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Maruyama S, Sawano K, Amaki S, Suzuki T, Narita S, Kimura K, Arakawa T, Yamada C, Ito Y, Dohmae N, Fujita K, Ishiwata A, Fushinobu S. Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase. Glycobiology 2021; 32:171-180. [PMID: 34735571 DOI: 10.1093/glycob/cwab103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/16/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
β-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At the active site of HypBA1, a cysteine residue (Cys417) coordinates with a Zn2+ atom and functions as the catalytic nucleophile for the anomer-retaining hydrolytic reaction. In this study, the role of Zn2+ ion and cysteine in catalysis as well as the substrate-bound structure were studied based on biochemical and crystallographic approaches. The enzymatic activity of HypBA1 decreased after dialysis in the presence of EDTA and guanidine hydrochloride and was then recovered by the addition of Zn2+. The Michaelis complex structure was determined using a crystal of a mutant at the acid/base catalyst residue (E322Q) soaked in a solution containing the substrate p-nitrophenyl-β-l-arabinofuranoside. To investigate the covalent thioglycosyl enzyme intermediate structure, synthetic inhibitors of l-arabinofuranosyl haloacetamide derivatives with different anomer configurations were used to target the nucleophilic cysteine. In the crystal structure of HypBA1, β-configured l-arabinofuranosylamide formed a covalent link with Cys417, whereas α-configured l-arabinofuranosylamide was linked to a noncatalytic residue Cys415. Mass spectrometric analysis indicated that Cys415 was also reactive with the probe molecule. With the β-configured inhibitor, the arabinofuranoside moiety was correctly positioned at the subsite and the active site integrity was retained to successfully mimic the covalent intermediate state.
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Affiliation(s)
- Shun Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kota Sawano
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoko Amaki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takehiro Suzuki
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Satoru Narita
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Kenta Kimura
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chihaya Yamada
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yukishige Ito
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Science, Osaka University, 1-1 Machikaneyamacho, Toyonaka, Osaka 560-0043, Japan
| | - Naoshi Dohmae
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Akihiro Ishiwata
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Schröder SP, Offen WA, Males A, Jin Y, de Boer C, Enotarpi J, Marino L, van der Marel GA, Florea BI, Codée JDC, Overkleeft HS, Davies GJ. Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on α-1,6 Mannanases. Chemistry 2021; 27:9519-9523. [PMID: 33878235 PMCID: PMC8362039 DOI: 10.1002/chem.202101255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 11/07/2022]
Abstract
There is a vast genomic resource for enzymes active on carbohydrates. Lagging far behind, however, are functional chemical tools for the rapid characterization of carbohydrate-active enzymes. Activity-based probes (ABPs) offer one chemical solution to these issues with ABPs based upon cyclophellitol epoxide and aziridine covalent and irreversible inhibitors representing a potent and widespread approach. Such inhibitors for enzymes active on polysaccharides are potentially limited by the requirement for several glycosidic bonds, themselves substrates for the enzyme targets. Here, it is shown that non-hydrolysable trisaccharide can be synthesized and applied even to enzymes with challenging subsite requirements. It was found that incorporation of carbasugar moieties, which was accomplished by cuprate-assisted regioselective trans-diaxial epoxide opening of carba-mannal synthesised for this purpose, yields inactivators that act as powerful activity-based inhibitors for α-1,6 endo-mannanases. 3-D structures at 1.35-1.47 Å resolutions confirm the design rationale and binding to the enzymatic nucleophile. Carbasugar oligosaccharide cyclophellitols offer a powerful new approach for the design of robust endoglycosidase inhibitors, while the synthesis procedures presented here should allow adaptation towards activity-based endoglycosidase probes as well as configurational isosteres targeting other endoglycosidase families.
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Affiliation(s)
- Sybrin P. Schröder
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Wendy A. Offen
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Alexandra Males
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Yi Jin
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Casper de Boer
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Jacopo Enotarpi
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Laura Marino
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | | | - Bogdan I. Florea
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Gideon J. Davies
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
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