1
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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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2
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Wei X, Wang P, Liu F, Ye X, Xiong D. Drug Discovery Based on Fluorine-Containing Glycomimetics. Molecules 2023; 28:6641. [PMID: 37764416 PMCID: PMC10536126 DOI: 10.3390/molecules28186641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Glycomimetics, which are synthetic molecules designed to mimic the structures and functions of natural carbohydrates, have been developed to overcome the limitations associated with natural carbohydrates. The fluorination of carbohydrates has emerged as a promising solution to dramatically enhance the metabolic stability, bioavailability, and protein-binding affinity of natural carbohydrates. In this review, the fluorination methods used to prepare the fluorinated carbohydrates, the effects of fluorination on the physical, chemical, and biological characteristics of natural sugars, and the biological activities of fluorinated sugars are presented.
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Affiliation(s)
- Xingxing Wei
- Department of Pharmacy, Changzhi Medical College, No. 161, Jiefang East Street, Changzhi 046012, China
| | - Pengyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| | - Fen Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| | - Xinshan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| | - Decai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
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3
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Neun S, Brear P, Campbell E, Tryfona T, El Omari K, Wagner A, Dupree P, Hyvönen M, Hollfelder F. Functional metagenomic screening identifies an unexpected β-glucuronidase. Nat Chem Biol 2022; 18:1096-1103. [PMID: 35799064 DOI: 10.1038/s41589-022-01071-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The abundance of recorded protein sequence data stands in contrast to the small number of experimentally verified functional annotation. Here we screened a million-membered metagenomic library at ultrahigh throughput in microfluidic droplets for β-glucuronidase activity. We identified SN243, a genuine β-glucuronidase with little homology to previously studied enzymes of this type, as a glycoside hydrolase 3 family member. This glycoside hydrolase family contains only one recently added β-glucuronidase, showing that a functional metagenomic approach can shed light on assignments that are currently 'unpredictable' by bioinformatics. Kinetic analyses of SN243 characterized it as a promiscuous catalyst and structural analysis suggests regions of divergence from homologous glycoside hydrolase 3 members creating a wide-open active site. With a screening throughput of >107 library members per day, picolitre-volume microfluidic droplets enable functional assignments that complement current enzyme database dictionaries and provide bridgeheads for the annotation of unexplored sequence space.
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Affiliation(s)
- Stefanie Neun
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Eleanor Campbell
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Australian Synchrotron, Clayton, VIC, Australia
| | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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4
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Abstract
![]()
Fluorinated
carbohydrates have found many applications in the glycosciences.
Typically, these contain fluorination at a single position. There
are not many applications involving polyfluorinated carbohydrates,
here defined as monosaccharides in which more than one carbon has
at least one fluorine substituent directly attached to it, with the
notable exception of their use as mechanism-based inhibitors. The
increasing attention to carbohydrate physical properties, especially
around lipophilicity, has resulted in a surge of interest for this
class of compounds. This review covers the considerable body of work
toward the synthesis of polyfluorinated hexoses, pentoses, ketosugars,
and aminosugars including sialic acids and nucleosides. An overview
of the current state of the art of their glycosidation is also provided.
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Affiliation(s)
- Kler Huonnic
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K
| | - Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.,Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, Krijgslaan 281-S4, Ghent, 9000, Belgium
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5
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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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6
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Functional and structural characterization of a GH3 β-N-acetylhexosaminidase from Akkermansia muciniphila involved in mucin degradation. Biochem Biophys Res Commun 2021; 589:186-191. [PMID: 34922201 DOI: 10.1016/j.bbrc.2021.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 01/06/2023]
Abstract
Akkermansia muciniphila is a probiotic that colonizes the outer layer of intestinal mucus and is negatively associated with metabolic disorders. Amuc_2109 protein, a β-N-acetylhexosaminidase from A. muciniphila, may be involved in the degradation of mucins and is associated with intestinal health. Here, we reported the crystal structure of Amuc_2109, which belongs to the GH family 3 enzymes and fell into the canonical (α/β)8 TIM barrel structure with GlcNAc bound to the active center. Biochemical assay characterization of Amuc_2109 revealed that Amuc_2109 is a GlcNAc-specific glycosidase active over a wide temperature and pH range, reflecting the survival advantage of Amuc_2109 in the intestinal environment. Our structural and biochemical results will contribute to the understanding of the catalytic mechanism of the GH3 β-N-acetylhexosaminidase and help to gain insight into the molecular mechanism of complex carbohydrate utilization and restoration of the intestinal barrier in A. muciniphila.
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7
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Franceus J, Lormans J, Cools L, D’hooghe M, Desmet T. Evolution of Phosphorylases from N-Acetylglucosaminide Hydrolases in Family GH3. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jolien Lormans
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Lore Cools
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Matthias D’hooghe
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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8
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Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253. Sci Rep 2020; 10:1329. [PMID: 31992772 PMCID: PMC6987092 DOI: 10.1038/s41598-020-58015-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/07/2020] [Indexed: 11/08/2022] Open
Abstract
The genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: β-N-acetyl-glucosaminidases, β-1,4-glucosidases/β-xylosidases and macrolide β-glucosidases. The RmNag3 with additional β-lactamase domain clustered with the deepest rooted GH3-lineage of β-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed β-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide β-glucosidases from Actinomycetes. The β-xylosidases, RmXyl3A and RmXyl3B, and the β-glucosidases RmBgl3A and RmBgl3C clustered within the major β-glucosidases/β-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed β-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed β-1,4-glucosidase/β-xylosidase activity while RmBgl3C was active on pNP-β-Glc and β-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252T (homolog strain). The analysis showed that in the homolog strain DSM 4252TRmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.
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9
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Meekrathok P, Thongsom S, Aunkham A, Kaewmaneewat A, Kitaoku Y, Choowongkomon K, Suginta W. Novel GH-20 β-N-acetylglucosaminidase inhibitors: Virtual screening, molecular docking, binding affinity, and anti-tumor activity. Int J Biol Macromol 2020; 142:503-512. [DOI: 10.1016/j.ijbiomac.2019.09.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 01/05/2023]
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10
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Rahfeld P, Wardman JF, Mehr K, Huff D, Morgan-Lang C, Chen HM, Hallam SJ, Withers SG. Prospecting for microbial α- N-acetylgalactosaminidases yields a new class of GH31 O-glycanase. J Biol Chem 2019; 294:16400-16415. [PMID: 31530641 DOI: 10.1074/jbc.ra119.010628] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/16/2019] [Indexed: 12/18/2022] Open
Abstract
α-Linked GalNAc (α-GalNAc) is most notably found at the nonreducing terminus of the blood type-determining A-antigen and as the initial point of attachment to the peptide backbone in mucin-type O-glycans. However, despite their ubiquity in saccharolytic microbe-rich environments such as the human gut, relatively few α-N-acetylgalactosaminidases are known. Here, to discover and characterize novel microbial enzymes that hydrolyze α-GalNAc, we screened small-insert libraries containing metagenomic DNA from the human gut microbiome. Using a simple fluorogenic glycoside substrate, we identified and characterized a glycoside hydrolase 109 (GH109) that is active on blood type A-antigen, along with a new subfamily of glycoside hydrolase 31 (GH31) that specifically cleaves the initial α-GalNAc from mucin-type O-glycans. This represents a new activity in this GH family and a potentially useful new enzyme class for analysis or modification of O-glycans on protein or cell surfaces.
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Affiliation(s)
- Peter Rahfeld
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jacob F Wardman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kevin Mehr
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Drew Huff
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Connor Morgan-Lang
- Department of Microbiology and Immunology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Hong-Ming Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada
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11
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Itoh T, Araki T, Nishiyama T, Hibi T, Kimoto H. Structural and functional characterization of a glycoside hydrolase family 3 β-N-acetylglucosaminidase from Paenibacillus sp. str. FPU-7. J Biochem 2019; 166:503-515. [DOI: 10.1093/jb/mvz072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/11/2019] [Indexed: 11/14/2022] Open
Abstract
AbstractChitin, a β-1,4-linked homopolysaccharide of N-acetyl-d-glucosamine (GlcNAc), is one of the most abundant biopolymers on Earth. Paenibacillus sp. str. FPU-7 produces several different chitinases and converts chitin into N,N′-diacetylchitobiose ((GlcNAc)2) in the culture medium. However, the mechanism by which the Paenibacillus species imports (GlcNAc)2 into the cytoplasm and divides it into the monomer GlcNAc remains unclear. The gene encoding Paenibacillus β-N-acetyl-d-glucosaminidase (PsNagA) was identified in the Paenibacillus sp. str. FPU-7 genome using an expression cloning system. The deduced amino acid sequence of PsNagA suggests that the enzyme is a part of the glycoside hydrolase family 3 (GH3). Recombinant PsNagA was successfully overexpressed in Escherichia coli and purified to homogeneity. As assessed by gel permeation chromatography, the enzyme exists as a 57-kDa monomer. PsNagA specifically hydrolyses chitin oligosaccharides, (GlcNAc)2–4, 4-nitrophenyl N-acetyl β-d-glucosamine (pNP-GlcNAc) and pNP-(GlcNAc)2–6, but has no detectable activity against 4-nitrophenyl β-d-glucose, 4-nitrophenyl β-d-galactosamine and colloidal chitin. In this study, we present a 1.9 Å crystal structure of PsNagA bound to GlcNAc. The crystal structure reveals structural features related to substrate recognition and the catalytic mechanism of PsNagA. This is the first study on the structural and functional characterization of a GH3 β-N-acetyl-d-glucosaminidase from Paenibacillus sp.
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Tomomitsu Araki
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Tomohiro Nishiyama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Takao Hibi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Hisashi Kimoto
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
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12
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β-N-Acetylhexosaminidases-the wizards of glycosylation. Appl Microbiol Biotechnol 2019; 103:7869-7881. [PMID: 31401752 DOI: 10.1007/s00253-019-10065-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/27/2022]
Abstract
β-N-Acetylhexosaminidases (EC 3.2.1.52) are a unique family of glycoside hydrolases with dual substrate specificity and a particular reaction mechanism. Though hydrolytic enzymes per se, their good stability, easy recombinant production, absolute stereoselectivity, and a broad substrate specificity predestine these enzymes for challenging applications in carbohydrate synthesis. This mini-review aims to demonstrate the catalytic potential of β-N-acetylhexosaminidases in a range of unusual reactions, processing of unnatural substrates, formation of unexpected products, and demanding reaction designs. The use of unconventional media can considerably alter the progress of transglycosylation reactions. By means of site-directed mutagenesis, novel catalytic machineries can be constructed. Glycosylation of difficult substrates such as sugar nucleotides was accomplished, and the range of afforded glycosidic bonds comprises unique non-reducing sugars. Specific functional groups may be tolerated in the substrate molecule, which makes β-N-acetylhexosaminidases invaluable allies in difficult synthetic problems.
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13
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Martínez-Pardo P, Blay G, Vila C, Sanz-Marco A, Muñoz MC, Pedro JR. Enantioselective Synthesis of 5-Trifluoromethyl-2-oxazolines under Dual Silver/Organocatalysis. J Org Chem 2018; 84:314-325. [DOI: 10.1021/acs.joc.8b02808] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pablo Martínez-Pardo
- Departament de Química Orgànica, Facultat de Química, Universitat de València, Burjassot, València 46100, Spain
| | - Gonzalo Blay
- Departament de Química Orgànica, Facultat de Química, Universitat de València, Burjassot, València 46100, Spain
| | - Carlos Vila
- Departament de Química Orgànica, Facultat de Química, Universitat de València, Burjassot, València 46100, Spain
| | - Amparo Sanz-Marco
- Departament de Química Orgànica, Facultat de Química, Universitat de València, Burjassot, València 46100, Spain
| | - M. Carmen Muñoz
- Departament de Física Aplicada, Universitat Politècnica de València, València 46022, Spain
| | - José R. Pedro
- Departament de Química Orgànica, Facultat de Química, Universitat de València, Burjassot, València 46100, Spain
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14
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Ho LA, Winogrodzki JL, Debowski AW, Madden Z, Vocadlo DJ, Mark BL, Stubbs KA. A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to β-lactams in Pseudomonas aeruginosa. Chem Commun (Camb) 2018; 54:10630-10633. [PMID: 30178799 DOI: 10.1039/c8cc05281f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of a potent mechanism-based inactivator of NagZ, an enzyme critical to the production of inducible AmpC β-lactamase in Gram-negative bacteria, is presented. This inactivator significantly reduces MIC values for important β-lactams against a clinically relevant strain of Pseudomonas aeruginosa.
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Affiliation(s)
- Louisa A Ho
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
| | - Judith L Winogrodzki
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
| | - Aleksandra W Debowski
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia. and School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Zarina Madden
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
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15
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Meekrathok P, Stubbs KA, Suginta W. Potent inhibition of a GH20 exo-β-N-acetylglucosaminidase from marine Vibrio bacteria by reaction intermediate analogues. Int J Biol Macromol 2018; 115:1165-1173. [DOI: 10.1016/j.ijbiomac.2018.04.193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/14/2018] [Accepted: 04/30/2018] [Indexed: 02/04/2023]
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16
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Dik DA, Fisher JF, Mobashery S. Cell-Wall Recycling of the Gram-Negative Bacteria and the Nexus to Antibiotic Resistance. Chem Rev 2018; 118:5952-5984. [PMID: 29847102 PMCID: PMC6855303 DOI: 10.1021/acs.chemrev.8b00277] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The importance of the cell wall to the viability of the bacterium is underscored by the breadth of antibiotic structures that act by blocking key enzymes that are tasked with cell-wall creation, preservation, and regulation. The interplay between cell-wall integrity, and the summoning forth of resistance mechanisms to deactivate cell-wall-targeting antibiotics, involves exquisite orchestration among cell-wall synthesis and remodeling and the detection of and response to the antibiotics through modulation of gene regulation by specific effectors. Given the profound importance of antibiotics to the practice of medicine, the assertion that understanding this interplay is among the most fundamentally important questions in bacterial physiology is credible. The enigmatic regulation of the expression of the AmpC β-lactamase, a clinically significant and highly regulated resistance response of certain Gram-negative bacteria to the β-lactam antibiotics, is the exemplar of this challenge. This review gives a current perspective to this compelling, and still not fully solved, 35-year enigma.
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Affiliation(s)
- David A. Dik
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jed F. Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
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17
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Bouquet J, King DT, Vadlamani G, Benzie GR, Iorga B, Ide D, Adachi I, Kato A, Vocadlo DJ, Mark BL, Blériot Y, Désiré J. Selective trihydroxylated azepane inhibitors of NagZ, a glycosidase involved in Pseudomonas aeruginosa resistance to β-lactam antibiotics. Org Biomol Chem 2018; 15:4609-4619. [PMID: 28513749 DOI: 10.1039/c7ob00838d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of a series of d-gluco-like configured 4,5,6-trihydroxyazepanes bearing a triazole, a sulfonamide or a fluorinated acetamide moiety at C-3 is described. These synthetic derivatives have been tested for their ability to selectively inhibit the muropeptide recycling glucosaminidase NagZ and to thereby increase sensitivity of Pseudomonas aeruginosa to β-lactams, a pathway with substantial therapeutic potential. While introduction of triazole and sulfamide groups failed to lead to glucosaminidase inhibitors, the NHCOCF3 analog proved to be a selective inhibitor of NagZ over other glucosaminidases including human O-GlcNAcase and lysosomal hexosaminidases HexA and B.
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Affiliation(s)
- J Bouquet
- Equipe Synthèse Organique, Groupe Glycochimie, IC2MP, UMR CNRS 7285, Université de Poitiers, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
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18
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Macdonald SS, Patel A, Larmour VLC, Morgan-Lang C, Hallam SJ, Mark BL, Withers SG. Structural and mechanistic analysis of a β-glycoside phosphorylase identified by screening a metagenomic library. J Biol Chem 2018; 293:3451-3467. [PMID: 29317495 DOI: 10.1074/jbc.ra117.000948] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/04/2018] [Indexed: 11/06/2022] Open
Abstract
Glycoside phosphorylases have considerable potential as catalysts for the assembly of useful glycans for products ranging from functional foods and prebiotics to novel materials. However, the substrate diversity of currently identified phosphorylases is relatively small, limiting their practical applications. To address this limitation, we developed a high-throughput screening approach using the activated substrate 2,4-dinitrophenyl β-d-glucoside (DNPGlc) and inorganic phosphate for identifying glycoside phosphorylase activity and used it to screen a large insert metagenomic library. The initial screen, based on release of 2,4-dinitrophenyl from DNPGlc in the presence of phosphate, identified the gene bglP, encoding a retaining β-glycoside phosphorylase from the CAZy GH3 family. Kinetic and mechanistic analysis of the gene product, BglP, confirmed a double displacement ping-pong mechanism involving a covalent glycosyl-enzyme intermediate. X-ray crystallographic analysis provided insights into the phosphate-binding mode and identified a key glutamine residue in the active site important for substrate recognition. Substituting this glutamine for a serine swapped the substrate specificity from glucoside to N-acetylglucosaminide. In summary, we present a high-throughput screening approach for identifying β-glycoside phosphorylases, which was robust, simple to implement, and useful in identifying active clones within a metagenomics library. Implementation of this screen enabled discovery of a new glycoside phosphorylase class and has paved the way to devising simple ways in which enzyme specificity can be encoded and swapped, which has implications for biotechnological applications.
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Affiliation(s)
- Spencer S Macdonald
- From the Departments of Chemistry and Biochemistry and.,the Genome Science and Technology Program.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, and
| | - Ankoor Patel
- the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2
| | - Veronica L C Larmour
- the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2
| | | | - Steven J Hallam
- the Genome Science and Technology Program.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, and.,Graduate Program in Bioinformatics, and.,the Department of Microbiology and Immunology and.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia V6T 1Z1
| | - Brian L Mark
- the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2
| | - Stephen G Withers
- From the Departments of Chemistry and Biochemistry and .,the Genome Science and Technology Program.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, and.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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19
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A Novel Multifunctional β-N-Acetylhexosaminidase Revealed through Metagenomics of an Oil-Spilled Mangrove. Bioengineering (Basel) 2017; 4:bioengineering4030062. [PMID: 28952541 PMCID: PMC5615308 DOI: 10.3390/bioengineering4030062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/25/2017] [Accepted: 07/06/2017] [Indexed: 11/22/2022] Open
Abstract
The use of culture-independent approaches, such as metagenomics, provides complementary access to environmental microbial diversity. Mangrove environments represent a highly complex system with plenty of opportunities for finding singular functions. In this study we performed a functional screening of fosmid libraries obtained from an oil contaminated mangrove site, with the purpose of identifying clones expressing hydrolytic activities. A novel gene coding for a β-N-acetylhexosaminidase with 355 amino acids and 43KDa was retrieved and characterized. The translated sequence showed only 38% similarity to a β-N-acetylhexosaminidase gene in the genome of Veillonella sp. CAG:933, suggesting that it might constitute a novel enzyme. The enzyme was expressed, purified, and characterized for its enzymatic activity on carboxymethyl cellulose, p-Nitrophenyl-2acetamide-2deoxy-β-d-glucopyranoside, p-Nitrophenyl-2acetamide-2deoxy-β-d-galactopyranoside, and 4-Nitrophenyl β-d-glucopyranoside, presenting β-N-acetylglucosaminidase, β-glucosidase, and β-1,4-endoglucanase activities. The enzyme showed optimum activity at 30 °C and pH 5.5. The characterization of the putative novel β-N-acetylglucosaminidase enzyme reflects similarities to characteristics of the environment explored, which differs from milder conditions environments. This work exemplifies the application of cultivation-independent molecular techniques to the mangrove microbiome for obtaining a novel biotechnological product.
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Alvarez-Dorta D, King DT, Legigan T, Ide D, Adachi I, Deniaud D, Désiré J, Kato A, Vocadlo D, Gouin SG, Blériot Y. Multivalency To Inhibit and Discriminate Hexosaminidases. Chemistry 2017; 23:9022-9025. [DOI: 10.1002/chem.201701756] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 01/17/2023]
Affiliation(s)
- Dimitri Alvarez-Dorta
- LUNAM Université; CEISAM; Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation; UMR CNRS 6230; UFR des Sciences et des Techniques; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Dustin T. King
- Department of Chemistry; Simon Fraser University; 8888 University Drive Burnaby British Columbia V5S 1P6 Canada
| | - Thibaut Legigan
- Equipe Synthèse Organique, Groupe Glycochimie, IC2MP; UMR CNRS 7285; Université de Poitiers; 4 rue Michel Brunet 86073 Poitiers cedex 09 France
| | - Daisuke Ide
- Department of Hospital Pharmacy; University of Toyama; 2630 Sugitani Toyama 930-0194 Japan
| | - Isao Adachi
- Department of Hospital Pharmacy; University of Toyama; 2630 Sugitani Toyama 930-0194 Japan
| | - David Deniaud
- LUNAM Université; CEISAM; Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation; UMR CNRS 6230; UFR des Sciences et des Techniques; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Jérôme Désiré
- Equipe Synthèse Organique, Groupe Glycochimie, IC2MP; UMR CNRS 7285; Université de Poitiers; 4 rue Michel Brunet 86073 Poitiers cedex 09 France
| | - Atsushi Kato
- Department of Hospital Pharmacy; University of Toyama; 2630 Sugitani Toyama 930-0194 Japan
| | - David Vocadlo
- Department of Chemistry; Simon Fraser University; 8888 University Drive Burnaby British Columbia V5S 1P6 Canada
| | - Sébastien G. Gouin
- LUNAM Université; CEISAM; Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation; UMR CNRS 6230; UFR des Sciences et des Techniques; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Yves Blériot
- Equipe Synthèse Organique, Groupe Glycochimie, IC2MP; UMR CNRS 7285; Université de Poitiers; 4 rue Michel Brunet 86073 Poitiers cedex 09 France
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21
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Acebrón I, Mahasenan KV, De Benedetti S, Lee M, Artola-Recolons C, Hesek D, Wang H, Hermoso JA, Mobashery S. Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa. J Am Chem Soc 2017; 139:6795-6798. [PMID: 28482153 DOI: 10.1021/jacs.7b01626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The N-acetylglucosaminidase NagZ of Pseudomonas aeruginosa catalyzes the first cytoplasmic step in recycling of muropeptides, cell-wall-derived natural products. This reaction regulates gene expression for the β-lactam resistance enzyme, β-lactamase. The enzyme catalyzes hydrolysis of N-acetyl-β-d-glucosamine-(1→4)-1,6-anhydro-N-acetyl-β-d-muramyl-peptide (1) to N-acetyl-β-d-glucosamine (2) and 1,6-anhydro-N-acetyl-β-d-muramyl-peptide (3). The structural and functional aspects of catalysis by NagZ were investigated by a total of seven X-ray structures, three computational models based on the X-ray structures, molecular-dynamics simulations and mutagenesis. The structural insights came from the unbound state and complexes of NagZ with the substrate, products and a mimetic of the transient oxocarbenium species, which were prepared by synthesis. The mechanism involves a histidine as acid/base catalyst, which is unique for glycosidases. The turnover process utilizes covalent modification of D244, requiring two transition-state species and is regulated by coordination with a zinc ion. The analysis provides a seamless continuum for the catalytic cycle, incorporating large motions by four loops that surround the active site.
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Affiliation(s)
- Iván Acebrón
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Stefania De Benedetti
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Cecilia Artola-Recolons
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid, Spain
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Huan Wang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid, Spain
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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22
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Vadlamani G, Stubbs KA, Désiré J, Blériot Y, Vocadlo DJ, Mark BL. Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress β-lactam antibiotic resistance. Protein Sci 2017; 26:1161-1170. [PMID: 28370529 DOI: 10.1002/pro.3166] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 11/10/2022]
Abstract
NagZ is an N-acetyl-β-d-glucosaminidase that participates in the peptidoglycan (PG) recycling pathway of Gram-negative bacteria by removing N-acetyl-glucosamine (GlcNAc) from PG fragments that have been excised from the cell wall during growth. The 1,6-anhydromuramoyl-peptide products generated by NagZ activate β-lactam resistance in many Gram-negative bacteria by inducing the expression of AmpC β-lactamase. Blocking NagZ activity can thereby suppress β-lactam antibiotic resistance in these bacteria. The NagZ active site is dynamic and it accommodates distortion of the glycan substrate during catalysis using a mobile catalytic loop that carries a histidine residue which serves as the active site general acid/base catalyst. Here, we show that flexibility of this catalytic loop also accommodates structural differences in small molecule inhibitors of NagZ, which could be exploited to improve inhibitor specificity. X-ray structures of NagZ bound to the potent yet non-selective N-acetyl-β-glucosaminidase inhibitor PUGNAc (O-(2-acetamido-2-deoxy-d-glucopyranosylidene) amino-N-phenylcarbamate), and two NagZ-selective inhibitors - EtBuPUG, a PUGNAc derivative bearing a 2-N-ethylbutyryl group, and MM-156, a 3-N-butyryl trihydroxyazepane, revealed that the phenylcarbamate moiety of PUGNAc and EtBuPUG completely displaces the catalytic loop from the NagZ active site to yield a catalytically incompetent form of the enzyme. In contrast, the catalytic loop was found positioned in the catalytically active conformation within the NagZ active site when bound to MM-156, which lacks the phenylcarbamate extension. Displacement of the catalytic loop by PUGNAc and its N-acyl derivative EtBuPUG alters the active site conformation of NagZ, which presents an additional strategy to improve the potency and specificity of NagZ inhibitors.
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Affiliation(s)
- Grishma Vadlamani
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3T2N2
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Jérôme Désiré
- IC2MP, UMR CNRS 7285, Équipe "Synthèse Organique" Groupe Glycochimie, Université de Poitiers, 4 rue Michel Brunet, 86073, Poitiers cedex 9, France
| | - Yves Blériot
- IC2MP, UMR CNRS 7285, Équipe "Synthèse Organique" Groupe Glycochimie, Université de Poitiers, 4 rue Michel Brunet, 86073, Poitiers cedex 9, France
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5S 1P6
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3T2N2
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23
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Carbohydrate recognition and lysis by bacterial peptidoglycan hydrolases. Curr Opin Struct Biol 2017; 44:87-100. [PMID: 28109980 DOI: 10.1016/j.sbi.2017.01.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/23/2016] [Accepted: 01/02/2017] [Indexed: 01/26/2023]
Abstract
The major component of bacterial cell wall is peptidoglycan (PG), a complex polymer formed by long glycan chains cross-linked by peptide stems. PG is in constant equilibrium requiring well-orchestrated coordination between synthesis and degradation. The resulting cell-wall fragments can be recycled, act as messengers for bacterial communication, as effector molecules in immune response or as signaling molecules triggering antibiotics resistance. Tailoring and recycling of PG requires the cleavage of different covalent bonds of the PG sacculi by a diverse set of specific enzymes whose activities are strictly regulated. Here, we review the molecular mechanisms that govern PG remodeling focusing on the structural information available for the bacterial lytic enzymes and the mechanisms by which they recognize their substrates.
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24
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Ducatti DRB, Carroll MA, Jakeman DL. On the phosphorylase activity of GH3 enzymes: A β-N-acetylglucosaminidase from Herbaspirillum seropedicae SmR1 and a glucosidase from Saccharopolyspora erythraea. Carbohydr Res 2016; 435:106-112. [PMID: 27744113 DOI: 10.1016/j.carres.2016.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/21/2016] [Accepted: 09/21/2016] [Indexed: 10/21/2022]
Abstract
A phosphorolytic activity has been reported for beta-N-acetylglucosaminidases from glycoside hydrolase family 3 (GH3) giving an interesting explanation for an unusual histidine as catalytic acid/base residue and suggesting that members from this family may be phosphorylases [J. Biol. Chem. 2015, 290, 4887]. Here, we describe the characterization of Hsero1941, a GH3 beta-N-acetylglucosaminidase from the endophytic nitrogen-fixing bacterium Herbaspirillum seropedicae SmR1. The enzyme has significantly higher activity against pNP-beta-D-GlcNAcp (Km = 0.24 mM, kcat = 1.2 s-1, kcat/Km = 5.0 mM-1s-1) than pNP-beta-D-Glcp (Km = 33 mM, kcat = 3.3 × 10-3 s-1, kcat/Km = 9 × 10-4 mM-1s-1). The presence of phosphate failed to significantly modify the kinetic parameters of the reaction. The enzyme showed a broad aglycone site specificity, being able to hydrolyze sugar phosphates beta-D-GlcNAc 1P and beta-D-Glc 1P, albeit at a fraction of the rate of hydrolysis of aryl glycosides. GH3 beta-glucosidase EryBI, that does not have a histidine as the general acid/base residue, also hydrolyzed beta-D-Glc 1P, at comparable rates to Hsero1941. These data indicate that Hsero1941 functions primarily as a hydrolase and that phosphorolytic activity is likely adventitious. The prevalence of histidine as a general acid/base residue is not predictive, nor correlative, with GH3 beta-N-acetylglucosaminidases having phosphorolytic activity.
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Affiliation(s)
- Diogo R B Ducatti
- College of Pharmacy, Dalhousie University, 5968 College Street, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada; Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Centro Politécnico, CEP 81-531-990, P.O. Box 19046, Curitiba, Paraná, Brazil
| | - Madison A Carroll
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
| | - David L Jakeman
- College of Pharmacy, Dalhousie University, 5968 College Street, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada; Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada.
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25
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Domínguez-Gil T, Molina R, Alcorlo M, Hermoso JA. Renew or die: The molecular mechanisms of peptidoglycan recycling and antibiotic resistance in Gram-negative pathogens. Drug Resist Updat 2016; 28:91-104. [PMID: 27620957 DOI: 10.1016/j.drup.2016.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance is one of the most serious health threats. Cell-wall remodeling processes are tightly regulated to warrant bacterial survival and in some cases are directly linked to antibiotic resistance. Remodeling produces cell-wall fragments that are recycled but can also act as messengers for bacterial communication, as effector molecules in immune response and as signaling molecules triggering antibiotic resistance. This review is intended to provide state-of-the-art information about the molecular mechanisms governing this process and gather structural information of the different macromolecular machineries involved in peptidoglycan recycling in Gram-negative bacteria. The growing body of literature on the 3D structures of the corresponding macromolecules reveals an extraordinary complexity. Considering the increasing incidence and widespread emergence of Gram-negative multidrug-resistant pathogens in clinics, structural information on the main actors of the recycling process paves the way for designing novel antibiotics disrupting cellular communication in the recycling-resistance pathway.
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Affiliation(s)
- Teresa Domínguez-Gil
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Martín Alcorlo
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.
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26
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Characterization of a Metagenome-Derived β-Glucosidase and Its Application in Conversion of Polydatin to Resveratrol. Catalysts 2016. [DOI: 10.3390/catal6030035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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27
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Meekrathok P, Suginta W. Probing the Catalytic Mechanism of Vibrio harveyi GH20 β-N-Acetylglucosaminidase by Chemical Rescue. PLoS One 2016; 11:e0149228. [PMID: 26870945 PMCID: PMC4752478 DOI: 10.1371/journal.pone.0149228] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 01/28/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Vibrio harveyi GH20 β-N-acetylglucosaminidase (VhGlcNAcase) is a chitinolytic enzyme responsible for the successive degradation of chitin fragments to GlcNAc monomers, activating the onset of the chitin catabolic cascade in marine Vibrios. METHODS Two invariant acidic pairs (Asp303-Asp304 and Asp437-Glu438) of VhGlcNAcase were mutated using a site-directed mutagenesis strategy. The effects of these mutations were examined and the catalytic roles of these active-site residues were elucidated using a chemical rescue approach. Enhancement of the enzymic activity of the VhGlcNAcase mutants was evaluated by a colorimetric assay using pNP-GlcNAc as substrate. RESULTS Substitution of Asp303, Asp304, Asp437 or Glu438 with Ala/Asn/Gln produced a dramatic loss of the GlcNAcase activity. However, the activity of the inactive D437A mutant was recovered in the presence of sodium formate. Our kinetic data suggest that formate ion plays a nucleophilic role by mimicking the β-COO-side chain of Asp437, thereby stabilizing the reaction intermediate during both the glycosylation and the deglycosylation steps. CONCLUSIONS Chemical rescue of the inactive D437A mutant of VhGlcNAcase by an added nucleophile helped to identify Asp437 as the catalytic nucleophile/base, and hence its acidic partner Glu438 as the catalytic proton donor/acceptor. GENERAL SIGNIFICANCE Identification of the catalytic nucleophile of VhGlcNAcases supports the proposal of a substrate-assisted mechanism of GH20 GlcNAcases, requiring the catalytic pair Asp437-Glu438 for catalysis. The results suggest the mechanistic basis of the participation of β-N-acetylglucosaminidase in the chitin catabolic pathway of marine Vibrios.
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Affiliation(s)
- Piyanat Meekrathok
- Biochemistry-Electrochemistry Research Unit and School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit and School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
- Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
- * E-mail:
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28
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Su H, Sheng X, Liu Y. Insights into the catalytic mechanism of N-acetylglucosaminidase glycoside hydrolase from Bacillus subtilis: a QM/MM study. Org Biomol Chem 2016; 14:3432-42. [DOI: 10.1039/c6ob00320f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
QM/MM calculations on NagZs fromBacillus subtilisfurther confirm NagZs to be glycoside phosphorylases rather than glycoside hydrolases.
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Affiliation(s)
- Hao Su
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Xiang Sheng
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Yongjun Liu
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
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29
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Kallemeijn WW, Witte MD, Wennekes T, Aerts JMFG. Mechanism-based inhibitors of glycosidases: design and applications. Adv Carbohydr Chem Biochem 2015; 71:297-338. [PMID: 25480507 DOI: 10.1016/b978-0-12-800128-8.00004-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This article covers recent developments in the design and application of activity-based probes (ABPs) for glycosidases, with emphasis on the different enzymes involved in metabolism of glucosylceramide in humans. Described are the various catalytic reaction mechanisms employed by inverting and retaining glycosidases. An understanding of catalysis at the molecular level has stimulated the design of different types of ABPs for glycosidases. Such compounds range from (1) transition-state mimics tagged with reactive moieties, which associate with the target active site—forming covalent bonds in a relatively nonspecific manner in or near the catalytic pocket—to (2) enzyme substrates that exploit the catalytic mechanism of retaining glycosidase targets to release a highly reactive species within the active site of the enzyme, to (3) probes based on mechanism-based, covalent, and irreversible glycosidase inhibitors. Some applications in biochemical and biological research of the activity-based glycosidase probes are discussed, including specific quantitative visualization of active enzyme molecules in vitro and in vivo, and as strategies for unambiguously identifying catalytic residues in glycosidases in vitro.
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Affiliation(s)
- Wouter W Kallemeijn
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Martin D Witte
- Department of Bio-Organic Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands.
| | - Tom Wennekes
- Department of Synthetic Organic Chemistry, Wageningen University, Wageningen, The Netherlands.
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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30
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Macdonald SS, Blaukopf M, Withers SG. N-acetylglucosaminidases from CAZy family GH3 are really glycoside phosphorylases, thereby explaining their use of histidine as an acid/base catalyst in place of glutamic acid. J Biol Chem 2014; 290:4887-4895. [PMID: 25533455 DOI: 10.1074/jbc.m114.621110] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
CAZy glycoside hydrolase family GH3 consists primarily of stereochemistry-retaining β-glucosidases but also contains a subfamily of β-N-acetylglucosaminidases. Enzymes from this subfamily were recently shown to use a histidine residue within a His-Asp dyad contained in a signature sequence as their catalytic acid/base residue. Reasons for their use of His rather than the Glu or Asp found in other glycosidases were not apparent. Through studies on a representative member, the Nag3 β-N-acetylglucosaminidase from Cellulomonas fimi, we now show that these enzymes act preferentially as glycoside phosphorylases. Their need to accommodate an anionic nucleophile within the enzyme active site explains why histidine is used as an acid/base catalyst in place of the anionic glutamate seen in other GH3 family members. Kinetic and mechanistic studies reveal that these enzymes also employ a double-displacement mechanism involving a covalent glycosyl-enzyme intermediate, which was directly detected by mass spectrometry. Phosphate has no effect on the rates of formation of the glycosyl-enzyme intermediate, but it accelerates turnover of the N-acetylglucosaminyl-enzyme intermediate ∼3-fold, while accelerating turnover of the glucosyl-enzyme intermediate several hundredfold. These represent the first reported examples of retaining β-glycoside phosphorylases, and the first instance of free β-GlcNAc-1-phosphate in a biological context.
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Affiliation(s)
- Spencer S Macdonald
- Centre for High-throughput Biology, Departments of Chemistry and of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Markus Blaukopf
- Centre for High-throughput Biology, Departments of Chemistry and of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stephen G Withers
- Centre for High-throughput Biology, Departments of Chemistry and of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
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31
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De novo design of a trans- -N-acetylglucosaminidase activity from a GH1 -glycosidase by mechanism engineering. Glycobiology 2014; 25:394-402. [DOI: 10.1093/glycob/cwu121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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32
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Mine S, Kado Y, Watanabe M, Fukuda Y, Abe Y, Ueda T, Kawarabayasi Y, Inoue T, Ishikawa K. The structure of hyperthermophilic β-N-acetylglucosaminidase reveals a novel dimer architecture associated with the active site. FEBS J 2014; 281:5092-103. [DOI: 10.1111/febs.13049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/02/2014] [Accepted: 09/11/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Shouhei Mine
- National Institute of Advanced Industrial Science and Technology (AIST); Hyogo Japan
| | - Yuji Kado
- Interdisciplinary Program for Biomedical Sciences; Institute for Academic Initiatives; Osaka University; Japan
- Graduate School of Engineering; Osaka University; Japan
| | | | - Yohta Fukuda
- Graduate School of Engineering; Osaka University; Japan
| | - Yoshito Abe
- Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Yutaka Kawarabayasi
- National Institute of Advanced Industrial Science and Technology (AIST); Hyogo Japan
- Faculty of Agriculture; Kyushu University; Fukuoka Japan
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33
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Willems LI, Jiang J, Li KY, Witte MD, Kallemeijn WW, Beenakker TJN, Schröder SP, Aerts JMFG, van der Marel GA, Codée JDC, Overkleeft HS. From Covalent Glycosidase Inhibitors to Activity-Based Glycosidase Probes. Chemistry 2014; 20:10864-72. [DOI: 10.1002/chem.201404014] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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34
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Mondon M, Hur S, Vadlamani G, Rodrigues P, Tsybina P, Oliver A, Mark BL, Vocadlo DJ, Blériot Y. Selective trihydroxyazepane NagZ inhibitors increase sensitivity of Pseudomonas aeruginosa to β-lactams. Chem Commun (Camb) 2014; 49:10983-5. [PMID: 24136176 DOI: 10.1039/c3cc46646a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AmpC β-lactamase confers resistance to β-lactam antibiotics in many Gram negative bacteria. Inducible expression of AmpC requires an N-acetylglucosaminidase termed NagZ. Here we describe the synthesis and characterization of hydroxyazepane inhibitors of NagZ. We find that these inhibitors enhance the susceptibility of clinically relevant Pseudomonas aeruginosa to β-lactams.
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Affiliation(s)
- Martine Mondon
- Université de Poitiers, IC2MP, UMR CNRS 7285, Équipe "Synthése Organique" Groupe Glycochimie, 4 rue Michel Brunet, 86022 Poitiers Cedex, France.
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35
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Jitonnom J, Limb MAL, Mulholland AJ. QM/MM free-energy simulations of reaction in Serratia marcescens Chitinase B reveal the protonation state of Asp142 and the critical role of Tyr214. J Phys Chem B 2014; 118:4771-83. [PMID: 24730355 DOI: 10.1021/jp500652x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Serratia marcescens Chitinase B (ChiB), belonging to the glycosidase family 18 (GH18), catalyzes the hydrolysis of β-1,4-glycosidic bond, with retention of configuration, via an unusual substrate-assisted mechanism, in which the substrate itself acts as an intramolecular nucleophile. Here, both elementary steps (glycosylation and deglycosylation) of the ChiB-catalyzed reaction are investigated by means of combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations at the SCC-DFTB/CHARMM22 level of theory. We examine the influence of the Asp142 protonation state on the reaction and the role that this residue performs in the reaction. Our simulations show that reaction with a neutral Asp142 is preferred and demonstrate that this residue provides electrostatic stabilization of the oxazolinium ion intermediate formed in the reaction. Insight into the conformational itinerary ((1,4)B↔(4)H5↔(4)C1) adopted by the substrate (bound in subsite -1) along the preferred reaction pathway is also provided by the simulations. The relative energies of the stationary points found along the reaction pathway calculated with SCC-DFTB and B3LYP were compared. The results suggest that SCC-DFTB is an accurate method for estimating the relative barriers for both steps of the reaction; however, it was found to overestimate the relative energy of an intermediate formed in the reaction when compared with the higher level of theory. Glycosylation is suggested to be a rate-determining step in the reaction with calculated overall reaction free-energy barrier of 20.5 kcal/mol, in a reasonable agreement with the 16.1 kcal/mol barrier derived from the experiment. The role of Tyr214 in catalysis was also investigated with the results, indicating that the residue plays a critical role in the deglycosylation step of the reaction. Simulations of the enzyme-product complex were also performed with an unbinding event suggested to have been observed, affording potential new mechanistic insight into the release of the product of ChiB.
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Affiliation(s)
- Jitrayut Jitonnom
- Division of Chemistry, School of Science, University of Phayao , Phayao 56000, Thailand
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36
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Stubbs KA, Bacik JP, Perley-Robertson GE, Whitworth GE, Gloster TM, Vocadlo DJ, Mark BL. The development of selective inhibitors of NagZ: increased susceptibility of Gram-negative bacteria to β-lactams. Chembiochem 2013; 14:1973-81. [PMID: 24009110 PMCID: PMC3920638 DOI: 10.1002/cbic.201300395] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Indexed: 11/21/2022]
Abstract
The increasing incidence of inducible chromosomal AmpC β-lactamases within the clinic is a growing concern because these enzymes deactivate a broad range of even the most recently developed β-lactam antibiotics. As a result, new strategies are needed to block the action of this antibiotic resistance enzyme. Presented here is a strategy to combat the action of inducible AmpC by inhibiting the β-glucosaminidase NagZ, which is an enzyme involved in regulating the induction of AmpC expression. A divergent route facilitating the rapid synthesis of a series of N-acyl analogues of 2-acetamido-2-deoxynojirimycin is reported here. Among these compounds are potent NagZ inhibitors that are selective against functionally related human enzymes. These compounds reduce minimum inhibitory concentration values for β-lactams against a clinically relevant Gram-negative bacterium bearing inducible chromosomal AmpC β-lactamase, Pseudomonas aeruginosa. The structure of a NagZ–inhibitor complex provides insight into the molecular basis for inhibition by these compounds.
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Affiliation(s)
- Keith A Stubbs
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 (Australia).
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37
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Identification of the acid/base catalyst of a glycoside hydrolase family 3 (GH3) beta-glucosidase from Aspergillus niger ASKU28. Biochim Biophys Acta Gen Subj 2013. [PMID: 23201198 DOI: 10.1016/j.bbagen.2012.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND The commercially important glycoside hydrolase family 3 (GH3) beta-glucosidases from Aspergillus niger are anomeric-configuration-retaining enzymes that operate through the canonical double-displacement glycosidase mechanism. Whereas the catalytic nucleophile is readily identified across all GH3 members by sequence alignments, the acid/base catalyst in this family is phylogenetically variable and less readily divined. METHODS In this report, we employed three-dimensional structure homology modeling and detailed kinetic analysis of site-directed mutants to identify the catalytic acid/base of a GH3 beta-glucosidase from A. niger ASKU28. RESULTS In comparison to the wild-type enzyme and other mutants, the E490A variant exhibited greatly reduced k(cat) and k(cat)/K(m) values toward the natural substrate cellobiose (67,000- and 61,000-fold, respectively). Correspondingly smaller kinetic effects were observed for artificial chromogenic substrates p-nitrophenyl beta-D-glucoside and 2,4-dinitrophenyl beta-D-glucoside, the aglycone leaving groups of which are less dependent on acid catalysis, although changes in the rate-determining catalytic step were revealed for both. pH-rate profile analyses also implicated E490 as the general acid/base catalyst. Addition of azide as an exogenous nucleophile partially rescued the activity of the E490A variant with the aryl beta-glucosides and yielded beta-glucosyl azide as a product. CONCLUSIONS AND GENERAL SIGNIFICANCE These results strongly support the assignment of E490 as the acid/base catalyst in a beta-glucosidase from A. niger ASKU28, and provide crucial experimental support for the bioinformatic identification of the homologous residue in a range of related GH3 subfamily members.
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38
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Bacik JP, Whitworth GE, Stubbs KA, Vocadlo DJ, Mark BL. Active site plasticity within the glycoside hydrolase NagZ underlies a dynamic mechanism of substrate distortion. ACTA ACUST UNITED AC 2013. [PMID: 23177201 DOI: 10.1016/j.chembiol.2012.09.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
NagZ is a glycoside hydrolase that participates in peptidoglycan (PG) recycling by removing β-N-acetylglucosamine from PG fragments that are excised from the bacterial cell wall during growth. Notably, the products formed by NagZ, 1,6-anhydroMurNAc-peptides, activate β-lactam resistance in many Gram-negative bacteria, making this enzyme of interest as a potential therapeutic target. Crystal structure determinations of NagZ from Salmonella typhimurium and Bacillus subtilis in complex with natural substrate, trapped as a glycosyl-enzyme intermediate, and bound to product, define the reaction coordinate of the NagZ family of enzymes. The structures, combined with kinetic studies, reveal an uncommon degree of structural plasticity within the active site of a glycoside hydrolase, and unveil how NagZ drives substrate distortion using a highly mobile loop that contains a conserved histidine that has been proposed as the general acid/base.
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Affiliation(s)
- John-Paul Bacik
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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39
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Hattie M, Debowski AW, Stubbs KA. Development of tools to study lacto-N-biosidase: an important enzyme involved in the breakdown of human milk oligosaccharides. Chembiochem 2012; 13:1128-31. [PMID: 22514018 DOI: 10.1002/cbic.201200135] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Indexed: 01/15/2023]
Abstract
Milk and sugar? The elucidation of the catalytic mechanism and the development of the first known inhibitor for lacto-N-biosidases, which are important enzymes involved in the breakdown of human milk oligosaccharides, are described.
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Affiliation(s)
- Mitchell Hattie
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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40
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Mark BL, Vocadlo DJ, Oliver A. Providing β-lactams a helping hand: targeting the AmpC β-lactamase induction pathway. Future Microbiol 2012; 6:1415-27. [PMID: 22122439 DOI: 10.2217/fmb.11.128] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A major cause of the clinical failure of broad-spectrum β-lactam antibiotics against Pseudomonas aeruginosa and many Enterobacteriaceae species are chromosomal mutations that lead to the hyperproduction of AmpC β-lactamase. These mutations typically affect proteins within the peptidoglycan (PG) recycling pathway, as well as proteins that are modulated by metabolic intermediates of this pathway. Blocking PG recycling and associated sensing mechanisms with small-molecule inhibitors holds promise as a strategy for overcoming AmpC-mediated resistance that results from the selection of mutations during β-lactam therapy, or from the direct acquisition of infections by AmpC-producing mutants. Here we report on the structural and functional biology of potential drug targets within the Gram-negative PG recycling pathway and the utility of blocking PG recycling as a means of attenuating AmpC-mediated resistance in P. aeruginosa.
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Affiliation(s)
- Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
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41
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Jitonnom J, Lee VS, Nimmanpipug P, Rowlands HA, Mulholland AJ. Quantum Mechanics/Molecular Mechanics Modeling of Substrate-Assisted Catalysis in Family 18 Chitinases: Conformational Changes and the Role of Asp142 in Catalysis in ChiB. Biochemistry 2011; 50:4697-711. [DOI: 10.1021/bi101362g] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jitrayut Jitonnom
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Vannajan S. Lee
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Piyarat Nimmanpipug
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Heather A. Rowlands
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
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42
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Witte MD, van der Marel GA, Aerts JMFG, Overkleeft HS. Irreversible inhibitors and activity-based probes as research tools in chemical glycobiology. Org Biomol Chem 2011; 9:5908-26. [DOI: 10.1039/c1ob05531c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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43
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Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, Mayer C. Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism. J Biol Chem 2010; 285:35675-84. [PMID: 20826810 PMCID: PMC2975192 DOI: 10.1074/jbc.m110.131037] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 09/03/2010] [Indexed: 11/06/2022] Open
Abstract
Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain β-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active site, at 1.84- and 1.40-Å resolution, respectively. The structures together with kinetic analyses of mutants revealed an Asp-His dyad involved in catalysis: His(234) of BsNagZ acts as general acid/base catalyst and is hydrogen bonded by Asp(232) for proper function. Replacement of both His(234) and Asp(232) with glycine reduced the rate of hydrolysis of the fluorogenic substrate 4'-methylumbelliferyl N-acetyl-β-D-glucosaminide 1900- and 4500-fold, respectively, and rendered activity pH-independent in the alkaline range consistent with a role of these residues in acid/base catalysis. N-Acetylglucosaminyl enzyme intermediate accumulated in the H234G mutant and β-azide product was formed in the presence of sodium azide in both mutants. The Asp-His dyad is conserved within β-N-acetylglucosaminidases but otherwise absent in β-glycosidases of family 3, which instead carry a "classical" glutamate acid/base catalyst. The acid/base glutamate of Hordeum vulgare exoglucanase (Exo1) superimposes with His(234) of the dyad of BsNagZ and, in contrast to the latter, protrudes from a second domain of the enzyme into the active site. This is the first report of an Asp-His catalytic dyad involved in hydrolysis of glycosides resembling in function the Asp-His-Ser triad of serine proteases. Our findings will facilitate the development of mechanism-based inhibitors that selectively target family 3 β-N-acetylglucosaminidases, which are involved in bacterial cell wall turnover, spore germination, and induction of β-lactamase.
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Affiliation(s)
| | - Stefanie Fischer
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
| | - Patrick Polzer
- the Max-Planck-Institute of Quantum Optics, 85748 Garching, Germany
| | - Kay Diederichs
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
| | - Wolfram Welte
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
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Slámová K, Bojarová P, Petrásková L, Křen V. β-N-Acetylhexosaminidase: What's in a name…? Biotechnol Adv 2010; 28:682-93. [DOI: 10.1016/j.biotechadv.2010.04.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 04/17/2010] [Accepted: 04/24/2010] [Indexed: 01/28/2023]
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Rivera-Mulia JC, Aranda-Anzaldo A. Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach. DNA Res 2010; 17:23-35. [PMID: 20047947 PMCID: PMC2818189 DOI: 10.1093/dnares/dsp027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nuclear DNA of metazoans is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). DNA is anchored to the NM by non-coding sequences known as matrix attachment regions (MARs). There are no consensus sequences for identification of MARs and not all potential MARs are actually bound to the NM constituting loop attachment regions (LARs). Fundamental processes of nuclear physiology occur at macromolecular complexes organized on the NM; thus, the topological organization of DNA loops must be important. Here, we describe a general method for determining the structural DNA loop organization in any large genomic region with a known sequence. The method exploits the topological properties of loop DNA attached to the NM and elementary topological principles such as that points in a deformable string (DNA) can be positionally mapped relative to a position-reference invariant (NM), and from such mapping, the configuration of the string in third dimension can be deduced. Therefore, it is possible to determine the specific DNA loop configuration without previous characterization of the LARs involved. We determined in hepatocytes and B-lymphocytes of the rat the DNA loop organization of a genomic region that contains four members of the albumin gene family.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, Toluca, Edo. Méx., México
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Balcewich MD, Stubbs KA, He Y, James TW, Davies GJ, Vocadlo DJ, Mark BL. Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ. Protein Sci 2009; 18:1541-51. [PMID: 19499593 DOI: 10.1002/pro.137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
NagZ is an exo-N-acetyl-beta-glucosaminidase, found within Gram-negative bacteria, that acts in the peptidoglycan recycling pathway to cleave N-acetylglucosamine residues off peptidoglycan fragments. This activity is required for resistance to cephalosporins mediated by inducible AmpC beta-lactamase. NagZ uses a catalytic mechanism involving a covalent glycosyl enzyme intermediate, unlike that of the human exo-N-acetyl-beta-glucosaminidases: O-GlcNAcase and the beta-hexosaminidase isoenzymes. These latter enzymes, which remove GlcNAc from glycoconjugates, use a neighboring-group catalytic mechanism that proceeds through an oxazoline intermediate. Exploiting these mechanistic differences we previously developed 2-N-acyl derivatives of O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc), which selectively inhibits NagZ over the functionally related human enzymes and attenuate antibiotic resistance in Gram-negatives that harbor inducible AmpC. To understand the structural basis for the selectivity of these inhibitors for NagZ, we have determined its crystallographic structure in complex with N-valeryl-PUGNAc, the most selective known inhibitor of NagZ over both the human beta-hexosaminidases and O-GlcNAcase. The selectivity stems from the five-carbon acyl chain of N-valeryl-PUGNAc, which we found ordered within the enzyme active site. In contrast, a structure determination of a human O-GlcNAcase homologue bound to a related inhibitor N-butyryl-PUGNAc, which bears a four-carbon chain and is selective for both NagZ and O-GlcNAcase over the human beta-hexosamnidases, reveals that this inhibitor induces several conformational changes in the active site of this O-GlcNAcase homologue. A comparison of these complexes, and with the human beta-hexosaminidases, reveals how selectivity for NagZ can be engineered by altering the 2-N-acyl substituent of PUGNAc to develop inhibitors that repress AmpC mediated beta-lactam resistance.
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Affiliation(s)
- Misty D Balcewich
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Hagena TL, Coward JK. Fluoridolysis of 5,6-epoxy carbohydrates: application to the synthesis of 5-fluoro lactosamine and isolactosamine glycosides. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.03.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Inactivation of the glycoside hydrolase NagZ attenuates antipseudomonal beta-lactam resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2009; 53:2274-82. [PMID: 19273679 DOI: 10.1128/aac.01617-08] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The overproduction of chromosomal AmpC beta-lactamase poses a serious challenge to the successful treatment of Pseudomonas aeruginosa infections with beta-lactam antibiotics. The induction of ampC expression by beta-lactams is mediated by the disruption of peptidoglycan (PG) recycling and the accumulation of cytosolic 1,6-anhydro-N-acetylmuramyl peptides, catabolites of PG recycling that are generated by an N-acetyl-beta-D-glucosaminidase encoded by nagZ (PA3005). In the absence of beta-lactams, ampC expression is repressed by three AmpD amidases encoded by ampD, ampDh2, and ampDh3, which act to degrade these 1,6-anhydro-N-acetylmuramyl peptide inducer molecules. The inactivation of ampD genes results in the stepwise upregulation of ampC expression and clinical resistance to antipseudomonal beta-lactams due to the accumulation of the ampC inducer anhydromuropeptides. To examine the role of NagZ on AmpC-mediated beta-lactam resistance in P. aeruginosa, we inactivated nagZ in P. aeruginosa PAO1 and in an isogenic triple ampD null mutant. We show that the inactivation of nagZ represses both the intrinsic beta-lactam resistance (up to 4-fold) and the high antipseudomonal beta-lactam resistance (up to 16-fold) that is associated with the loss of AmpD activity. We also demonstrate that AmpC-mediated resistance to antipseudomonal beta-lactams can be attenuated in PAO1 and in a series of ampD null mutants using a selective small-molecule inhibitor of NagZ. Our results suggest that the blockage of NagZ activity could provide a strategy to enhance the efficacies of beta-lactams against P. aeruginosa and other gram-negative organisms that encode inducible chromosomal ampC and to counteract the hyperinduction of ampC that occurs from the selection of ampD null mutations during beta-lactam therapy.
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Vocadlo DJ, Davies GJ. Mechanistic insights into glycosidase chemistry. Curr Opin Chem Biol 2009; 12:539-55. [PMID: 18558099 DOI: 10.1016/j.cbpa.2008.05.010] [Citation(s) in RCA: 300] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 11/16/2022]
Abstract
The enzymatic hydrolysis of the glycosidic bond continues to gain importance, reflecting the critically important roles complex glycans play in health and disease as well as the rekindled interest in enzymatic biomass conversion. Recent advances include the broadening of our understanding of enzyme reaction coordinates, through both computational and structural studies, improved understanding of enzyme inhibition through transition state mimicry and fascinating insights into mechanism yielded by physical organic chemistry approaches.
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Affiliation(s)
- David J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, Canada.
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Rempel BP, Withers SG. Non-Stick Sugars: Synthesis of Difluorosugar Fluorides as Potential Glycosidase Inactivators. Aust J Chem 2009. [DOI: 10.1071/ch09223] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Four new difluorosugar fluorides, 2-deoxy-2,5-difluoro-α-l-idopyranosyl fluoride, 1,5-difluoro-d-glucopyranosyl fluoride, 1,5-difluoro-l-idopyranosyl fluoride, and 2-deoxy-1,2-difluoro-d-glucopyranosyl fluoride, were synthesized from known precursors by a radical bromination/fluoride displacement sequence, followed by deprotection. The compounds were tested as time-dependent inactivators of the β-glucosidase from Agrobacterium sp. (Abg, EC 3.2.1.21) and, while they were shown to bind to the enzyme active site as reversible competitive inhibitors, the only time-dependent inactivation observed was traced to the presence of an extremely small amount (<0.1%) of a highly reactive contaminating impurity.
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