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Rajakumara E, Abhishek S, Nitin K, Saniya D, Bajaj P, Schwaneberg U, Davari MD. Structure and Cooperativity in Substrate-Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design. ACS Chem Biol 2022; 17:266-280. [PMID: 35041385 DOI: 10.1021/acschembio.1c00500] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure-function relationship, cooperativity in binding of substrates, and dynamics of substrate-enzyme-cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure-activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes' structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Kulhar Nitin
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Dubey Saniya
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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Han X, Chen CC, Kuo CJ, Huang CH, Zheng Y, Ko TP, Zhu Z, Feng X, Wang K, Oldfield E, Wang AHJ, Liang PH, Guo RT, Ma Y. Crystal structures of ligand-bound octaprenyl pyrophosphate synthase from Escherichia coli reveal the catalytic and chain-length determining mechanisms. Proteins 2015; 83:37-45. [PMID: 24895191 PMCID: PMC4256133 DOI: 10.1002/prot.24618] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 05/12/2014] [Accepted: 05/27/2014] [Indexed: 01/07/2023]
Abstract
Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of one allylic substrate farnesyl pyrophosphate (FPP) and five homoallylic substrate isopentenyl pyrophosphate (IPP) molecules to form a C40 long-chain product OPP, which serves as a side chain of ubiquinone and menaquinone. OPPs belongs to the trans-prenyltransferase class of proteins. The structures of OPPs from Escherichia coli were solved in the apo-form as well as in complexes with IPP and a FPP thio-analog, FsPP, at resolutions of 2.2-2.6 Å, and revealed the detailed interactions between the ligands and enzyme. At the bottom of the active-site tunnel, M123 and M135 act in concert to form a wall which determines the final chain length. These results represent the first ligand-bound crystal structures of a long-chain trans-prenyltransferase and provide new information on the mechanisms of catalysis and product chain elongation.
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Affiliation(s)
- Xu Han
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chun-Chi Chen
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Chun-Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yingying Zheng
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Zhen Zhu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xinxin Feng
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Ke Wang
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan,Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan,Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan,Contact information of corresponding authors: Yanhe Ma Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861977, Fax number: +86 22 84861926. Rey-Ting Guo Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861999, Fax number: +86 22 24828701. Po-Huang Liang Ph.D., Address: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, , Telephone number: +886-2-2785-5696 ext. 6070, Fax number:+886-2-2788-9759
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Contact information of corresponding authors: Yanhe Ma Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861977, Fax number: +86 22 84861926. Rey-Ting Guo Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861999, Fax number: +86 22 24828701. Po-Huang Liang Ph.D., Address: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, , Telephone number: +886-2-2785-5696 ext. 6070, Fax number:+886-2-2788-9759
| | - Yanhe Ma
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Contact information of corresponding authors: Yanhe Ma Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861977, Fax number: +86 22 84861926. Rey-Ting Guo Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861999, Fax number: +86 22 24828701. Po-Huang Liang Ph.D., Address: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, , Telephone number: +886-2-2785-5696 ext. 6070, Fax number:+886-2-2788-9759
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