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Meelua W, Wanjai T, Thinkumrob N, Oláh J, Mujika JI, Ketudat-Cairns JR, Hannongbua S, Jitonnom J. Active site dynamics and catalytic mechanism in arabinan hydrolysis catalyzed by GH43 endo-arabinanase from QM/MM molecular dynamics simulation and potential energy surface. J Biomol Struct Dyn 2021; 40:7439-7449. [PMID: 33715601 DOI: 10.1080/07391102.2021.1898469] [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] [Indexed: 10/21/2022]
Abstract
The endo-1,5-α-L-arabinanases, belonging to glycoside hydrolase family 43 (GH43), catalyse the hydrolysis of α-1,5-arabinofuranosidic bonds in arabinose-containing polysaccharides. These enzymes are proposed targets for industrial and medical applications. Here, molecular dynamics (MD), potential energy surface and free energy (potential of mean force) simulations are undertaken using hybrid quantum mechanical/molecular mechanical (QM/MM) potentials to understand the active site dynamics, catalytic mechanism and the electrostatic influence of active site residues of the GH43 endo-arabinanase from G. stearothermophilus. The calculated results give support to the single-displacement mechanism proposed for the inverting GH43 enzymes: first a proton is transferred from the general acid E201 to the substrate, followed by a nucleophilic attack by water, activated by the general base D27, on the anomer carbon. A conformational change (2E ↔E3 ↔ 4E) in the -1 sugar ring is observed involving a transition state featuring an oxocarbenium ion character. Residues D87, K106, H271 are highlighted as potential targets for future mutation experiments in order to increase the efficiency of the reaction. To our knowledge, this is the first QM/MM study providing molecular insights into the glycosidic bond hydrolysis of a furanoside substrate by an inverting GH in solution.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wijitra Meelua
- Demonstration School, University of Phayao, Phayao, Thailand.,Division of Chemistry, School of Science, University of Phayao, Phayao, Thailand
| | | | | | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Jon I Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, and Donostia International Physics Center (DIPC), Donostia, Euskadi, Spain
| | - James R Ketudat-Cairns
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Jitrayut Jitonnom
- Division of Chemistry, School of Science, University of Phayao, Phayao, Thailand
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Wang J, Tang X, Zhang Y, Li Y, Zhu L, Zhang Q, Wang W. How to complete the tautomerization and substrate-assisted activation prior to C–C bond fission by meta-cleavage product hydrolase LigY? Catal Sci Technol 2020. [DOI: 10.1039/d0cy01102a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two feasible binding modes could complete the C–C bond fission of the substrate. One is the bidentate mode and five-coordination, and the other is the monodentate mode and five-coordination.
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Affiliation(s)
- Junjie Wang
- Environment Research Institute
- Shandong University
- Qingdao 266237
- P. R. China
| | - Xiaowen Tang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- P. R. China
| | - Yixin Zhang
- Environment Research Institute
- Shandong University
- Qingdao 266237
- P. R. China
| | - Yanwei Li
- Environment Research Institute
- Shandong University
- Qingdao 266237
- P. R. China
| | - Ledong Zhu
- Environment Research Institute
- Shandong University
- Qingdao 266237
- P. R. China
| | - Qingzhu Zhang
- Environment Research Institute
- Shandong University
- Qingdao 266237
- P. R. China
| | - Wenxing Wang
- Environment Research Institute
- Shandong University
- Qingdao 266237
- P. R. China
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