Structure and Cooperativity in Substrate–Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design

ACS Chemical Biology, vol. 17, pp. 266–280

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.

Authors 7

1. Eerappa Rajakumara corresponding

   Indian Institute of Technology Hyderabad

   Affiliation as printed

   Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India

2. Suman Abhishek

   Indian Institute of Technology Hyderabad

   Affiliation as printed

   Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India

3. Kulhar Nitin

   Indian Institute of Technology Hyderabad

   Affiliation as printed

   Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India

4. Dubey Saniya

   Indian Institute of Technology Hyderabad

   Affiliation as printed

   Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India

5. Priyanka Bajaj

   National Institute of Pharmaceutical Education and Research

   Affiliation as printed

   National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India

6. Ulrich Schwaneberg Aachen DWI - Leibniz Institute for Interactive Materials Institute of Biotechnology

   DWI – Leibniz Institute for Interactive Materials · RWTH Aachen University

   Affiliation as printed

   DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany

   Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany

7. Mehdi D. Davari corresponding

   Leibniz Institute of Plant Biochemistry

   Affiliation as printed

   Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany