discovered systems are poorly characterized. One such system is the Thoeris defense system, which consists of two genes, thsA and thsB. Here, we report structural and functional analyses of ThsA and ThsB. ThsA exhibits robust NAD+ cleavage activity and a two-domain architecture containing sirtuin-like and SLOG-like domains. Mutation analysis suggests that NAD+ cleavage is linked to the antiphage function of Thoeris. ThsB exhibits a structural resemblance to TIR domain proteins such as nucleotide hydrolases and Toll-like receptors, but no enzymatic activity is detected in our in vitro assays. These results further our understanding of the molecular mechanism underlying the Thoeris defense system, highlighting a unique strategy for bacterial antiphage resistance via NAD+ degradation. The Thoeris defense system is a recently discovered bacterial defense system that protects bacteria against phage infection and consists of the two genes thsA and thsB. Here, the authors present the crystal structures of Bacillus cereus ThsA and ThsB and show that ThsA is a NAD+ cleaving enzyme.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Hyejin Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea.,Department of Applied Biology and Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Eunyoung Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Jeong-Han Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea. .,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
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36
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Soroko M, Kwan DH. Enzymatic Synthesis of a Fluorogenic Reporter Substrate and the Development of a High-Throughput Assay for Fucosyltransferase VIII Provide a Toolkit to Probe and Inhibit Core Fucosylation. Biochemistry 2020; 59:2100-2110. [PMID: 32441090 DOI: 10.1021/acs.biochem.0c00286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maxim Soroko
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
| | - David H. Kwan
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
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37
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In silico analysis of the effects of disease-associated mutations of β-hexosaminidase A in Tay‒Sachs disease. J Genet 2020. [DOI: 10.1007/s12041-020-01208-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Meekrathok P, Stubbs KA, Aunkham A, Kaewmaneewat A, Kardkuntod A, Bulmer DM, Berg B, Suginta W. NAG‐thiazoline is a potent inhibitor of the
Vibrio campbellii
GH20 β‐
N
‐Acetylglucosaminidase. FEBS J 2020; 287:4982-4995. [DOI: 10.1111/febs.15283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/15/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Piyanat Meekrathok
- School of Chemistry Suranaree University of Technology Nakhon Ratchasima Thailand
| | - Keith A. Stubbs
- School of Molecular Sciences The University of Western Australia Crawley WA Australia
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE) Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Anuphon Kaewmaneewat
- School of Biomolecular Science and Engineering (BSE) Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Apinya Kardkuntod
- School of Biomolecular Science and Engineering (BSE) Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - David M. Bulmer
- Institute for Cell and Molecular Biosciences Newcastle University UK
| | - Bert Berg
- Institute for Cell and Molecular Biosciences Newcastle University UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE) Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
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39
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Sørlie M, Horn SJ, Vaaje-Kolstad G, Eijsink VG. Using chitosan to understand chitinases and the role of processivity in the degradation of recalcitrant polysaccharides. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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40
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Acceptor Specificity of β- N-Acetylhexosaminidase from Talaromyces flavus: A Rational Explanation. Int J Mol Sci 2019; 20:ijms20246181. [PMID: 31817903 PMCID: PMC6940953 DOI: 10.3390/ijms20246181] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023] Open
Abstract
Fungal β-N-acetylhexosaminidases, though hydrolytic enzymes in vivo, are useful tools in the preparation of oligosaccharides of biological interest. The β-N-acetylhexosaminidase from Talaromyces flavus is remarkable in terms of its synthetic potential, broad substrate specificity, and tolerance to substrate modifications. It can be heterologously produced in Pichia pastoris in a high yield. The mutation of the Tyr470 residue to histidine greatly enhances its transglycosylation capability. The aim of this work was to identify the structural requirements of this model β-N-acetylhexosaminidase for its transglycosylation acceptors and formulate a structure-activity relationship study. Enzymatic reactions were performed using an activated glycosyl donor, 4-nitrophenyl N-acetyl-β-d-glucosaminide or 4-nitrophenyl N-acetyl-β-d-galactosaminide, and a panel of glycosyl acceptors of varying structural features (N-acetylglucosamine, glucose, N-acetylgalactosamine, galactose, N-acetylmuramic acid, and glucuronic acid). The transglycosylation products were isolated and structurally characterized. The C-2 N-acetamido group in the acceptor molecule was found to be essential for recognition by the enzyme. The presence of the C-2 hydroxyl moiety strongly hindered the normal course of transglycosylation, yielding unique non-reducing disaccharides in a low yield. Moreover, whereas the gluco-configuration at C-4 steered the glycosylation into the β(1-4) position, the galacto-acceptor afforded a β(1-6) glycosidic linkage. The Y470H mutant enzyme was tested with acceptors based on β-glycosides of uronic acid and N-acetylmuramic acid. With the latter acceptor, we were able to isolate and characterize one glycosylation product in a low yield. To our knowledge, this is the first example of enzymatic glycosylation of an N-acetylmuramic acid derivative. In order to explain these findings and predict enzyme behavior, a modeling study was accomplished that correlated with the acquired experimental data.
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41
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Structural basis for the specific cleavage of core-fucosylated N-glycans by endo-β- N-acetylglucosaminidase from the fungus Cordyceps militaris. J Biol Chem 2019; 294:17143-17154. [PMID: 31548313 PMCID: PMC6851319 DOI: 10.1074/jbc.ra119.010842] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/20/2019] [Indexed: 01/07/2023] Open
Abstract
N-Linked glycans play important roles in various cellular and immunological events. Endo-β-N-acetylglucosaminidase (ENGase) can release or transglycosylate N-glycans and is a promising tool for the chemoenzymatic synthesis of glycoproteins with homogeneously modified glycans. The ability of ENGases to act on core-fucosylated glycans is a key factor determining their therapeutic utility because mammalian N-glycans are frequently α-1,6-fucosylated. Although the biochemistries and structures of various ENGases have been studied extensively, the structural basis for the recognition of the core fucose and the asparagine-linked GlcNAc is unclear. Herein, we determined the crystal structures of a core fucose-specific ENGase from the caterpillar fungus Cordyceps militaris (Endo-CoM), which belongs to glycoside hydrolase family 18. Structures complexed with fucose-containing ligands were determined at 1.75-2.35 Å resolutions. The fucose moiety linked to GlcNAc is extensively recognized by protein residues in a round-shaped pocket, whereas the asparagine moiety linked to the GlcNAc is exposed to the solvent. The N-glycan-binding cleft of Endo-CoM is Y-shaped, and several lysine and arginine residues are present at its terminal regions. These structural features were consistent with the activity of Endo-CoM on fucose-containing glycans on rituximab (IgG) and its preference for a sialobiantennary substrate. Comparisons with other ENGases provided structural insights into their core fucose tolerance and specificity. In particular, Endo-F3, a known core fucose-specific ENGase, has a similar fucose-binding pocket, but the surrounding residues are not shared with Endo-CoM. Our study provides a foothold for protein engineering to develop enzymatic tools for the preparation of more effective therapeutic antibodies.
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42
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Wang S, Breslawec AP, Alvarez E, Tyrlik M, Li C, Poulin MB. Differential Recognition of Deacetylated PNAG Oligosaccharides by a Biofilm Degrading Glycosidase. ACS Chem Biol 2019; 14:1998-2005. [PMID: 31430121 DOI: 10.1021/acschembio.9b00467] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Exopolysaccharides consisting of partially de-N-acetylated poly-β-d-(1→6)-N-acetyl-glucosamine (dPNAG) are key structural components of the biofilm extracellular polymeric substance of both Gram-positive and Gram-negative human pathogens. De-N-acetylation is required for the proper assembly and function of dPNAG in biofilm development suggesting that different patterns of deacetylation may be preferentially recognized by proteins that interact with dPNAG, such as Dispersin B (DspB). The enzymatic degradation of dPNAG by the Aggregatibacter actinomycetemcomitans native β-hexosaminidase enzyme DspB plays a role in biofilm dispersal. To test the role of substrate de-N-acetylation on substrate recognition by DspB, we applied an efficient preactivation-based one-pot glycosylation approach to prepare a panel of dPNAG trisaccharide analogs with defined acetylation patterns. These analogs served as effective DspB substrates, and the rate of hydrolysis was dependent on the specific substrate de-N-acetylation pattern, with glucosamine (GlcN) located +2 from the site of cleavage being preferentially hydrolyzed. The product distributions support a primarily exoglycosidic cleavage activity following a substrate assisted cleavage mechanism, with the exception of substrates containing a nonreducing GlcN that were cleaved endo leading to the exclusive formation of a nonreducing disaccharide product. These observations provide critical insight into the substrate specificity of dPNAG specific glycosidase that can help guide their design as biocatalysts.
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Affiliation(s)
- Shaochi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Alexandra P. Breslawec
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Elaine Alvarez
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Michal Tyrlik
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Crystal Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Myles B. Poulin
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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43
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Ka D, An SY, Suh JY, Bae E. Crystal structure of an anti-CRISPR protein, AcrIIA1. Nucleic Acids Res 2019; 46:485-492. [PMID: 29182776 PMCID: PMC5758886 DOI: 10.1093/nar/gkx1181] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/14/2017] [Indexed: 11/16/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide bacteria with RNA-based adaptive immunity against phage infection. To counteract this defense mechanism, phages evolved anti-CRISPR (Acr) proteins that inactivate the CRISPR-Cas systems. AcrIIA1, encoded by Listeria monocytogenes prophages, is the most prevalent among the Acr proteins targeting type II-A CRISPR-Cas systems and has been used as a marker to identify other Acr proteins. Here, we report the crystal structure of AcrIIA1 and its RNA-binding affinity. AcrIIA1 forms a dimer with a novel two helical-domain architecture. The N-terminal domain of AcrIIA1 exhibits a helix-turn-helix motif similar to transcriptional factors. When overexpressed in Escherichia coli, AcrIIA1 associates with RNAs, suggesting that AcrIIA1 functions via nucleic acid recognition. Taken together, the unique structural and functional features of AcrIIA1 suggest its distinct mode of Acr activity, expanding the diversity of the inhibitory mechanisms employed by Acr proteins.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - So Young An
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano 399 4598, Japan
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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44
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Ka D, Jang DM, Han BW, Bae E. Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. Nucleic Acids Res 2019; 46:9805-9815. [PMID: 30102386 PMCID: PMC6182153 DOI: 10.1093/nar/gky702] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against invading foreign nucleic acids. In type II-A CRISPR–Cas systems, the Cas1–Cas2 integrase complex and the subtype-specific Csn2 comprise the CRISPR adaptation module, which cooperates with the Cas9 nuclease effector for spacer selection. Here, we report the molecular organization of the Streptococcus pyogenes type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. We determined the crystal structure of S. pyogenes type II-A Cas2. Chromatographic and calorimetric analyses revealed the stoichiometry and topology of the type II-A adaptation module composed of Cas1, Cas2 and Csn2. We also demonstrated that Cas9 interacts with Csn2 in a direct and stoichiometric manner. Our results reveal a network of molecular interactions among type II-A Cas proteins and highlight the role of Csn2 in coordinating Cas components involved in the adaptation and interference stages of CRISPR-mediated immunity.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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45
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Dong L, Shen S, Lu H, Jin S, Zhang J. Novel Glycosylated Naphthalimide-Based Activatable Fluorescent Probe: A Tool for the Assessment of Hexosaminidase Activity and Intracellular Hexosaminidase Imaging. ACS Sens 2019; 4:1222-1229. [PMID: 31001975 DOI: 10.1021/acssensors.8b01617] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of effective detection methods for hexosaminidase is of great importance for the rapid screening of potential inhibitors in vitro and for the early diagnosis of related diseases ex vivo. In this study, the activatable fluorescent probes that are based on naphthalimide decorated with ethylene glycol units were synthesized using N-acetyl-β-d-glucosaminide as a hexosaminidase-responsive group. When exposed to this enzyme, the glucoside-linked naphthalimide moiety of 1c can be cleaved quickly with significant changes in both color (from colorless to yellow) and fluorescence (from blue to green). Probe 1c shows better water-solubility and fluorescence properties than common substrate 4-methylumbelliferyl N-acetyl-β-d-glucosaminide. Furthermore, the response mechanism of 1c to hexosaminidase was evaluated using HPLC analysis and TD-DFT calculations. Molecular docking was performed to investigate the interaction mode. In addition, 1c has successfully achieved the straightforward rapid discovery of effective hexosaminidase inhibitors. Fluorescence imaging experiments indicate that 1c has good cell safety and can be employed as a useful tool for detecting intracellular hexosaminidase activity.
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Affiliation(s)
- Lili Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
| | - Shengqiang Shen
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
| | - Huizhe Lu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
| | - Shuhui Jin
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
| | - Jianjun Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
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46
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Zhang X, Chen F, Petrella A, Chacón-Huete F, Covone J, Tsai TW, Yu CC, Forgione P, Kwan DH. A High-Throughput Glycosyltransferase Inhibition Assay for Identifying Molecules Targeting Fucosylation in Cancer Cell-Surface Modification. ACS Chem Biol 2019; 14:715-724. [PMID: 30831024 DOI: 10.1021/acschembio.8b01123] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In cancers, increased fucosylation (attachment of fucose sugar residues) on cell-surface glycans, resulting from the abnormal upregulation of the expression of specific fucosyltransferase enzymes (FUTs), is one of the most important types of glycan modifications associated with malignancy. Fucosylated glycans on cell surfaces are involved in a multitude of cellular interactions and signal regulation in normal biological processes, as well as in disease. For example, sialyl LewisX is a fucosylated cell-surface glycan that is abnormally abundant in some cancers where it has been implicated in facilitating metastasis, allowing circulating tumor cells to bind to the epithelial tissue within blood vessels and invade into secondary sites by taking advantage of glycan-mediated interactions. To identify inhibitors of FUT enzymes as potential cancer therapeutics, we have developed a novel high-throughput assay that makes use of a fluorogenically labeled oligosaccharide as a probe of fucosylation. This probe, which consists of a 4-methylumbelliferyl glycoside, is recognized and hydrolyzed by specific glycoside hydrolase enzymes to release fluorescent 4-methylumbelliferone, yet when the probe is fucosylated prior to treatment with the glycoside hydrolases, hydrolysis does not occur and no fluorescent signal is produced. We have demonstrated that this assay can be used to measure the inhibition of FUT enzymes by small molecules, because blocking fucosylation will allow glycosidase-catalyzed hydrolysis of the labeled oligosaccharide to produce a fluorescent signal. Employing this assay, we have screened a focused library of small molecules for inhibitors of a human FUT enzyme involved in the synthesis of sialyl LewisX and demonstrated that our approach can be used to identify potent FUT inhibitors from compound libraries in microtiter plate format.
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Affiliation(s)
| | | | | | | | | | - Teng-Wei Tsai
- Department of Chemistry and Biochemistry, National Chung-Cheng University, 168 University Road, Min-Hsiung, Chiayi 62102, Taiwan
| | - Ching-Ching Yu
- Department of Chemistry and Biochemistry, National Chung-Cheng University, 168 University Road, Min-Hsiung, Chiayi 62102, Taiwan
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47
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Dong L, Shen S, Xu Y, Wang L, Feng R, Zhang J, Lu H. Computational Studies on the Potency and Selectivity of PUGNAc Derivatives Against GH3, GH20, and GH84 β-N-acetyl-D-hexosaminidases. Front Chem 2019; 7:235. [PMID: 31111026 PMCID: PMC6499197 DOI: 10.3389/fchem.2019.00235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/25/2019] [Indexed: 02/05/2023] Open
Abstract
β-N-acetyl-D-hexosaminidases have attracted significant attention due to their crucial role in diverse physiological functions including antibacterial synergists, pathogen defense, virus infection, lysosomal storage, and protein glycosylation. In particular, the GH3 β-N-acetyl-D-hexosaminidase of V. cholerae (VcNagZ), human GH20 β-N-acetyl-D-hexosaminidase B (HsHexB), and human GH84 β-N-acetyl-D-hexosaminidase (hOGA) are three important representative glycosidases. These have been found to be implicated in β-lactam resistance (VcNagZ), lysosomal storage disorders (HsHexB) and Alzheimer's disease (hOGA). Considering the profound effects of these three enzymes, many small molecule inhibitors with good potency and selectivity have been reported to regulate the corresponding physiological functions. In this paper, the best-known inhibitors PUGNAc and two of its derivatives (N-valeryl-PUGNAc and EtBuPUG) were selected as model compounds and docked into the active pockets of VcNagZ, HsHexB, and hOGA, respectively. Subsequently, molecular dynamics simulations of the nine systems were performed to systematically compare their binding modes from active pocket architecture and individual interactions. Furthermore, the binding free energy and free energy decomposition are calculated using the MM/GBSA methods to predict the binding affinities of enzyme-inhibitor systems and to quantitatively analyze the contribution of each residue. The results show that PUGNAc is deeply-buried in the active pockets of all three enzymes, which indicates its potency (but not selectivity) against VcNagZ, HsHexB, and hOGA. However, EtBuPUG, bearing branched 2-isobutamido, adopted strained conformations and was only located in the active pocket of VcNagZ. It has completely moved out of the pocket of HsHexB and lacks interactions with HsHexB. This indicates why the selectivity of EtBuPUG to VcNagZ/HsHexB is the largest, reaching 968-fold. In addition, the contributions of the catalytic residue Asp253 (VcNagZ), Asp254 (VcNagZ), Asp175 (hOGA), and Asp354 (HsHexB) are important to distinguish the activity and selectivity of these inhibitors. The results of this study provide a helpful structural guideline to promote the development of novel and selective inhibitors against specific β-N-acetyl-D-hexosaminidases.
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Affiliation(s)
- Lili Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Shengqiang Shen
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Yefei Xu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Leng Wang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Ruirui Feng
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Jianjun Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Huizhe Lu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
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Wang M, Zheng F, Wang T, Lyu YM, Alteen MG, Cai ZP, Cui ZL, Liu L, Voglmeir J. Characterization of Stackebrandtia nassauensis GH 20 Beta-Hexosaminidase, a Versatile Biocatalyst for Chitobiose Degradation. Int J Mol Sci 2019; 20:ijms20051243. [PMID: 30871033 PMCID: PMC6429369 DOI: 10.3390/ijms20051243] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022] Open
Abstract
An unstudied β-N-acetylhexosaminidase (SnHex) from the soil bacterium Stackebrandtia nassauensis was successfully cloned and subsequently expressed as a soluble protein in Escherichia coli. Activity tests and the biochemical characterization of the purified protein revealed an optimum pH of 6.0 and a robust thermal stability at 50 °C within 24 h. The addition of urea (1 M) or sodium dodecyl sulfate (1% w/v) reduced the activity of the enzyme by 44% and 58%, respectively, whereas the addition of divalent metal ions had no effect on the enzymatic activity. PUGNAc (O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate) strongly inhibited the enzyme in sub-micromolar concentrations. The β-N-acetylhexosaminidase was able to hydrolyze β1,2-linked, β1,3-linked, β1,4-linked, and β1,6-linked GlcNAc residues from the non-reducing end of various tested glycan standards, including bisecting GlcNAc from one of the tested hybrid-type N-glycan substrates. A mutational study revealed that the amino acids D306 and E307 bear the catalytically relevant side acid/base side chains. When coupled with a chitinase, the β-N-acetylhexosaminidase was able to generate GlcNAc directly from colloidal chitin, which showed the potential of this enzyme for biotechnological applications.
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Affiliation(s)
- Meng Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Zheng
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yong-Mei Lyu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Matthew G Alteen
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Zhi-Peng Cai
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhong-Li Cui
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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49
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Chen X, Wang J, Liu M, Yang W, Wang Y, Tang R, Zhang M. Crystallographic evidence for substrate-assisted catalysis of β-N-acetylhexosaminidas from Akkermansia muciniphila. Biochem Biophys Res Commun 2019; 511:833-839. [PMID: 30846208 DOI: 10.1016/j.bbrc.2019.02.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 12/21/2022]
Abstract
β-N-acetylhexosaminidases from Akkermansia muciniphila was reported to perform the crystal structure with GlcNAc complex, which proved to be the substrate of Am2301. Domain II of Am2301 is consisted of amino acid residues 111-489 and is folded as a (β/α)8 barrel with the active site combined of the glycosyl hydrolases. Crystallographic evidence showed that Asp-278 and Glu-279 could be the catalytic site and Tyr-373 may plays a role on binding the substrate. Moreover, Am2301 prefers to bind Zn ion, which similar to other GH 20 family. Enzyme activity and kinetic parameters of wild-type Am2301 and mutants proved that Asp-278 and Glu-279 are the catalytic sites and they play a critical role on the catalytic process. Overall, our results demonstrate that Am2301 and its complex with GlcNAC provide obvious structural evidence for substrate-assisted catalysis. Obviously, this expands our understanding on the mode of substrate-assisted reaction for this enzyme family in Akkermansia muciniphila.
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Affiliation(s)
- Xi Chen
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Department of Biological and Food Engineering, Bozhou University, 2266 Tangwang Road, Bozhou, Anhui, China
| | - Junchao Wang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Mingjie Liu
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Wenyi Yang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Yongzhong Wang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Rupei Tang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.
| | - Min Zhang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.
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50
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Brockerman JA, Okon M, Withers SG, McIntosh LP. The pK a values of the catalytic residues in the retaining glycoside hydrolase T26H mutant of T4 lysozyme. Protein Sci 2018; 28:620-632. [PMID: 30537432 DOI: 10.1002/pro.3562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/24/2022]
Abstract
T4 phage lysozyme (T4L) is an enzyme that cleaves bacterial cell wall peptidoglycan. Remarkably, the single substitution of the active site Thr26 to a His (T26H) converts T4L from an inverting to a retaining glycoside hydrolase with transglycosylase activity. It has been proposed that T26H-T4L follows a double displacement mechanism with His26 serving as a nucleophile to form a covalent glycosyl-enzyme intermediate (Kuroki et al., PNAS 1999; 96:8949-8954). To gain further insights into this or alternative mechanisms, we used NMR spectroscopy to measure the acid dissociation constants (pKa values) and/or define the ionization states of the Asp, Glu, His, and Arg residues in the T4L mutant. Most notably, the pKa value of the putative nucleophile His26 is 6.8 ± 0.1, whereas that of the general acid Glu11 is 4.7 ± 0.1. If the proposed mechanism holds true, then T26H-T4L follows a reverse protonation pathway in which only a minor population of the free enzyme is in its catalytically competent ionization state with His26 deprotonated and Glu11 protonated. Our studies also confirm that all arginines in T26H-T4L, including the active site Arg145, are positively charged under neutral pH conditions. BRIEF STATEMENT: The replacement of a single amino acid changes T4 lysozyme from an inverting to a retaining glycoside hydrolase. Using NMR spectroscopy, we measured the pKa values of the ionizable residues in the active site of this mutant enzyme. Along with previously reported data, these results provide important constraints for understanding the catalytic mechanisms by which the wild-type and mutant form of T4 lysozyme cleave bacterial peptidoglycan.
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Affiliation(s)
- Jacob A Brockerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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