1
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Doherty GG, Ler GJM, Wimmer N, Bernhardt PV, Ashmus RA, Vocadlo DJ, Armstrong Z, Davies GJ, Maccarana M, Li JP, Kayal Y, Ferro V. Synthesis of Uronic Acid 1-Azasugars as Putative Inhibitors of α-Iduronidase, β-Glucuronidase and Heparanase. Chembiochem 2023; 24:e202200619. [PMID: 36453606 DOI: 10.1002/cbic.202200619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/03/2022]
Abstract
1-Azasugar analogues of l-iduronic acid (l-IdoA) and d-glucuronic acid (d-GlcA) and their corresponding enantiomers have been synthesized as potential pharmacological chaperones for mucopolysaccharidosis I (MPS I), a lysosomal storage disease caused by mutations in the gene encoding α-iduronidase (IDUA). The compounds were efficiently synthesized in nine or ten steps from d- or l-arabinose, and the structures were confirmed by X-ray crystallographic analysis of key intermediates. All compounds were inactive against IDUA, although l-IdoA-configured 8 moderately inhibited β-glucuronidase (β-GLU). The d-GlcA-configured 9 was a potent inhibitor of β-GLU and a moderate inhibitor of the endo-β-glucuronidase heparanase. Co-crystallization of 9 with heparanase revealed that the endocyclic nitrogen of 9 forms close interactions with both the catalytic acid and catalytic nucleophile.
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Affiliation(s)
- Gareth G Doherty
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Geraldine Jia Ming Ler
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Norbert Wimmer
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Paul V Bernhardt
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Roger A Ashmus
- Department of Chemistry and, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - David J Vocadlo
- Department of Chemistry and, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Zachary Armstrong
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
- Current address: Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
- Current address: Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Marco Maccarana
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, University of Uppsala, 75123, Uppsala, Sweden
| | - Jin-Ping Li
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, University of Uppsala, 75123, Uppsala, Sweden
| | - Yasmin Kayal
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Vito Ferro
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
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2
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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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3
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Artola M, Kuo CL, McMahon SA, Oehler V, Hansen T, van der Lienden M, He X, van den Elst H, Florea BI, Kermode AR, van der Marel GA, Gloster TM, Codée JDC, Overkleeft HS, Aerts JMFG. New Irreversible α-l-Iduronidase Inhibitors and Activity-Based Probes. Chemistry 2018; 24:19081-19088. [PMID: 30307091 PMCID: PMC6343074 DOI: 10.1002/chem.201804662] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/10/2018] [Indexed: 11/20/2022]
Abstract
Cyclophellitol aziridines are potent irreversible inhibitors of retaining glycosidases and versatile intermediates in the synthesis of activity‐based glycosidase probes (ABPs). Direct 3‐amino‐2‐(trifluoromethyl)quinazolin‐4(3H)‐one‐mediated aziridination of l‐ido‐configured cyclohexene has enabled the synthesis of new covalent inhibitors and ABPs of α‐l‐iduronidase, deficiency of which underlies the lysosomal storage disorder mucopolysaccharidosis type I (MPS I). The iduronidase ABPs react covalently and irreversibly in an activity‐based manner with human recombinant α‐l‐iduronidase (rIDUA, Aldurazyme®). The structures of IDUA when complexed with the inhibitors in a non‐covalent transition state mimicking form and a covalent enzyme‐bound form provide insights into its conformational itinerary. Inhibitors 1–3 adopt a half‐chair conformation in solution (4H3 and 3H4), as predicted by DFT calculations, which is different from the conformation of the Michaelis complex observed by crystallographic studies. Consequently, 1–3 may need to overcome an energy barrier in order to switch from the 4H3 conformation to the transition state (2, 5B) binding conformation before reacting and adopting a covalent 5S1 conformation. rIDUA can be labeled with fluorescent Cy5 ABP 2, which allows monitoring of the delivery of therapeutic recombinant enzyme to lysosomes, as is intended in enzyme replacement therapy for the treatment of MPS I patients.
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Affiliation(s)
- Marta Artola
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Chi-Lin Kuo
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Verena Oehler
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Thomas Hansen
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Martijn van der Lienden
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Xu He
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Hans van den Elst
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bogdan I Florea
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Allison R Kermode
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Gijsbert A van der Marel
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Jeroen D C Codée
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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4
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Vickers C, Liu F, Abe K, Salama-Alber O, Jenkins M, Springate CMK, Burke JE, Withers SG, Boraston AB. Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29. J Biol Chem 2018; 293:18296-18308. [PMID: 30282808 DOI: 10.1074/jbc.ra118.005134] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Indexed: 11/06/2022] Open
Abstract
Fucoidans are chemically complex and highly heterogeneous sulfated marine fucans from brown macro algae. Possessing a variety of physicochemical and biological activities, fucoidans are used as gelling and thickening agents in the food industry and have anticoagulant, antiviral, antitumor, antibacterial, and immune activities. Although fucoidan-depolymerizing enzymes have been identified, the molecular basis of their activity on these chemically complex polysaccharides remains largely uninvestigated. In this study, we focused on three glycoside hydrolase family 107 (GH107) enzymes: MfFcnA and two newly identified members, P5AFcnA and P19DFcnA, from a bacterial species of the genus Psychromonas Using carbohydrate-PAGE, we show that P5AFcnA and P19DFcnA are active on fucoidans that differ from those depolymerized by MfFcnA, revealing differential substrate specificity within the GH107 family. Using a combination of X-ray crystallography and NMR analyses, we further show that GH107 family enzymes share features of their structures and catalytic mechanisms with GH29 α-l-fucosidases. However, we found that GH107 enzymes have the distinction of utilizing a histidine side chain as the proposed acid/base catalyst in its retaining mechanism. Further interpretation of the structural data indicated that the active-site architectures within this family are highly variable, likely reflecting the specificity of GH107 enzymes for different fucoidan substructures. Together, these findings begin to illuminate the molecular details underpinning the biological processing of fucoidans.
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Affiliation(s)
- Chelsea Vickers
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Feng Liu
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada, and
| | - Kento Abe
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Orly Salama-Alber
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Meredith Jenkins
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | | | - John E Burke
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Stephen G Withers
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada, and
| | - Alisdair B Boraston
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada,.
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5
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Cheng WC, Lin CK, Li HY, Chang YC, Lu SJ, Chen YS, Chang SY. A combinatorial approach towards the synthesis of non-hydrolysable triazole–iduronic acid hybrid inhibitors of human α-l-iduronidase: discovery of enzyme stabilizers for the potential treatment of MPSI. Chem Commun (Camb) 2018; 54:2647-2650. [DOI: 10.1039/c7cc09642a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis and bioevaluation of substituent-diverse triazole–iduronic acid hybrid molecules are highlighted.
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Affiliation(s)
- Wei-Chieh Cheng
- Genomics Research Center
- Academia Sinica
- Taipei
- Taiwan
- Department of Chemistry
| | | | - Huang-Yi Li
- Department of Life Sciences and Institute of Genome Sciences
- National Yang-Ming University
- Taipei
- Taiwan
| | - Yu-Chien Chang
- Department of Chemistry
- National Cheng Kung University
- Tainan City
- Taiwan
| | | | - Yu-Shin Chen
- Genomics Research Center
- Academia Sinica
- Taipei
- Taiwan
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6
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Ali-Ahmad A, Garron ML, Zamboni V, Lenfant N, Nurizzo D, Henrissat B, Berrin JG, Bourne Y, Vincent F. Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2. J Struct Biol 2017; 197:227-235. [DOI: 10.1016/j.jsb.2016.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/18/2016] [Accepted: 11/19/2016] [Indexed: 12/16/2022]
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7
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Biochemical characterization of a novel cold-adapted GH39 β-agarase, AgaJ9, from an agar-degrading marine bacterium Gayadomonas joobiniege G7. Appl Microbiol Biotechnol 2016; 101:1965-1974. [DOI: 10.1007/s00253-016-7951-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/11/2016] [Accepted: 10/20/2016] [Indexed: 11/28/2022]
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8
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Stütz AE, Wrodnigg TM. Carbohydrate-Processing Enzymes of the Lysosome: Diseases Caused by Misfolded Mutants and Sugar Mimetics as Correcting Pharmacological Chaperones. Adv Carbohydr Chem Biochem 2016; 73:225-302. [PMID: 27816107 DOI: 10.1016/bs.accb.2016.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lysosomal storage diseases are hereditary disorders caused by mutations on genes encoding for one of the more than fifty lysosomal enzymes involved in the highly ordered degradation cascades of glycans, glycoconjugates, and other complex biomolecules in the lysosome. Several of these metabolic disorders are associated with the absence or the lack of activity of carbohydrate-processing enzymes in this cell compartment. In a recently introduced therapy concept, for susceptible mutants, small substrate-related molecules (so-called pharmacological chaperones), such as reversible inhibitors of these enzymes, may serve as templates for the correct folding and transport of the respective protein mutant, thus improving its concentration and, consequently, its enzymatic activity in the lysosome. Carbohydrate-processing enzymes in the lysosome, related lysosomal diseases, and the scope and limitations of reported reversible inhibitors as pharmacological chaperones are discussed with a view to possibly extending and improving research efforts in this area of orphan diseases.
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Affiliation(s)
- Arnold E Stütz
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| | - Tanja M Wrodnigg
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
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9
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Baker P, Whitfield GB, Hill PJ, Little DJ, Pestrak MJ, Robinson H, Wozniak DJ, Howell PL. Characterization of the Pseudomonas aeruginosa Glycoside Hydrolase PslG Reveals That Its Levels Are Critical for Psl Polysaccharide Biosynthesis and Biofilm Formation. J Biol Chem 2015; 290:28374-28387. [PMID: 26424791 DOI: 10.1074/jbc.m115.674929] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Indexed: 01/04/2023] Open
Abstract
A key component of colonization, biofilm formation, and protection of the opportunistic human pathogen Pseudomonas aeruginosa is the biosynthesis of the exopolysaccharide Psl. Composed of a pentameric repeating unit of mannose, glucose, and rhamnose, the biosynthesis of Psl is proposed to occur via a Wzx/Wzy-dependent mechanism. Previous genetic studies have shown that the putative glycoside hydrolase PslG is essential for Psl biosynthesis. To understand the function of this protein, the apo-structure of the periplasmic domain of PslG (PslG(31-442)) and its complex with mannose were determined to 2.0 and 1.9 Å resolution, respectively. Despite a domain architecture and positioning of catalytic residues similar to those of other family 39 glycoside hydrolases, PslG(31-442) exhibits a unique 32-Å-long active site groove that is distinct from other structurally characterized family members. PslG formed a complex with two mannose monosaccharides in this groove, consistent with binding data obtained from intrinsic tryptophan fluorescence. PslG was able to catalyze the hydrolysis of surface-associated Psl, and this activity was abolished in a E165Q/E276Q double catalytic variant. Surprisingly, P. aeruginosa variants with these chromosomal mutations as well as a pslG deletion mutant were still capable of forming Psl biofilms. However, overexpression of PslG in a pslG deletion background impaired biofilm formation and resulted in less surface-associated Psl, suggesting that regulation of this enzyme is important during polysaccharide biosynthesis.
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Affiliation(s)
- Perrin Baker
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Gregory B Whitfield
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Preston J Hill
- Division of Infectious Disease, Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio 43210
| | - Dustin J Little
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthew J Pestrak
- Division of Infectious Disease, Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio 43210
| | - Howard Robinson
- Photon Sciences Division, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - Daniel J Wozniak
- Division of Infectious Disease, Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio 43210.
| | - P Lynne Howell
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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10
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Chuang HY, Suen CS, Hwang MJ, Roffler SR. Toward reducing immunogenicity of enzyme replacement therapy: altering the specificity of human β-glucuronidase to compensate for α-iduronidase deficiency. Protein Eng Des Sel 2015; 28:519-29. [DOI: 10.1093/protein/gzv041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/31/2015] [Indexed: 11/13/2022] Open
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11
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Bie H, Yin J, He X, Kermode AR, Goddard-Borger ED, Withers SG, James MNG. Insights into mucopolysaccharidosis I from the structure and action of α-L-iduronidase. Nat Chem Biol 2013; 9:739-45. [PMID: 24036510 PMCID: PMC4954775 DOI: 10.1038/nchembio.1357] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 09/05/2013] [Indexed: 02/06/2023]
Abstract
Mucopolysaccharidosis type I (MPS I), caused by mutations in the gene encoding α-L-iduronidase (IDUA), is one of approximately 70 genetic disorders collectively known as the lysosomal storage diseases. To gain insight into the basis for MPS I, we crystallized human IDUA produced in an Arabidopsis thaliana cgl mutant. IDUA consists of a TIM barrel domain containing the catalytic site, a β-sandwich domain and a fibronectin-like domain. Structures of IDUA bound to iduronate analogs illustrate the Michaelis complex and reveal a (2,5)B conformation in the glycosyl-enzyme intermediate, which suggest a retaining double displacement reaction involving the nucleophilic Glu299 and the general acid/base Glu182. Unexpectedly, the N-glycan attached to Asn372 interacts with iduronate analogs in the active site and is required for enzymatic activity. Finally, these IDUA structures and biochemical analysis of the disease-relevant P533R mutation have enabled us to correlate the effects of mutations in IDUA to clinical phenotypes.
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Affiliation(s)
- Haiying Bie
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Jiang Yin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Xu He
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
| | - Allison R. Kermode
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
| | - Ethan D. Goddard-Borger
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z1
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z1
| | - Michael N. G. James
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
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12
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Human α-L-iduronidase uses its own N-glycan as a substrate-binding and catalytic module. Proc Natl Acad Sci U S A 2013; 110:14628-33. [PMID: 23959878 DOI: 10.1073/pnas.1306939110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
N-glycosylation is a major posttranslational modification that endows proteins with various functions. It is established that N-glycans are essential for the correct folding and stability of some enzymes; however, the actual effects of N-glycans on their activities are poorly understood. Here, we show that human α-l-iduronidase (hIDUA), of which a dysfunction causes accumulation of dermatan/heparan sulfate leading to mucopolysaccharidosis type I, uses its own N-glycan as a substrate binding and catalytic module. Structural analysis revealed that the mannose residue of the N-glycan attached to N372 constituted a part of the substrate-binding pocket and interacted directly with a substrate. A deglycosylation study showed that enzyme activity was highly correlated with the N-glycan attached to N372. The kinetics of native and deglycosylated hIDUA suggested that the N-glycan is also involved in catalytic processes. Our study demonstrates a previously unrecognized function of N-glycans.
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13
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Esmurziev AM, Reimers A, Andreassen T, Simic N, Sundby E, Hoff BH. Benzoylated uronic acid building blocks and synthesis of N-uronate conjugates of lamotrigine. Molecules 2012; 17:820-35. [PMID: 22269868 PMCID: PMC6268592 DOI: 10.3390/molecules17010820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 01/02/2012] [Accepted: 01/04/2012] [Indexed: 11/24/2022] Open
Abstract
A chemoenzymatic approach towards benzoylated uronic acid building blocks has been investigated starting with benzoylated hexapyranosides using regioselective C-6 enzymatic hydrolysis as the key step. Two of the building blocks were reacted with the antiepileptic drug lamotrigine. Glucuronidation of lamotrigine using methyl (2,3,4-tri-O-benzoyl-α-D-glycopyranosyl bromide)uronate proceeded to give the N2-conjugate. However, lamotrigine-N2-glucuronide was most efficiently synthesised from methyl (2,3,4-tri-O-acetyl-α-D-glucopyranosyl bromide)uronate. Employing nitromethane as solvent with CdCO(3) as a base lamotrigine-N2 glucuronide was prepared in a high yield (41%). Also methyl (2,3-di-O-benzoyl-4-deoxy-4-fluoro-α-D-glucosyl bromide)uronate underwent N-glucuronidation, but the product was unstable, eliminating hydrogen fluoride to give the corresponding enoate conjugate.
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Affiliation(s)
- Aslan M. Esmurziev
- Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Trondheim NO-7491, Norway
- Sør-Trøndelag University College, E.C. Dahls Gate 2, Trondheim NO-7004, Norway
| | - Arne Reimers
- Department of Neuroscience, Faculty of Medicine, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Trygve Andreassen
- Department of Biotechnology, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Nebojsa Simic
- Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Trondheim NO-7491, Norway
| | - Eirik Sundby
- Sør-Trøndelag University College, E.C. Dahls Gate 2, Trondheim NO-7004, Norway
| | - Bård Helge Hoff
- Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Trondheim NO-7491, Norway
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14
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Kang TS, Stevens RC. Structural aspects of therapeutic enzymes to treat metabolic disorders. Hum Mutat 2010; 30:1591-610. [PMID: 19790257 DOI: 10.1002/humu.21111] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein therapeutics represents a niche subset of pharmacological agents that is rapidly gaining importance in medicine. In addition to the exceptional specificity that is characteristic of protein therapeutics, several classes of proteins have also been effectively utilized for treatment of conditions that would otherwise lack effective pharmacotherapeutic options. A particularly striking class of protein therapeutics is exogenous enzymes administered for replacement therapy in patients afflicted with metabolic disorders. To date, at least 11 enzymes have either been approved for use, or are in clinical trials for the treatment of selected inherited metabolic disorders. With the recent advancement in structural biology, a significantly larger amount of structural information for several of these enzymes is now available. This article is an overview of the correlation between structural perturbations of these enzymes with the clinical presentation of the respective metabolic conditions, as well as a discussion of the relevant structural modification strategies engaged in improving these enzymes for replacement therapies.
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Affiliation(s)
- Tse Siang Kang
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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15
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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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Yip VLY, Thompson J, Withers SG. Mechanism of GlvA from Bacillus subtilis: a detailed kinetic analysis of a 6-phospho-alpha-glucosidase from glycoside hydrolase family 4. Biochemistry 2007; 46:9840-52. [PMID: 17676871 DOI: 10.1021/bi700536p] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
GlvA, a 6-phospho-alpha-glucosidase from Bacillus subtilis assigned to glycoside hydrolase family 4, catalyzes the hydrolysis of maltose 6'-phosphate via a redox-elimination-addition mechanism requiring NAD+ as cofactor. In contrast to previous reports and consistent with the proposed mechanism, GlvA is only activated in the presence of the nicotinamide cofactor in its oxidized, and not the reduced NADH, form. Significantly, GlvA catalyzes the hydrolysis of both 6-phospho-alpha- and 6-phospho-beta-glucosides containing activated leaving groups such as p-nitrophenol and does so with retention and inversion, respectively, of anomeric configuration. Mechanistic details of the individual bond cleaving and forming steps were probed using a series of 6-phospho-alpha- and 6-phospho-beta-glucosides. Primary deuterium kinetic isotope effects (KIEs) were measured for both classes of substrates in which either the C2 or the C3 protons have been substituted with a deuterium, consistent with C-H bond cleavage at each center being partially rate-limiting. Kinetic parameters were also determined for 1-[2H]-substituted substrates, and depending on the substrates and the reaction conditions, the measurements of kcat and kcat/KM produced either no KIEs or inverse KIEs. In conjunction with results of Brønsted analyses with both aryl 6-phospho-alpha- and beta-glucosides, the kinetic data suggest that GlvA utilizes an E1cb mechanism analogous to that proposed for the Thermotoga maritima BglT, a 6-phospho-beta-glucosidase in glycoside hydrolase family 4 (Yip, V.L.Y et al. (2006) Biochemistry 45, 571-580). The pattern of isotope effects measured and the observation of very similar kcat values for all substrates, including unactivated and natural substrates, indicate that the oxidation and deprotonation steps are rate-limiting steps in essentially all cases. This mechanism permits the cleavage of both alpha- and beta-glycosides within the same active site motif and, for activated substrates that do not require acid catalysis for cleavage, within the same active site, yielding the product sugar-6-phosphate in the same anomeric form in the two cases.
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Affiliation(s)
- Vivian L Y Yip
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
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17
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Yip VLY, Withers SG. Breakdown of oligosaccharides by the process of elimination. Curr Opin Chem Biol 2006; 10:147-55. [PMID: 16495121 DOI: 10.1016/j.cbpa.2006.02.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Accepted: 02/09/2006] [Indexed: 12/22/2022]
Abstract
Several new mechanisms for enzyme-catalyzed breakdown of oligosaccharides have been uncovered in recent years. A common feature is the recruitment of elimination steps rather than direct displacements. Bond cleavage can proceed via E1 mechanisms with cationic transition states or E1(cb) mechanisms with anionic transition states, and can even involve NAD(+)-mediated redox steps. A common feature emerging from studies on disparate syn-eliminating enzymes is the use of a single catalytic residue, often tyrosine, as both general acid and base.
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Affiliation(s)
- Vivian L Y Yip
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
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18
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Pabba J, Rempel B, Withers S, Vasella A. Synthesis of Glycaro-1,5-lactams and Tetrahydrotetrazolopyridine-5-carboxylates: Inhibitors ofβ-D-Glucuronidase andα-L-Iduronidase. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690066] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kakavanos R, Lehn P, Callebaut I, Meikle PJ, Parkinson-Lawrence EJ, Hopwood JJ, Brooks DA. Common antigenicity for two glycosidases. FEBS Lett 2005; 580:87-92. [PMID: 16359666 DOI: 10.1016/j.febslet.2005.11.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Accepted: 11/22/2005] [Indexed: 11/23/2022]
Abstract
Enzyme replacement therapy (ERT) has proven to be an effective therapy for some lysosomal storage disorder (LSD) patients. A potential complication during ERT is the generation of an immune response against the replacement protein. We have investigated the antigenicity of two distantly related glycosidases, alpha-glucosidase (Pompe disease or glycogen storage disease type II, GSD II), and alpha-L-iduronidase (Hurler syndrome, mucopolysaccharidosis type I, MPS I). The linear sequence epitope reactivity of affinity purified polyclonal antibodies to recombinant human alpha-glucosidase and alpha-L-iduronidase was defined, to both glycosidases. The polyclonal antibodies exhibited some cross-reactive epitopes on the two proteins. Moreover, a monoclonal antibody to the active site of alpha-glucosidase showed cross-reactivity with a catalytic structural element of alpha-L-iduronidase. In a previous study, in MPS I patients who developed an immune response to ERT, this same site on alpha-L-iduronidase was highly antigenic and the last to tolerise following repeated enzyme infusions. We conclude that glycosidases can exhibit cross-reactive epitopes, and infer that this may relate to common structural elements associated with their active sites.
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Affiliation(s)
- Revecca Kakavanos
- Lysosomal Diseases Research Unit, Department of Genetic Medicine, Children Youth and Women's Health Service, 72 King William Road, North Adelaide, Adelaide, SA 5006, Australia
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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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21
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Rempel BP, Clarke LA, Withers SG. A homology model for human alpha-l-iduronidase: insights into human disease. Mol Genet Metab 2005; 85:28-37. [PMID: 15862278 DOI: 10.1016/j.ymgme.2004.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Revised: 12/10/2004] [Accepted: 12/10/2004] [Indexed: 10/25/2022]
Abstract
Genotype-phenotype correlations in genetic diseases for which missense mutations lead to disease remain a challenge. This is particularly true for diseases caused by alterations of proteins for which no three-dimensional structure is available. One such disease is Mucopolysaccharidosis type I, a disorder arising from a lack of activity of the lysosomal enzyme alpha-l-iduronidase (IDUA, EC 3.2.1.76). This deficiency compromises the degradation pathway of glycosaminoglycans such as heparan sulfate and dermatan sulfate, leading to substrate accumulation, which ultimately results in a multisystem disorder. Patients with IDUA deficiency have a wide spectrum of disease ranging from an early onset, rapidly progressive form leading to death in the first decade of life, to an attenuated disease which manifests in adolescence and leads to progressive joint and cardiac disease but is associated with a normal life span. Many patients fit into a disease phenotype intermediate to these extremes. While a number of point mutations have been described as leading to varying degrees of disease severity, a structural basis for these genotype-phenotype correlations has not been available owing to the lack of a three-dimensional structure for IDUA. A homology model for the IDUA enzyme was constructed based on the recently solved crystal structure of the beta-xylosidase from Thermoanaerobacterium saccharolyticum (XyTS, EC 3.2.1.37), both of which belong to the same sequence-related family (CAZY family 39). This model provides insights into why certain point mutations produce severely misfolded proteins and thus lead to severe disease, and why other mutations produce proteins with only minor structural perturbations and therefore the attenuated form of the disease.
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Affiliation(s)
- Brian P Rempel
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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Blériot Y, Vadivel SK, Herrera AJ, Greig IR, Kirby AJ, Sinaÿ P. Synthesis and acid catalyzed hydrolysis of B2,5 type conformationally constrained glucopyranosides: incorporation into a cellobiose analogue. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Yip VLY, Varrot A, Davies GJ, Rajan SS, Yang X, Thompson J, Anderson WF, Withers SG. An Unusual Mechanism of Glycoside Hydrolysis Involving Redox and Elimination Steps by a Family 4 β-Glycosidase fromThermotoga maritima. J Am Chem Soc 2004; 126:8354-5. [PMID: 15237973 DOI: 10.1021/ja047632w] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among the numerous well-characterized families of glycosidases, family 4 appears to be the anomaly, requiring both catalytic NAD+ and a divalent metal for activity. The unusual cofactor requirement prompted the proposal of a mechanism involving key NAD+-mediated redox steps as well as elimination of the glycosidic oxygen. Primary kinetic isotope effects for the 2- and 3-deutero substrate analogues, isotopic exchange with solvent, and structural analysis of a 6-phospho-beta-glucosidase, BglT (E.C. 3.2.1.6), provided evidence in support of the proposed mechanism, which has striking resemblances to that of the sugar dehydratases. Furthermore, analysis of the stereochemical outcome indicated that family 4 enzymes are retaining glycosidases.
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Affiliation(s)
- Vivian L Y Yip
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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24
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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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