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Grayfer T, Yamani K, Jung E, Chesnokov GA, Ferrara I, Hsiao CC, Georgiou A, Michel J, Bailly A, Sieber S, Eberl L, Gademann K. Allylic Carbocyclic Inhibitors Covalently Bind Glycoside Hydrolases. JACS AU 2023; 3:1151-1161. [PMID: 37124289 PMCID: PMC10131216 DOI: 10.1021/jacsau.3c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 05/03/2023]
Abstract
Allylic cyclitols were investigated as covalent inhibitors of glycoside hydrolases by chemical, enzymatic, proteomic, and computational methods. This approach was inspired by the C7 cyclitol natural product streptol glucoside, which features a potential carbohydrate leaving group in the 4-position (carbohydrate numbering). To test this hypothesis, carbocyclic inhibitors with leaving groups in the 4- and 6- positions were prepared. The results of enzyme kinetics analyses demonstrated that dinitrophenyl ethers covalently inhibit α-glucosidases of the GH13 family without reactivation. The labeled enzyme was studied by proteomics, and the active site residue Asp214 was identified as modified. Additionally, computational studies, including enzyme homology modeling and density functional theory (DFT) calculations, further delineate the electronic and structural requirements for activity. This study demonstrates that previously unexplored 4- and 6-positions can be exploited for successful inhibitor design.
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Affiliation(s)
- Tatyana
D. Grayfer
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Khalil Yamani
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Erik Jung
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Gleb A. Chesnokov
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Isabella Ferrara
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Chien-Chi Hsiao
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Antri Georgiou
- Department
of Plant and Microbial Biology, University
of Zurich, Zollikerstrasse
107, 8008 Zürich, Switzerland
| | - Jeremy Michel
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Aurélien Bailly
- Department
of Plant and Microbial Biology, University
of Zurich, Zollikerstrasse
107, 8008 Zürich, Switzerland
| | - Simon Sieber
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Leo Eberl
- Department
of Plant and Microbial Biology, University
of Zurich, Zollikerstrasse
107, 8008 Zürich, Switzerland
| | - Karl Gademann
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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Collet L, Vander Wauven C, Oudjama Y, Galleni M, Dutoit R. Glycoside hydrolase family 5: structural snapshots highlighting the involvement of two conserved residues in catalysis. Acta Crystallogr D Struct Biol 2021; 77:205-216. [PMID: 33559609 DOI: 10.1107/s2059798320015557] [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: 08/21/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
The ability of retaining glycoside hydrolases (GHs) to transglycosylate is inherent to the double-displacement mechanism. Studying reaction intermediates, such as the glycosyl-enzyme intermediate (GEI) and the Michaelis complex, could provide valuable information to better understand the molecular factors governing the catalytic mechanism. Here, the GEI structure of RBcel1, an endo-1,4-β-glucanase of the GH5 family endowed with transglycosylase activity, is reported. It is the first structure of a GH5 enzyme covalently bound to a natural oligosaccharide with the two catalytic glutamate residues present. The structure of the variant RBcel1_E135A in complex with cellotriose is also reported, allowing a description of the entire binding cleft of RBcel1. Taken together, the structures deliver different snapshots of the double-displacement mechanism. The structural analysis revealed a significant movement of the nucleophilic glutamate residue during the reaction. Enzymatic assays indicated that, as expected, the acid/base glutamate residue is crucial for the glycosylation step and partly contributes to deglycosylation. Moreover, a conserved tyrosine residue in the -1 subsite, Tyr201, plays a determinant role in both the glycosylation and deglycosylation steps, since the GEI was trapped in the RBcel1_Y201F variant. The approach used to obtain the GEI presented here could easily be transposed to other retaining GHs in clan GH-A.
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Affiliation(s)
| | | | | | - Moreno Galleni
- Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, 13 Allée du 6 Août, 4000 Liège, Belgium
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Kytidou K, Artola M, Overkleeft HS, Aerts JMFG. Plant Glycosides and Glycosidases: A Treasure-Trove for Therapeutics. FRONTIERS IN PLANT SCIENCE 2020; 11:357. [PMID: 32318081 PMCID: PMC7154165 DOI: 10.3389/fpls.2020.00357] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/11/2020] [Indexed: 05/10/2023]
Abstract
Plants contain numerous glycoconjugates that are metabolized by specific glucosyltransferases and hydrolyzed by specific glycosidases, some also catalyzing synthetic transglycosylation reactions. The documented value of plant-derived glycoconjugates to beneficially modulate metabolism is first addressed. Next, focus is given to glycosidases, the central theme of the review. The therapeutic value of plant glycosidases is discussed as well as the present production in plant platforms of therapeutic human glycosidases used in enzyme replacement therapies. The increasing knowledge on glycosidases, including structure and catalytic mechanism, is described. The novel insights have allowed the design of functionalized highly specific suicide inhibitors of glycosidases. These so-called activity-based probes allow unprecedented visualization of glycosidases cross-species. Here, special attention is paid on the use of such probes in plant science that promote the discovery of novel enzymes and the identification of potential therapeutic inhibitors and chaperones.
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Affiliation(s)
- Kassiani Kytidou
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Marta Artola
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
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High-Throughput Recovery and Characterization of Metagenome-Derived Glycoside Hydrolase-Containing Clones as a Resource for Biocatalyst Development. mSystems 2019; 4:4/4/e00082-19. [PMID: 31164449 PMCID: PMC6550366 DOI: 10.1128/msystems.00082-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The generation of new biocatalysts for plant biomass degradation and glycan synthesis has typically relied on the characterization and investigation of one or a few enzymes at a time. By coupling functional metagenomic screening and high-throughput functional characterization, we can progress beyond the current scale of catalyst discovery and provide rapid annotation of catalyst function. By functionally screening environmental DNA from many diverse sources, we have generated a suite of active glycoside hydrolase-containing clones and demonstrated their reaction parameters. We then demonstrated the utility of this collection through the generation of a new catalyst for the formation of azido-modified glycans. Further interrogation of this collection of clones will expand our biocatalytic toolbox, with potential application to biomass deconstruction and synthesis of glycans. Functional metagenomics is a powerful tool for both the discovery and development of biocatalysts. This study presents the high-throughput functional screening of 22 large-insert fosmid libraries containing over 300,000 clones sourced from natural and engineered ecosystems, characterization of active clones, and a demonstration of the utility of recovered genes or gene cassettes in the development of novel biocatalysts. Screening was performed in a 384-well-plate format with the fluorogenic substrate 4-methylumbelliferyl cellobioside, which releases a fluorescent molecule when cleaved by β-glucosidases or cellulases. The resulting set of 164 active clones was subsequently interrogated for substrate preference, reaction mechanism, thermal stability, and optimal pH. The environmental DNA harbored within each active clone was sequenced, and functional annotation revealed a cornucopia of carbohydrate-degrading enzymes. Evaluation of genomic-context information revealed both synteny and polymer-targeting loci within a number of sequenced clones. The utility of these fosmids was then demonstrated by identifying clones encoding activity on an unnatural glycoside (4-methylumbelliferyl 6-azido-6-deoxy-β-d-galactoside) and transforming one of the identified enzymes into a glycosynthase capable of forming taggable disaccharides. IMPORTANCE The generation of new biocatalysts for plant biomass degradation and glycan synthesis has typically relied on the characterization and investigation of one or a few enzymes at a time. By coupling functional metagenomic screening and high-throughput functional characterization, we can progress beyond the current scale of catalyst discovery and provide rapid annotation of catalyst function. By functionally screening environmental DNA from many diverse sources, we have generated a suite of active glycoside hydrolase-containing clones and demonstrated their reaction parameters. We then demonstrated the utility of this collection through the generation of a new catalyst for the formation of azido-modified glycans. Further interrogation of this collection of clones will expand our biocatalytic toolbox, with potential application to biomass deconstruction and synthesis of glycans.
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Ben Bdira F, Artola M, Overkleeft HS, Ubbink M, Aerts JMFG. Distinguishing the differences in β-glycosylceramidase folds, dynamics, and actions informs therapeutic uses. J Lipid Res 2018; 59:2262-2276. [PMID: 30279220 PMCID: PMC6277158 DOI: 10.1194/jlr.r086629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
Glycosyl hydrolases (GHs) are carbohydrate-active enzymes that hydrolyze a specific β-glycosidic bond in glycoconjugate substrates; β-glucosidases degrade glucosylceramide, a ubiquitous glycosphingolipid. GHs are grouped into structurally similar families that themselves can be grouped into clans. GH1, GH5, and GH30 glycosidases belong to clan A hydrolases with a catalytic (β/α)8 TIM barrel domain, whereas GH116 belongs to clan O with a catalytic (α/α)6 domain. In humans, GH abnormalities underlie metabolic diseases. The lysosomal enzyme glucocerebrosidase (family GH30), deficient in Gaucher disease and implicated in Parkinson disease etiology, and the cytosol-facing membrane-bound glucosylceramidase (family GH116) remove the terminal glucose from the ceramide lipid moiety. Here, we compare enzyme differences in fold, action, dynamics, and catalytic domain stabilization by binding site occupancy. We also explore other glycosidases with reported glycosylceramidase activity, including human cytosolic β-glucosidase, intestinal lactase-phlorizin hydrolase, and lysosomal galactosylceramidase. Last, we describe the successful translation of research to practice: recombinant glycosidases and glucosylceramide metabolism modulators are approved drug products (enzyme replacement therapies). Activity-based probes now facilitate the diagnosis of enzyme deficiency and screening for compounds that interact with the catalytic pocket of glycosidases. Future research may deepen the understanding of the functional variety of these enzymes and their therapeutic potential.
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Affiliation(s)
- Fredj Ben Bdira
- Departments of Macromolecular Biochemistry,Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Marta Artola
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Herman S Overkleeft
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Marcellus Ubbink
- Departments of Macromolecular Biochemistry,Leiden Institute of Chemistry, Leiden, The Netherlands
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Sharifzadeh S, Shirley JD, Carlson EE. Activity-Based Protein Profiling Methods to Study Bacteria: The Power of Small-Molecule Electrophiles. Curr Top Microbiol Immunol 2018; 420:23-48. [PMID: 30232601 DOI: 10.1007/82_2018_135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ABPP methods have been utilized for the last two decades as a means to investigate complex proteomes in all three domains of life. Extensive use in eukaryotes has provided a more fundamental understanding of the biological processes involved in numerous diseases and has driven drug discovery and treatment campaigns. However, the use of ABPP in prokaryotes has been less common, although it has gained more attention over the last decade. The urgent need for understanding bacteriophysiology and bacterial pathogenicity at a foundational level has never been more apparent, as the rise in antibiotic resistance has resulted in the inadequate and ineffective treatment of infections. This is not only a result of resistance to clinically used antibiotics, but also a lack of new drugs and equally as important, new drug targets. ABPP provides a means for which new, clinically relevant drug targets may be identified through gaining insight into biological processes. In this chapter, we place particular focus on the discussion of ABPP strategies that have been applied to study different classes of bacterial enzymes.
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Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA.
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Murugan V, Parasuraman P, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Theoretical investigation on the binding specificity of fluorinated sialyldisaccharides Neu5Acα(2–3)Gal and Neu5Acα(2–6)Gal with influenza hemagglutinin H1 – A Molecular Dynamics Study. J Carbohydr Chem 2017. [DOI: 10.1080/07328303.2017.1365153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Veeramani Murugan
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
| | - Ponnusamy Parasuraman
- Department of Physical Sciences, Bannari Amman Institute of Technology, Erode, Tamilnadu, India
| | | | - Michael M. Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
| | - Kazuhiko Fukui
- National Institute of Advanced Industrial Science and Technology (AIST), Molecular Profiling Research Center for Drug Discovery (molprof), 2-4-7 Aomi, Koto-ku, Tokyo, Japan
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9
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Stubbs KA. Activity-based proteomics probes for carbohydrate-processing enzymes: current trends and future outlook. Carbohydr Res 2014; 390:9-19. [DOI: 10.1016/j.carres.2014.02.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/21/2014] [Accepted: 02/22/2014] [Indexed: 11/27/2022]
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10
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Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1317-31. [PMID: 24721563 DOI: 10.1016/j.bbapap.2014.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 01/14/2023]
Abstract
Bovine CD38/NAD(+) glycohydrolase catalyzes the hydrolysis of NAD(+) to nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose via a stepwise reaction mechanism. Our recent crystallographic study of its Michaelis complex and covalently-trapped intermediates provided insights into the modalities of substrate binding and the molecular mechanism of bCD38. The aim of the present work was to determine the precise role of key conserved active site residues (Trp118, Glu138, Asp147, Trp181 and Glu218) by focusing mainly on the cleavage of the nicotinamide-ribosyl bond. We analyzed the kinetic parameters of mutants of these residues which reside within the bCD38 subdomain in the vicinity of the scissile bond of bound NAD(+). To address the reaction mechanism we also performed chemical rescue experiments with neutral (methanol) and ionic (azide, formate) nucleophiles. The crucial role of Glu218, which orients the substrate for cleavage by interacting with the N-ribosyl 2'-OH group of NAD(+), was highlighted. This contribution to catalysis accounts for almost half of the reaction energy barrier. Other contributions can be ascribed notably to Glu138 and Asp147 via ground-state destabilization and desolvation in the vicinity of the scissile bond. Key interactions with Trp118 and Trp181 were also proven to stabilize the ribooxocarbenium ion-like transition state. Altogether we propose that, as an alternative to a covalent acylal reaction intermediate with Glu218, catalysis by bCD38 proceeds through the formation of a discrete and transient ribooxocarbenium intermediate which is stabilized within the active site mostly by electrostatic interactions.
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Lee SS, Greig IR, Vocadlo DJ, McCarter JD, Patrick BO, Withers SG. Structural, Mechanistic, and Computational Analysis of the Effects of Anomeric Fluorines on Anomeric Fluoride Departure in 5-Fluoroxylosyl Fluorides. J Am Chem Soc 2011; 133:15826-9. [DOI: 10.1021/ja204829r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Seung Seo Lee
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Ian R. Greig
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - David J. Vocadlo
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - John D. McCarter
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Brian O. Patrick
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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Rempel BP, Tropak MB, Mahuran DJ, Withers SG. Tailoring the Specificity and Reactivity of a Mechanism-Based Inactivator of Glucocerebrosidase for Potential Therapeutic Applications. Angew Chem Int Ed Engl 2011; 50:10381-3. [DOI: 10.1002/anie.201103924] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Indexed: 01/07/2023]
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13
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Rempel BP, Tropak MB, Mahuran DJ, Withers SG. Tailoring the Specificity and Reactivity of a Mechanism-Based Inactivator of Glucocerebrosidase for Potential Therapeutic Applications. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103924] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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14
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Gandy MN, Debowski AW, Stubbs KA. A general method for affinity-based proteomic profiling of exo-α-glycosidases. Chem Commun (Camb) 2011; 47:5037-9. [PMID: 21431156 DOI: 10.1039/c1cc10308c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of iminosugar-based affinity-based proteomics probes for use in probing exo-α-glycosidase activity.
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Affiliation(s)
- Michael N Gandy
- Chemistry M313, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA Australia6009
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Schilling CI, Jung N, Biskup M, Schepers U, Bräse S. Bioconjugation via azide–Staudinger ligation: an overview. Chem Soc Rev 2011; 40:4840-71. [DOI: 10.1039/c0cs00123f] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Demir Ö, Roitberg AE. Modulation of catalytic function by differential plasticity of the active site: case study of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase. Biochemistry 2009; 48:3398-406. [PMID: 19216574 PMCID: PMC2713503 DOI: 10.1021/bi802230y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
trans-Sialidase is an essential enzyme for Trypanosoma cruzi, the causative agent of Chagas' disease, to escape from the host immune system and to invade the host cells. Therefore, T. cruzi trans-sialidase (TcTS) presents a potential and appealing therapeutic target for this lethal disease. The availability of a structurally very similar enzyme with strict hydrolase activity (Trypanosoma rangeli sialidase, TrSA) provides us a unique opportunity to understand the determinants of their structure and catalytic mechanism. In this study, we compare the catalytic cleft plasticity of free (apo) and ligand-bound (holo) forms of the two enzymes using molecular dynamics simulations. We focus on the mouth of the catalytic cleft that is defined by two residues: W312 and Y119 in TcTS and W312 and S119 in TrSA. Our results indicate that TcTS has a very flexible, widely open catalytic cleft, mostly due to W312 loop motion, in apo form. However, when the catalytic cleft is occupied by a ligand, the flexibility and solvent exposure of TcTS is significantly reduced. On the other hand, TrSA maintains a more open catalytic cleft compared to its crystal structures in both apo and holo forms (and compared to TcTS in holo forms). The reduced solvent exposure of TcTS catalytic cleft might be partially or fully responsible for TcTS to be a less efficient hydrolase than TrSA.
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Affiliation(s)
- Özlem Demir
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-8435, USA
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
| | - Adrian E. Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-8435, USA
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
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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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Berkowitz DB, Karukurichi KR, de la Salud-Bea R, Nelson DL, McCune CD. Use of Fluorinated Functionality in Enzyme Inhibitor Development: Mechanistic and Analytical Advantages. J Fluor Chem 2008; 129:731-742. [PMID: 19727327 PMCID: PMC2598403 DOI: 10.1016/j.jfluchem.2008.05.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
On the one hand, owing to its electronegativity, relatively small size, and notable leaving group ability from anionic intermediates, fluorine offers unique opportunities for mechanism-based enzyme inhibitor design. On the other, the "bio-orthogonal" and NMR-active 19-fluorine nucleus allows the bioorganic chemist to follow the mechanistic fate of fluorinated substrate analogues or inhibitors as they are enzymatically processed. This article takes an overview of the field, highlighting key developments along these lines. It begins by highlighting new screening methodologies for drug discovery that involve appropriate tagging of either substrate or the target protein itself with (19)F-markers, that then report back on turnover and binding, respectively, via an the NMR screen. Taking this one step further, substrate-tagging with fluorine can be done is such a manner as to provide stereochemical information on enzyme mechanism. For example, substitution of one of the terminal hydrogens in phosphoenolpyruvate, provides insight into the, otherwise latent, facial selectivity of C-C bond formation in KDO synthase. Perhaps, most importantly, from the point of view of this discussion, appropriately tailored fluorinated functionality can be used to form to stabilized "transition state analogue" complexes with a target enzymes. Thus, 5-fluorinated pyrimidines, alpha-fluorinated ketones, and 2-fluoro-2-deoxysugars each lead to covalent adduction of catalytic active site residues in thymidylate synthase, serine protease and glycosidase enzymes, respectively. In all such cases, (19)F NMR allows the bioorganic chemist to spectrally follow "transition state analogue" formation. Finally, the use of specific fluorinated functionality to engineer "suicide substrates" is highlighted in a discussion of the development of the alpha-(2'Z-fluoro)vinyl trigger for amino acid decarboxylase inactivation. Here (19)F NMR allows the bioorganic chemist to glean useful partition ratio data directly out of the NMR tube.
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Affiliation(s)
- David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304
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Piens K, Fauré R, Sundqvist G, Baumann MJ, Saura-Valls M, Teeri TT, Cottaz S, Planas A, Driguez H, Brumer H. Mechanism-based Labeling Defines the Free Energy Change for Formation of the Covalent Glycosyl-enzyme Intermediate in a Xyloglucan endo-Transglycosylase. J Biol Chem 2008; 283:21864-72. [DOI: 10.1074/jbc.m803057200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Noguchi J, Hayashi Y, Baba Y, Okino N, Kimura M, Ito M, Kakuta Y. Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase. Biochem Biophys Res Commun 2008; 374:549-52. [PMID: 18662675 DOI: 10.1016/j.bbrc.2008.07.089] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2008] [Accepted: 07/16/2008] [Indexed: 10/21/2022]
Abstract
Human cytosolic beta-glucosidase, also known as klotho-related protein (KLrP, GBA3), is an enzyme that hydrolyzes various beta-D-glucosides, including glucosylceramide. We recently reported the crystal structure of KLrP in complex with glucose [Y. Hayashi, N. Okino, Y. Kakuta, T. Shikanai, M. Tani, H. Narimatsu, M. Ito, Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase, J. Biol. Chem. 282 (2007) 30889-30900]. Here, we report the crystal structure of a covalent intermediate of the KLrP mutant E165Q, in which glucose was covalently bound to a nucleophile, Glu(373). The structure confirms the double displacement mechanism of the retaining beta-glucosidase. In addition, the structure suggests that a water molecule could be involved in the stabilization of transition states through a sugar, 2-hydroxyl.
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Affiliation(s)
- Junji Noguchi
- Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8581, Japan
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22
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Zhang R, McCarter JD, Braun C, Yeung W, Brayer GD, Withers SG. Synthesis and testing of 2-deoxy-2,2-dihaloglycosides as mechanism-based inhibitors of alpha-glycosidases. J Org Chem 2008; 73:3070-7. [PMID: 18345685 DOI: 10.1021/jo702565q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of a series of 2-deoxy-2,2-dihaloglycosyl halides as potential alpha-glycosidase inactivators has been achieved via the halogenation of protected 2-fluoroglycal precursors. Direct chlorination of per-O-acetylated 2-fluoro-d-glucal and 2-fluoromaltal followed by basic deprotection yielded the corresponding 2-chloro-2-deoxy-2-fluoroglycosyl chlorides. Reaction of the per-O-acetylated 2-fluoroglycals with acetyl hypofluorite or Selectfluor yielded the 2-deoxy-2,2-difluoroglycosyl derivatives, which were converted to their alpha-chlorides using thionyl chloride and deprotected under basic conditions. Trinitrophenyl glycosides of the 2-deoxy-2,2-difluoro mono- and disaccharides were synthesized by arylation of the hemiacetals with picryl fluoride, then deprotected with HCl in methanol. All three monosaccharide derivatives caused active site-directed, time-dependent inactivation of yeast alpha-glucosidase via the trapping of covalent glycosyl-enzyme intermediates, and kinetic parameters for inactivation by each compound were determined. Surprisingly neither of the 2-deoxy-2,2-dihalomaltosyl chlorides caused time-dependent inactivation of human pancreatic alpha-amylase, despite the fact that the trinitrophenyl 2-deoxy-2,2-difluoromaltoside functioned in that mode. The trinitrophenyl glycosides appear to be approximately 1000-fold more reactive than the corresponding chlorides in the enzyme active sites.
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Affiliation(s)
- Ran Zhang
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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23
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Hekmat O, Florizone C, Kim YW, Eltis LD, Warren RAJ, Withers SG. Specificity Fingerprinting of Retaining β-1,4-Glycanases in theCellulomonas fimi Secretome Using Two Fluorescent Mechanism-Based Probes. Chembiochem 2007; 8:2125-32. [DOI: 10.1002/cbic.200700481] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Goto T, Abe Y, Kakuta Y, Takeshita K, Imoto T, Ueda T. Crystal Structure of Tapes japonica Lysozyme with Substrate Analogue. J Biol Chem 2007; 282:27459-27467. [PMID: 17631496 DOI: 10.1074/jbc.m704555200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tapes japonica lysozyme (TJL) is classified as a member of the recently established i-type lysozyme family. In this study, we solved the crystal structure of TJL complexed with a trimer of N-acetylglucosamine to 1.6A resolution. Based on structure and mutation analyses, we demonstrated that Glu-18 and Asp-30 are the catalytic residues of TJL. Furthermore, the present findings suggest that the catalytic mechanism of TJL is a retaining mechanism that proceeds through a covalent sugar-enzyme intermediate. On the other hand, the quaternary structure in the crystal revealed a dimer formed by the electrostatic interactions of catalytic residues (Glu-18 and Asp-30) in one molecule with the positive residues at the C terminus in helix 6 of the other molecule. Gel chromatography analysis revealed that the TJL dimer remained intact under low salt conditions but that it dissociated to TJL monomers under high salt conditions. With increasing salt concentrations, the chitinase activity of TJL dramatically increased. Therefore, this study provides novel evidence that the lysozyme activity of TJL is modulated by its quaternary structure.
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Affiliation(s)
- Takashi Goto
- Graduate School of Pharmaceutical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 and
| | - Yoshito Abe
- Graduate School of Pharmaceutical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 and
| | - Yoshimitsu Kakuta
- Agricultural Sciences of Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 and
| | - Kohei Takeshita
- Graduate School of Pharmaceutical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 and
| | - Taiji Imoto
- Faculty of Biotechnology and Life Science, Sojo University, Kumamoto 860-0082, Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 and.
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25
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Affiliation(s)
- Michael J Evans
- The Skaggs Institute for Chemical Biology and Departments of Cell Biology and Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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26
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Gloster TM, Madsen R, Davies GJ. Structural basis for cyclophellitol inhibition of a beta-glucosidase. Org Biomol Chem 2006; 5:444-6. [PMID: 17252125 DOI: 10.1039/b616590g] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural basis for beta-glucosidase inhibition by cyclophellitol is demonstrated using X-ray crystallography, enzyme kinetics and mass spectrometry.
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Affiliation(s)
- Tracey M Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK YO10 5YW
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27
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Watts AG, Oppezzo P, Withers SG, Alzari PM, Buschiazzo A. Structural and Kinetic Analysis of Two Covalent Sialosyl-Enzyme Intermediates on Trypanosoma rangeli Sialidase. J Biol Chem 2006; 281:4149-55. [PMID: 16298994 DOI: 10.1074/jbc.m510677200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosoma rangeli sialidase is a glycoside hydrolase (family GH33) that catalyzes the cleavage of alpha-2-->3-linked sialic acid residues from sialoglycoconjugates with overall retention of anomeric configuration. Retaining glycosidases usually operate through a ping-pong mechanism, wherein a covalent intermediate is formed between the carbohydrate and an active site carboxylic acid of the enzyme. Sialidases, instead, appear to use a tyrosine as the catalytic nucleophile, leaving the possibility of an essentially different catalytic mechanism. Indeed, a direct nucleophilic role for a tyrosine was shown for the homologous trans-sialidase from Trypanosoma cruzi, although itself not a typical sialidase. Here we present the three-dimensional structures of the covalent glycosyl-enzyme complexes formed by the T. rangeli sialidase with two different mechanism-based inactivators at 1.9 and 1.7 Angstroms resolution. To our knowledge, these are the first reported structures of enzymatically competent covalent intermediates for a strictly hydrolytic sialidase. Kinetic analyses have been carried out on the formation and turnover of both intermediates, showing that structural modifications to these inactivators can be used to modify the lifetimes of covalent intermediates. These results provide further evidence that all sialidases likely operate through a similar mechanism involving the transient formation of a covalently sialylated enzyme. Furthermore, we believe that the ability to "tune" the inactivation and reactivation rates of mechanism-based inactivators toward specific enzymes represents an important step toward developing this class of inactivators into therapeutically useful compounds.
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Affiliation(s)
- Andrew G Watts
- Department of Chemistry, University of British Columbia, Vancouver, Canada
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28
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Williams SJ, Hekmat O, Withers SG. Synthesis and Testing of Mechanism-Based Protein-Profiling Probes for Retaining Endo-glycosidases. Chembiochem 2006; 7:116-24. [PMID: 16397879 DOI: 10.1002/cbic.200500279] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
New functional proteomics methods are required for targeting and identification of subsets of a proteome in an activity-based fashion. Glycosidases play critical roles in biology, yet a robust method for functional analysis of their activities and identities in biological proteomes is still lacking. An aryl 2-deoxy-2-fluoro xylobioside inactivator was conjugated through cleavable and noncleavable linker arms to a biotin tag, thereby yielding two new active-site-directed reagents for activity-based profiling of retaining beta-glycanases in complex proteomes. Crucially, these tagged reagents possess high specificity for their target enzymes with kinetic parameters similar to those of the untagged reagent. Western blotting showed that these reagents bind and covalently label active retaining beta-glycanases both in pure enzyme samples and in the secreted proteome of the soil bacterium Cellulomonas fimi. Such reagents therefore show great promise for future activity-based targeting of glycanases.
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Affiliation(s)
- Spencer J Williams
- Protein Engineering Network of Centres of Excellence of Canada, Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada
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29
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Stubbs KA, Vocadlo DJ. Functional Proteomic Profiling of Glycan‐Processing Enzymes. Methods Enzymol 2006; 415:253-68. [PMID: 17116479 DOI: 10.1016/s0076-6879(06)15016-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Glycoconjugates play critical roles in regulating cellular and organismal functions. Consequently, defining the relative levels of these glycoconjugates under varied physiological conditions is important. Thus identifying and understanding the regulation of the enzymes that process these glycoconjugates are essential steps in understanding the role of this "glycocode" in development and disease. Activity-based affinity reagents are useful tools for probing these enzymes and should facilitate the unraveling of proteomes. One advantage of activity-based affinity probes is that they can simultaneously reveal multiple enzymes having similar activities. These probes can also be used to enrich proteomes of interest, thereby facilitating identification and cloning of new carbohydrate-processing enzymes. Here we review the current state of activity-based affinity probes for profiling carbohydrate-processing enzymes, focusing on successes and limitations, general design features, and a specific example describing profiling of exoglycosidases from cell lysates.
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Affiliation(s)
- Keith A Stubbs
- Department of Chemistry, Simon Frasier University, Burnaby, British Columbia, Canada
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30
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Salleh HM, Müllegger J, Reid SP, Chan WY, Hwang J, Warren RAJ, Withers SG. Cloning and characterization of Thermotoga maritima beta-glucuronidase. Carbohydr Res 2005; 341:49-59. [PMID: 16303119 DOI: 10.1016/j.carres.2005.10.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Revised: 10/05/2005] [Accepted: 10/07/2005] [Indexed: 11/17/2022]
Abstract
The putative beta-glucuronidase from Thermotoga maritima, comprising 563 amino acid residues conjugated with a Hisx6 tag, was cloned and expressed in Escherichia coli. The enzyme has a moderately broad specificity, hydrolysing a range of p-nitrophenyl glycoside substrates, but has greatest activity on p-nitrophenyl beta-D-glucosiduronic acid (kcat=68 s(-1), kcat/K(M)= 4.5x10(5) M(-1) s(-1)). The enzyme also shows a relatively broad pH-dependence with activity from pH4.5 to 7.5 and a maximum at pH6.5. As expected the enzyme is stable towards heat denaturation, with a half life of 3h at 85 degrees C, in contrast to the mesophilic E. coli enzyme, which has a half life of 2.6h at 50 degrees C. The identity of the catalytic nucleophile was confirmed as Glu476 within the sequence VTEFGAD by trapping the glycosyl-enzyme intermediate using the mechanism-based inactivator, 2-deoxy-2-fluoro-beta-D-glucosyluronic acid fluoride and identifying the labeled peptide in peptic digests by HPLC-MS/MS methodologies. Consistent with this, the Glu476Ala mutant was shown to be hydrolytically inactive. The acid/base catalyst was confirmed as Glu383 by generation and kinetic analysis of enzyme mutants modified at that position, Glu383Ala and Glu383Gln. The demonstration of activity rescue by azide is consistent with the proposed role for this residue. This enzyme therefore appears suitable for use in enzymatic oligosaccharide synthesis in either the transglycosylation mode or by use of glycosynthase and thioglycoligase approaches.
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Affiliation(s)
- Hamzah M Salleh
- Protein Engineering Network of Centres of Excellence of Canada, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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31
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Czjzek M, Ben David A, Bravman T, Shoham G, Henrissat B, Shoham Y. Enzyme–Substrate Complex Structures of a GH39 β-Xylosidase from Geobacillus stearothermophilus. J Mol Biol 2005; 353:838-46. [PMID: 16212978 DOI: 10.1016/j.jmb.2005.09.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 08/31/2005] [Accepted: 09/01/2005] [Indexed: 10/25/2022]
Abstract
Beta-D-Xylosidases are glycoside hydrolases that catalyse the release of xylose units from short xylooligosaccharides and are engaged in the final breakdown of plant cell-wall hemicelluloses. beta-D-Xylosidases are found in glycoside hydrolase families 3, 39, 43, 52 and 54. The first crystal structure of a GH39 beta-xylosidase revealed a multi-domain organization with the catalytic domain having the canonical (beta/alpha)8 barrel fold. Here, we report the crystal structure of the GH39 Geobacillus stearothermophilus beta-D-xylosidase, inactivated by a point mutation of the general acid-base residue E160A, in complex with the chromogenic substrate molecule 2,5-dinitrophenyl-beta-D-xyloside. Surprisingly, six of the eight active sites present in the crystallographic asymmetric unit contain the trapped covalent glycosyl-enzyme intermediate, while two of them still contain the uncleaved substrate. The structural characterization of these two critical species along the reaction coordinate of this enzyme identifies the residues forming its xyloside-binding pocket as well as those essential for its aglycone recognition.
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Affiliation(s)
- Mirjam Czjzek
- Station Biologique de Roscoff, Végétaux Marins et Biomolécules, UMR7139-CNRS-UPMC, Place George Teissier, BP74, 29682 Roscoff, France.
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32
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Hommalai G, Chaiyen P, Svasti J. Studies on the transglucosylation reactions of cassava and Thai rosewood β-glucosidases using 2-deoxy-2-fluoro-glycosyl-enzyme intermediates. Arch Biochem Biophys 2005; 442:11-20. [PMID: 16139237 DOI: 10.1016/j.abb.2005.07.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Revised: 07/25/2005] [Accepted: 07/27/2005] [Indexed: 10/25/2022]
Abstract
Beta-glucosidases from cassava and Thai rosewood can synthesize a variety of alkyl glucosides using various alcohols as glucosyl acceptors for transglucosylation. Both enzymes were inactivated by 2-deoxy-2-fluoro-sugar analogues to form the covalent glycosyl-enzyme intermediates, indicating that the reaction mechanism was of the double-replacement type. The trapped enzyme intermediates were used for investigating transglucosylation specificity, by measuring the rate of reactivation by various alcohols. The glucosyl-enzyme intermediate from the cassava enzyme showed a 20- to 120-fold higher rate of glucose transfer to alcohols than the glucosyl-enzyme intermediate from the Thai rosewood enzyme. Kinetic analysis indicated that the aglycone binding site of the cassava enzyme was hydrophobic, since the enzyme bound better to more hydrophobic alcohols and showed poor transfer of glucose to hydrophilic sugars. With butanol, transglucosylation was faster with the primary alcohols than with the secondary or tertiary alcohol. Studies with ethanol and chloro-substituted ethanols indicated that the rate of transglucosylation was significantly faster with alcohols with lower pKa values, where the reactive alkoxide was more readily generated, indicating that the formation of the alkoxide species was a major step governing the formation of the transition state in the cassava enzyme.
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Affiliation(s)
- Greanggrai Hommalai
- Department of Biochemistry, Center for Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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33
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Hekmat O, Kim YW, Williams SJ, He S, Withers SG. Active-site peptide "fingerprinting" of glycosidases in complex mixtures by mass spectrometry. Discovery of a novel retaining beta-1,4-glycanase in Cellulomonas fimi. J Biol Chem 2005; 280:35126-35. [PMID: 16085650 DOI: 10.1074/jbc.m508434200] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
New proteomics methods are required for targeting and identification of subsets of a proteome in an activity-based fashion. Here, we report the first gel-free, mass spectrometry-based strategy for mechanism-based profiling of retaining beta-endoglycosidases in complex proteomes. Using a biotinylated, cleavable 2-deoxy-2-fluoroxylobioside inactivator, we have isolated and identified the active-site peptides of target retaining beta-1,4-glycanases in systems of increasing complexity: pure enzymes, artificial proteomes, and the secreted proteome of the aerobic mesophilic soil bacterium Cellulomonas fimi. The active-site peptide of a new C. fimi beta-1,4-glycanase was identified in this manner, and the peptide sequence, which includes the catalytic nucleophile, is highly conserved among glycosidase family 10 members. The glycanase gene (GenBank accession number DQ146941) was cloned using inverse PCR techniques, and the protein was found to comprise a catalytic domain that shares approximately 70% sequence identity with those of xylanases from Streptomyces sp. and a family 2b carbohydrate-binding module. The new glycanase hydrolyzes natural and artificial xylo-configured substrates more efficiently than their cello-configured counterparts. It has a pH dependence very similar to that of known C. fimi retaining glycanases.
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Affiliation(s)
- Omid Hekmat
- Protein Engineering Network of Centres of Excellence of Canada, Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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34
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Tarling CA, Withers SG. The synthesis of a series of modified mannotrisaccharides as probes of the enzymes involved in the early stages of mammalian complex N-glycan formation. Carbohydr Res 2005; 339:2487-97. [PMID: 15476709 DOI: 10.1016/j.carres.2004.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2004] [Accepted: 08/17/2004] [Indexed: 11/29/2022]
Abstract
A series of mannotrisaccharides were synthesized by two distinct chemical pathways as probes of the enzymes involved in the early stages of mammalian complex N-glycan formation. Methyl (alpha-D-mannopyranosyl)-(1-->3)-[(alpha-D-mannopyranosyl)-(1-->6)]-beta-D-mannopyranoside (6) and methyl (2-deoxy-2-fluoro-alpha-D-mannopyranosyl)-(1-->3)-[(2-deoxy-2-fluoro-alpha-D-mannopyranosyl)-(1-->6)]-beta-D-mannopyranoside (8) were rapidly synthesized from unprotected methyl beta-D-mannopyranoside (12). Methyl (2-deoxy-2-fluoro-alpha-D-mannopyranosyl)-(1-->3)-[(alpha-D-mannopyranosyl)-(1-->6)]-beta-D-mannopyranoside (7) and methyl (alpha-D-mannopyranosyl)-(1-->3)-[(2-deoxy-2-fluoro-alpha-D-mannopyranosyl)-(1-->6)]-beta-D-mannopyranoside (9) were synthesized from the common orthogonally protected precursor methyl 2-O-acetyl-4,6-O-benzylidene-beta-D-mannopyranoside (15). The 2-deoxy-2-fluoro substitution common to trisaccharides 7-9 renders these analogues resistant to enzyme action in two distinct ways. Firstly the fluorine serves as a non-nucleophilic isostere for the acceptor hydroxyl in studies with glycosyl transferases GnT-I and GnT-II (7 and 9, respectively). Secondly it should render trisaccharide 8 stable to hydrolysis by the mannosidases Man-II and Man-III by inductive destabilization of their oxocarbenium ion-like transition states. These analogues should be useful for structural studies on these enzymes.
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Affiliation(s)
- Chris A Tarling
- Department of Chemistry, 2036 Main Mall, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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35
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Cox LR, DeBoos GA, Fullbrook JJ, Percy JM, Spencer N. Applying asymmetric dihydroxylation to the synthesis of difluorinated carbohydrate analogues: a 1,1-difluoro-1-deoxy-d-xylulose. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2004.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Sandgren M, Ståhlberg J, Mitchinson C. Structural and biochemical studies of GH family 12 cellulases: improved thermal stability, and ligand complexes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2004; 89:246-91. [PMID: 15950056 DOI: 10.1016/j.pbiomolbio.2004.11.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this review we will describe how we have gathered structural and biochemical information from several homologous cellulases from one class of glycoside hydrolases (GH family 12), and used this information within the framework of a protein-engineering program for the design of new variants of these enzymes. These variants have been characterized to identify some of the positions and the types of mutations in the enzymes that are responsible for some of the biochemical differences in thermal stability and activity between the homologous enzymes. In this process we have solved the three-dimensional structure of four of these homologous GH 12 cellulases: Three fungal enzymes, Humicola grisea Cel12A, Hypocrea jecorina Cel12A and Hypocrea schweinitzii Cel12A, and one bacterial, Streptomyces sp. 11AG8 Cel12A. We have also determined the three-dimensional structures of the two most stable H. jecorina Cel12A variants. In addition, four ligand-complex structures of the wild-type H. grisea Cel12A enzyme have been solved and have made it possible to characterize some of the interactions between substrate and enzyme. The structural and biochemical studies of these related GH 12 enzymes, and their variants, have provided insight on how specific residues contribute to protein thermal stability and enzyme activity. This knowledge can serve as a structural toolbox for the design of Cel12A enzymes with specific properties and features suited to existing or new applications.
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Affiliation(s)
- Mats Sandgren
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden.
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37
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Watts AG, Withers SG. The synthesis of some mechanistic probes for sialic acid processing enzymes and the labeling of a sialidase from Trypanosoma rangeli. CAN J CHEM 2004. [DOI: 10.1139/v04-125] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sialyl hydrolases, trans-sialidases, and sialyl transferases are biologically important enzymes that are responsible for the incorporation and removal of sialic acid residues, which decorate many cell surface glycocongugates. Two fluorinated sialic acid derivatives have been synthesized as mechanism-based inactivators, to probe the catalytic mechanisms through which sialidases and trans-sialidases operate. Both compounds are known to be covalent inactivators of a trans-sialidase from Trypanosoma cruzi. Here, 3-fluorosialosyl fluoride has been found to covalently label the catalytic nucleophile of a sialidase from T. rangeli, and the residue involved is shown to be Tyr346 within the sequence DENSGYSSVL. This is the first demonstration that sialidases operate through a covalent glycosyl-enzyme intermediate, strongly suggesting a common catalytic mechanism amongst all members of the sialidase superfamily. CMP-3-fluoro sialic acid is a competitive inhibitor of sialyl transferases and was synthesized via a two-step enzymatic process from commercially available N-acetyl mannosamine, 3-fluoropyruvic acid, and cytidine triphosphate in around 84% yield.Key words: sialidase, mechanism, labeling, nucleophile, inhibitor.
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38
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Yu Y, Kirkup CE, Pi N, Leary JA. Characterization of noncovalent protein-ligand complexes and associated enzyme intermediates of GlcNAc-6-O-sulfotransferase by electrospray ionization FT-ICR mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1400-1407. [PMID: 15465352 DOI: 10.1016/j.jasms.2004.06.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2004] [Revised: 05/21/2004] [Accepted: 06/02/2004] [Indexed: 05/24/2023]
Abstract
In this study, a GlcNAc-6-O-Sulfotransferase, NodST and its complexation with the substrate 3'-phosphoadenosine 5'-phosphosulfate (PAPS) and the inhibitor 3'-phosphoadenosine 5'-phosphate (PAP) were studied using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. In addition, using isotopically labeled substrate, we have successfully confirmed a sulfated enzyme intermediate, which was predicted by the MS kinetic measurement. It is also shown that information regarding solution binding affinities can be obtained using electrospray ionization (ESI)-FTICR mass spectrometry. The relative binding constants, Kd(PAPS)/Kd(PAP), derived from the solution and gas phase were very similar, which suggests that the binding domain of this particular enzyme system, given known structures of other sulfotransferases, may be preserved during the transmission of the complex from solution to the gas phase.
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Affiliation(s)
- Yonghao Yu
- Department of Chemistry, University of California at Berkeley, 410 Latimer Hall, 94720, Berkeley, CA, USA
| | - Colleen E Kirkup
- Department of Chemistry, University of California at Berkeley, 410 Latimer Hall, 94720, Berkeley, CA, USA
| | - Na Pi
- Department of Chemistry, University of California at Berkeley, 410 Latimer Hall, 94720, Berkeley, CA, USA
| | - Julie A Leary
- Department of Chemistry, University of California at Berkeley, 410 Latimer Hall, 94720, Berkeley, CA, USA.
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Sandgren M, Berglund GI, Shaw A, Ståhlberg J, Kenne L, Desmet T, Mitchinson C. Crystal Complex Structures Reveal How Substrate is Bound in the −4 to the +2 Binding Sites of Humicola grisea Cel12A. J Mol Biol 2004; 342:1505-17. [PMID: 15364577 DOI: 10.1016/j.jmb.2004.07.098] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Revised: 07/19/2004] [Accepted: 07/30/2004] [Indexed: 11/27/2022]
Abstract
As part of an ongoing enzyme discovery program to investigate the properties and catalytic mechanism of glycoside hydrolase family 12 (GH 12) endoglucanases, a GH family that contains several cellulases that are of interest in industrial applications, we have solved four new crystal structures of wild-type Humicola grisea Cel12A in complexes formed by soaking with cellobiose, cellotetraose, cellopentaose, and a thio-linked cellotetraose derivative (G2SG2). These complex structures allow mapping of the non-covalent interactions between the enzyme and the glucosyl chain bound in subsites -4 to +2 of the enzyme, and shed light on the mechanism and function of GH 12 cellulases. The unhydrolysed cellopentaose and the G2SG2 cello-oligomers span the active site of the catalytically active H.grisea Cel12A enzyme, with the pyranoside bound in subsite -1 displaying a S31 skew boat conformation. After soaking in cellotetraose, the cello-oligomer that is found bound in site -4 to -1 contains a beta-1,3-linkage between the two cellobiose units in the oligomer, which is believed to have been formed by a transglycosylation reaction that has occurred during the ligand soak of the protein crystals. The close fit of this ligand and the binding sites occupied suggest a novel mixed beta-glucanase activity for this enzyme.
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Affiliation(s)
- Mats Sandgren
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
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40
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Amaya MF, Watts AG, Damager I, Wehenkel A, Nguyen T, Buschiazzo A, Paris G, Frasch AC, Withers SG, Alzari PM. Structural Insights into the Catalytic Mechanism of Trypanosoma cruzi trans-Sialidase. Structure 2004; 12:775-84. [PMID: 15130470 DOI: 10.1016/j.str.2004.02.036] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2004] [Revised: 02/27/2004] [Accepted: 02/29/2004] [Indexed: 11/17/2022]
Abstract
Sialidases are a superfamily of sialic-acid-releasing enzymes that are of significant interest due to their implication as virulence factors in the pathogenesis of a number of diseases. However, extensive studies of viral and microbial sialidases have failed to provide a comprehensive picture of their mechanistic properties, in part because the structures of competent enzyme-substrate complexes and reaction intermediates have never been described. Here we report these structures for the Trypanosoma cruzi trans-sialidase (TcTS), showing that catalysis by sialidases occurs via a similar mechanism to that of other retaining glycosidases, but with some intriguing differences that may have evolved in response to the substrate structure.
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Affiliation(s)
- María Fernanda Amaya
- Unité de Biochimie Structurale, CNRS URA 2185, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris, France
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41
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Paal K, Ito M, Withers SG. Paenibacillus sp. TS12 glucosylceramidase: kinetic studies of a novel sub-family of family 3 glycosidases and identification of the catalytic residues. Biochem J 2004; 378:141-9. [PMID: 14561218 PMCID: PMC1223920 DOI: 10.1042/bj20031028] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2003] [Revised: 10/02/2003] [Accepted: 10/16/2003] [Indexed: 11/17/2022]
Abstract
GCase (glucosylceramidase) from Paenibacillus sp. TS12, a family 3 glycosidase, hydrolyses the beta-glycosidic linkage of glucosylceramide with retention of anomeric configuration via a two-step, double-displacement mechanism. Two carboxyl residues are essential for catalysis, one functioning as a nucleophile and the other as a general acid/base catalyst. p-nitrophenyl beta-D-glucopyranoside [K(m)=0.27+/-0.02 mM and kcat/K(m)=(2.1+/-0.2)x10(6) M(-1) x s(-1)] and 2,4-dinitrophenyl beta-D-glucopyranoside [K(m)=0.16+/-0.02 mM and k(cat)/K(m)=(2.9+/-0.4)x10(6) M(-1) x s(-1)] were used for continuous assay of the enzyme. The dependence of kcat (and kcat/K(m)) on pH revealed a dependence on a group of pK(a)< or =7.8 in the enzyme-substrate complex which must be protonated for catalysis. Incubation of GCase with 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside caused time-dependent inactivation (K(i)=2.4+/-0.7 mM and k(i)=0.59+/-0.05 min(-1)) due to the accumulation of a trapped glycosyl-enzyme intermediate. Electrospray ionization MS analysis of the peptic digest of this complex showed that the enzyme was covalently labelled by the reagent at Asp-223, consistent with its role as nucleophile. A mutant modified at this residue (D223G) showed substantially reduced activity compared with the wild type (>10(4)), but this activity could be partially restored by addition of formate as an external nucleophile. Kinetic analysis of the mutant E411A indicated that Glu-411 serves as the general acid/base catalytic residue since this mutant was pH-independent and since considerable GCase activity was restored upon addition of azide to E411A, along with formation of a glycosyl azide product.
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Affiliation(s)
- Krisztina Paal
- Protein Engineering Network of Centres of Excellence of Canada and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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42
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Lee JK, Bain AD, Berti PJ. Probing the Transition States of Four Glucoside Hydrolyses with13C Kinetic Isotope Effects Measured at Natural Abundance by NMR Spectroscopy. J Am Chem Soc 2004; 126:3769-76. [PMID: 15038730 DOI: 10.1021/ja0394028] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinetic isotope effects (KIEs) were measured for methyl glucoside (4) hydrolysis on unlabeled material by NMR. Twenty-eight (13)C KIEs were measured on the acid-catalyzed hydrolysis of alpha-4 and beta-4, as well as enzymatic hydrolyses with yeast alpha-glucosidase and almond beta-glucosidase. The 1-(13)C KIEs on the acid-catalyzed reactions of alpha-4 and beta-4, 1.007(2) and 1.010(6), respectively, were in excellent agreement with the previously reported values (1.007(1), 1.011(2): Bennet and Sinnott, J. Am. Chem. Soc. 1986, 108, 7287). Transition state analysis of the acid-catalyzed reactions using the (13)C KIEs, along with the previously reported (2)H KIEs, confirmed that both reactions proceed with a stepwise D(N)A(N) mechanism and showed that the glucosyl oxocarbenium ion intermediate exists in an E(3) sofa or (4)H(3) half-chair conformation. (13)C KIEs showed that the alpha-glucosidase reaction also proceeded through a D(N)*A(N) mechanism, with a 1-(13)C KIE of 1.010(4). The secondary (13)C KIEs showed evidence of distortions in the glucosyl ring at the transition state. For the beta-glucosidase-catalyzed reaction, the 1-(13)C KIE of 1.032(1) demonstrated a concerted A(N)D(N) mechanism. The pattern of secondary (13)C KIEs was similar to the acid-catalyzed reaction, showing no signs of distortion. KIE measurement at natural abundance makes it possible to determine KIEs much more quickly than previously, both by increasing the speed of KIE measurement and by obviating the need for synthesis of isotopically labeled compounds.
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Affiliation(s)
- Jason K Lee
- Department of Chemistry, Antimicrobial Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada
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Jensen MH, Mirza O, Albenne C, Remaud-Simeon M, Monsan P, Gajhede M, Skov LK. Crystal Structure of the Covalent Intermediate of Amylosucrase fromNeisseria polysaccharea†. Biochemistry 2004; 43:3104-10. [PMID: 15023061 DOI: 10.1021/bi0357762] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The alpha-retaining amylosucrase from the glycoside hydrolase family 13 performs a transfer reaction of a glucosyl moiety from sucrose to an acceptor molecule. Amylosucrase has previously been shown to be able to use alpha-D-glucopyranosyl fluoride as a substrate, which suggested that it could also be used for trapping the reaction intermediate for crystallographic studies. In this paper, the crystal structure of the acid/base catalyst mutant, E328Q, with a covalently bound glucopyranosyl moiety is presented. Sucrose cocrystallized crystals were soaked with alpha-D-glucopyranosyl fluoride, which resulted in the trapping of a covalent intermediate in the active site of the enzyme. The structure is refined to a resolution of 2.2 A and showed that binding of the covalent intermediate resulted in a backbone movement of 1 A around the location of the nucleophile, Asp286. This structure reveals the first covalent intermediate of an alpha-retaining glycoside hydrolase where the glucosyl moiety is identical to the expected biologically relevant entity. Comparison to other enzymes with anticipated glucosylic covalent intermediates suggests that this structure is a representative model for such intermediates. Analysis of the active site shows how oligosaccharide binding disrupts the putative nucleophilic water binding site found in the hydrolases of the GH family 13. This reveals important parts of the structural background for the shift in function from hydrolase to transglycosidase seen in amylosucrase.
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Affiliation(s)
- Malene H Jensen
- Structural Biology Group, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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Tarling CA, He S, Sulzenbacher G, Bignon C, Bourne Y, Henrissat B, Withers SG. Identification of the catalytic nucleophile of the family 29 alpha-L-fucosidase from Thermotoga maritima through trapping of a covalent glycosyl-enzyme intermediate and mutagenesis. J Biol Chem 2003; 278:47394-9. [PMID: 12975375 DOI: 10.1074/jbc.m306610200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fucose-containing glycoconjugates are key antigenic determinants in many biological processes. A change in expression levels of the enzymes responsible for tailoring these glycoconjugates has been associated with many pathological conditions and it is therefore surprising that little information is known regarding the mechanism of action of these important catabolic enzymes. Thermotoga maritima, a thermophilic bacterium, produces a wide range of carbohydrate-processing enzymes including a 52-kDa alpha-L-fucosidase that has 38% sequence identity and 56% similarity to human fucosidases. The catalytic nucleophile of this enzyme was identified to be Asp-224 within the peptide sequence 222WNDMGWPEKGKEDL235 using the mechanism-based covalent inactivator 2-deoxy-2-fluoro-alpha-L-fucosyl fluoride. The 10(4)-fold lower activity (kcat/Km) of the site-directed mutant D224A, and the subsequent rescue of activity upon addition of exogenous nucleophiles, conclusively confirms this assignment. This article presents the first direct identification of the catalytic nucleophile of an alpha-L-fucosidase, a key step in the understanding of these important enzymes.
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Affiliation(s)
- Chris A Tarling
- Department of Chemistry, University of British Columbia, Vancouver V6T 1Z1, Canada
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Golan G, Shallom D, Teplitsky A, Zaide G, Shulami S, Baasov T, Stojanoff V, Thompson A, Shoham Y, Shoham G. Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications. J Biol Chem 2003; 279:3014-24. [PMID: 14573597 DOI: 10.1074/jbc.m310098200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alpha-glucuronidases cleave the alpha-1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid and short xylooligomers as part of the hemicellulose degradation system. To date, all of the alpha-glucuronidases are classified as family 67 glycosidases, which catalyze the hydrolysis via the investing mechanism. Here we describe several high resolution crystal structures of the alpha-glucuronidase (AguA) from Geobacillus stearothermophilus, in complex with its substrate and products. In the complex of AguA with the intact substrate, the 4-O-methyl-d-glucuronic acid sugar ring is distorted into a half-chair conformation, which is closer to the planar conformation required for the oxocarbenium ion-like transition state structure. In the active site, a water molecule is coordinated between two carboxylic acids, in an appropriate position to act as a nucleophile. From the structural data it is likely that two carboxylic acids, Asp(364) and Glu(392), activate together the nucleophilic water molecule. The loop carrying the catalytic general acid Glu(285) cannot be resolved in some of the structures but could be visualized in its "open" and "closed" (catalytic) conformations in other structures. The protonated state of Glu(285) is presumably stabilized by its proximity to the negative charge of the substrate, representing a new variation of substrate-assisted catalysis mechanism.
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Affiliation(s)
- Gali Golan
- Department of Inorganic Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Hövel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D. Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J 2003; 22:4922-32. [PMID: 14517232 PMCID: PMC204477 DOI: 10.1093/emboj/cdg494] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.
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Affiliation(s)
- Klaus Hövel
- Institute for Biochemistry, University of Cologne, Cologne 50674, Germany
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47
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Watts AG, Damager I, Amaya ML, Buschiazzo A, Alzari P, Frasch AC, Withers SG. Trypanosoma cruzi trans-sialidase operates through a covalent sialyl-enzyme intermediate: tyrosine is the catalytic nucleophile. J Am Chem Soc 2003; 125:7532-3. [PMID: 12812490 DOI: 10.1021/ja0344967] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Modified sialic acid substrates have been used to label Trypanosoma cruzi trans-sialidase, demonstrating that the enzyme catalyses the transfer of sialic acid through a covalent glycosyl-enzyme intermediate, a mechanism common to most retaining glycosidases. Peptic digestion of labeled protein, followed by LC-MS/MS analysis of the digest, identified Tyr342 as the catalytic nucleophile. This is the first such example of a retaining glycosidase utilizing an aryl glycoside intermediate. It is suggested that this alternative choice of nucleophile is a consequence of the chemical nature of sialic acid. A Tyr/Glu couple is invoked to relay charge from a remote glutamic acid, thereby avoiding electrostatic repulsion with the sialic acid carboxylate group.
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Affiliation(s)
- Andrew G Watts
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada V6T 1Z1
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