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Kumar V, Johnson BP, Mandal PS, Sheffield DR, Dimas DA, Das R, Maity S, Distefano MD, Singh S. The utility of Streptococcus mutans undecaprenol kinase for the chemoenzymatic synthesis of diverse non-natural isoprenoids. Bioorg Chem 2024; 151:107707. [PMID: 39128243 DOI: 10.1016/j.bioorg.2024.107707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/08/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Isoprene chemoenzymatic cascades (ICCs) overcome the complexity of natural pathways by leveraging a streamlined two-enzyme cascade, facilitating efficient synthesis of C5-isoprene diphosphate precursors from readily available alcohol derivatives. Despite the documented promiscuity of enzymes in ICCs, exploration of their potential for accessing novel compounds remains limited, and existing methods require additional enzymes for generating longer-chain diphosphates. In this study, we present the utility of Streptococcus mutans undecaprenol kinase (SmUdpK) for the chemoenzymatic synthesis of diverse non-natural isoprenoids. Using a library of 50 synthetic alcohols, we demonstrate that SmUdpK's promiscuity extends to allylic chains as small as four carbons and benzylic alcohols with various substituents. Subsequently, SmUdpK is utilized in an ICC with isopentenyl phosphate kinase and aromatic prenyltransferase to generate multiple non-natural isoprenoids. This work provides evidence that, with proper optimization, SmUdpK can act as the first enzyme in these ICCs, enhancing access to both valuable and novel compounds.
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Affiliation(s)
- Vikas Kumar
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Bryce P Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Prashant S Mandal
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Daniel R Sheffield
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Dustin A Dimas
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Riki Das
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, United States
| | - Sanjay Maity
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, United States
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States.
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Johnson BP, Mandal PS, Brown SM, Thomas LM, Singh S. Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity. Proteins 2024; 92:808-818. [PMID: 38333996 PMCID: PMC11147733 DOI: 10.1002/prot.26674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic "isoprenol pathways," which seek to reduce the synthesis of the isoprenoid precursors to two enzymatic steps. Furthermore, the natural promiscuity of IPKs toward non-natural alkyl-monophosphates (alkyl-Ps) as substrates has hinted at the isoprenol pathways' potential to access novel isoprenoids with potentially useful activities. However, only a handful of IPK crystal structures have been solved to date, and even fewer of these contain non-natural substrates bound in the active site. The current study sought to elucidate additional ternary complexes bound to non-natural substrates using the IPK homolog from Thermococcus paralvinellae (TcpIPK). Four such structures were solved, each bound to a different non-natural alkyl-P and the phosphoryl donor substrate/product adenosine triphosphate (ATP)/adenosine diphosphate (ADP). As expected, the quaternary, tertiary, and secondary structures of TcpIPK closely resembled those of IPKs published previously, and kinetic analysis of a novel alkyl-P substrate highlighted the potentially dramatic effects of altering the core scaffold of the natural substrate. Even more interesting, though, was the discovery of a trend correlating the position of two α helices in the active site with the magnitude of an IPK homolog's reaction rate for the natural reaction. Overall, the current structures of TcpIPK highlight the importance of continued structural analysis of the IPKs to better understand and optimize their activity with both natural and non-natural substrates.
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Affiliation(s)
- Bryce P Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Prashant S Mandal
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Sara M Brown
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Leonard M Thomas
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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Zhang X, Wang X, Zhang Y, Wang F, Zhang C, Li X. Development of isopentenyl phosphate kinases and their application in terpenoid biosynthesis. Biotechnol Adv 2023; 64:108124. [PMID: 36863457 DOI: 10.1016/j.biotechadv.2023.108124] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/20/2023] [Accepted: 02/26/2023] [Indexed: 03/04/2023]
Abstract
As the largest class of natural products, terpenoids (>90,000) have multiple biological activities and a wide range of applications (e.g., pharmaceutical, agricultural, personal care and food industries). Therefore, the sustainable production of terpenoids by microorganisms is of great interest. Microbial terpenoid production depends on two common building blocks: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In addition to the natural biosynthetic pathways, mevalonate and methyl-D-erythritol-4-phosphate pathways, IPP and DMAPP can be produced through the conversion of isopentenyl phosphate and dimethylallyl monophosphate by isopentenyl phosphate kinases (IPKs), offering an alternative route for terpenoid biosynthesis. This review summarizes the properties and functions of various IPKs, novel IPP/DMAPP synthesis pathways involving IPKs, and their applications in terpenoid biosynthesis. Furthermore, we have discussed strategies to exploit novel pathways and unleash their potential for terpenoid biosynthesis.
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Affiliation(s)
- Xinyi Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xun Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yu Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Fei Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.
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