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Wu X, Zhao S, Tian Z, Han C, Jiang X, Wang L. Dynamics of loops surrounding the active site architecture in GH5_2 subfamily TfCel5A for cellulose degradation. Biotechnol Biofuels Bioprod 2023; 16:154. [PMID: 37853500 PMCID: PMC10583438 DOI: 10.1186/s13068-023-02411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Lignocellulose is the most abundant natural biomass resource for the production of biofuels and other chemicals. The efficient degradation of cellulose by cellulases is a critical step for the lignocellulose bioconversion. Understanding the structure-catalysis relationship is vital for rational design of more stable and highly active enzymes. Glycoside hydrolase (GH) family 5 is the largest and most functionally diverse group of cellulases, with a conserved TIM barrel structure. The important roles of the various loop regions of GH5 enzymes in catalysis, however, remain poorly understood. RESULTS In the present study, we investigated the relationship between the loops surrounding active site architecture and its catalytic efficiency, taking TfCel5A, an enzyme from GH5_2 subfamily of Thermobifida fusca, as an example. Large-scale computational simulations and site-directed mutagenesis experiments revealed that three loops (loop 8, 3, and 7) around active cleft played diverse roles in substrate binding, intermediate formation, and product release, respectively. The highly flexible and charged residue triad of loop 8 was responsible for capturing the ligand into the active cleft. Severe fluctuation of loop 3 led to the distortion of sugar conformation at the - 1 subsite. The wobble of loop 7 might facilitate product release, and the enzyme activity of the mutant Y361W in loop 7 was increased by approximately 40%. CONCLUSION This study unraveled the vital roles of loops in active site architecture and provided new insights into the catalytic mechanism of the GH5_2 cellulases.
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Affiliation(s)
- Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Sha Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhennan Tian
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Chao Han
- Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Ringel M, Dimos N, Himpich S, Haack M, Huber C, Eisenreich W, Schenk G, Loll B, Brück T. Biotechnological potential and initial characterization of two novel sesquiterpene synthases from Basidiomycota Coniophora puteana for heterologous production of δ-cadinol. Microb Cell Fact 2022; 21:64. [PMID: 35440053 PMCID: PMC9018054 DOI: 10.1186/s12934-022-01791-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/07/2022] [Indexed: 01/01/2023] Open
Abstract
Background Terpene synthases are versatile catalysts in all domains of life, catalyzing the formation of an enormous variety of different terpenoid secondary metabolites. Due to their diverse bioactive properties, terpenoids are of great interest as innovative ingredients in pharmaceutical and cosmetic applications. Recent advances in genome sequencing have led to the discovery of numerous terpene synthases, in particular in Basidiomycota like the wood rotting fungus Coniophora puteana, which further enhances the scope for the manufacture of terpenes for industrial purposes. Results In this study we describe the identification of two novel (+)-δ-cadinol synthases from C. puteana, Copu5 and Copu9. The sesquiterpene (+)-δ-cadinol was previously shown to exhibit cytotoxic activity therefore having an application as possible, new, and sustainably sourced anti-tumor agent. In an Escherichia coli strain, optimized for sesquiterpene production, titers of 225 mg l−1 and 395 mg l−1, respectively, could be achieved. Remarkably, both enzymes share the same product profile thereby representing the first two terpene synthases from Basidiomycota with identical product profiles. We solved the crystal structure of Copu9 in its closed conformation, for the first time providing molecular details of sesquiterpene synthase from Basidiomycota. Based on the Copu9 structure, we conducted structure-based mutagenesis of amino acid residues lining the active site, thereby altering the product profile. Interestingly, the mutagenesis study also revealed that despite the conserved product profiles of Copu5 and Copu9 different conformational changes may accompany the catalytic cycle of the two enzymes. This observation suggests that the involvement of tertiary structure elements in the reaction mechanism(s) employed by terpene synthases may be more complex than commonly expected. Conclusion The presented product selectivity and titers of Copu5 and Copu9 may pave the way towards a sustainable, biotechnological production of the potentially new bioactive (+)-δ-cadinol. Furthermore, Copu5 and Copu9 may serve as model systems for further mechanistic studies of terpenoid catalysis. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01791-8.
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Affiliation(s)
- Marion Ringel
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Nicole Dimos
- Institute for Chemistry and Biochemistry, Structural Biochemistry Laboratory, Freie Universität Berlin, Takustr. 6, 14195, Berlin, Germany
| | - Stephanie Himpich
- Institute for Chemistry and Biochemistry, Structural Biochemistry Laboratory, Freie Universität Berlin, Takustr. 6, 14195, Berlin, Germany
| | - Martina Haack
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Claudia Huber
- Bavarian NMR Center - Structural Membrane Biochemistry, Department of Chemistry, Technical University of Munich, 85748, Garching, Germany
| | - Wolfgang Eisenreich
- Bavarian NMR Center - Structural Membrane Biochemistry, Department of Chemistry, Technical University of Munich, 85748, Garching, Germany
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Cooper Rd, Brisbane, 4702, Australia
| | - Bernhard Loll
- Institute for Chemistry and Biochemistry, Structural Biochemistry Laboratory, Freie Universität Berlin, Takustr. 6, 14195, Berlin, Germany.
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany.
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Lv K, Shao W, Pedroso MM, Peng J, Wu B, Li J, He B, Schenk G. Enhancing the catalytic activity of a GH5 processive endoglucanase from Bacillus subtilis BS-5 by site-directed mutagenesis. Int J Biol Macromol 2020; 168:442-452. [PMID: 33310097 DOI: 10.1016/j.ijbiomac.2020.12.060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 11/16/2022]
Abstract
Processive endoglucanases possess both endo- and exoglucanase activity, making them attractive discovery and engineering targets. Here, a processive endoglucanase EG5C-1 from Bacillus subtilis was employed as the starting point for enzyme engineering. Referring to the complex structure information of EG5C-1 and cellohexaose, the amino acid residues in the active site architecture were identified and subjected to alanine scanning mutagenesis. The residues were chosen for a saturation mutagenesis since their variants showed similar activities to EG5C-1. Variants D70Q and S235W showed increased activity towards the substrates CMC and Avicel, an increase was further enhanced in D70Q/S235W double mutant, which displayed a 2.1- and 1.7-fold improvement in the hydrolytic activity towards CMC and Avicel, respectively. In addition, kinetic measurements showed that double mutant had higher substrate affinity (Km) and a significantly higher catalytic efficiency (kcat/Km). The binding isotherms of wild-type EG5C-1 and double mutant D70Q/S235W suggested that the binding capability of EG5C-1 for the insoluble substrate was weaker than that of D70Q/S235W. Molecular dynamics simulations suggested that the collaborative substitutions of D70Q and S235W altered the hydrogen bonding network within the active site architecture and introduced new hydrogen bonds between the enzyme and cellohexaose, thus enhancing both substrate affinity and catalytic efficiency.
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Affiliation(s)
- Kemin Lv
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Wenyu Shao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jiayu Peng
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China.
| | - Jiahuang Li
- School of Life Science, Nanjing University, Nanjing 210023, Jiangsu, China.
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
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