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Dalwani S, Wierenga RK. Enzymes of the crotonase superfamily: Diverse assembly and diverse function. Curr Opin Struct Biol 2023; 82:102671. [PMID: 37542911 DOI: 10.1016/j.sbi.2023.102671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/08/2023] [Accepted: 07/10/2023] [Indexed: 08/07/2023]
Abstract
The crotonase fold is generated by a framework of four repeats of a ββα-unit, extended by two helical regions. The active site of crotonase superfamily (CS) enzymes is located at the N-terminal end of the helix of the third repeat, typically being covered by a C-terminal helix. A major subset of CS-enzymes catalyzes acyl-CoA-dependent reactions, allowing for a diverse range of acyl-tail modifications. Most of these enzymes occur as trimers or hexamers (dimers of trimers), but monomeric forms are also observed. A common feature of the active sites of CS-enzymes is an oxyanion hole, formed by two peptide-NH hydrogen bond donors, which stabilises the negatively charged thioester oxygen atom of the reaction intermediate. Structural properties and possible use of these enzymes for biotechnological applications are discussed.
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Affiliation(s)
- Subhadra Dalwani
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland.
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2
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Thioester-mediated biocatalytic amide bond synthesis with in situ thiol recycling. Nat Catal 2022. [DOI: 10.1038/s41929-022-00889-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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3
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Chen Q, Jiang Y, Kang Z, Cheng J, Xiong X, Hu CY, Meng Y. Engineering a Feruloyl-Coenzyme A Synthase for Bioconversion of Phenylpropanoid Acids into High-Value Aromatic Aldehydes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9948-9960. [PMID: 35917470 DOI: 10.1021/acs.jafc.2c02980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aromatic aldehydes find extensive applications in food, perfume, pharmaceutical, and chemical industries. However, a limited natural enzyme selectivity has become the bottleneck of bioconversion of aromatic aldehydes from natural phenylpropanoid acids. Here, based on the original structure of feruloyl-coenzyme A (CoA) synthetase (FCS) from Streptomyces sp. V-1, we engineered five substrate-binding domains to match specific phenylpropanoid acids. FcsCIAE407A/K483L, FcsMAE407R/I481R/K483R, FcsHAE407K/I481K/K483I, FcsCAE407R/I481R/K483T, and FcsFAE407R/I481K/K483R showed 9.96-, 10.58-, 4.25-, 6.49-, and 8.71-fold enhanced catalytic efficiency for degrading CoA thioesters of cinnamic acid, 4-methoxycinnamic acid, 4-hydroxycinnamic acid, caffeic acid, and ferulic acid, respectively. Molecular dynamics simulation illustrated that novel substrate-binding domains formed strong interaction forces with substrates' methoxy/hydroxyl group and provided hydrophobic/alkaline catalytic surfaces. Five recombinant E. coli with FCS mutants were constructed with the maximum benzaldehyde, p-anisaldehyde, p-hydroxybenzaldehyde, protocatechualdehyde, and vanillin productivity of 6.2 ± 0.3, 5.1 ± 0.23, 4.1 ± 0.25, 7.1 ± 0.3, and 8.7 ± 0.2 mM/h, respectively. Hence, our study provided novel and efficient enzymes for the bioconversion of phenylpropanoid acids into aromatic aldehydes.
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Affiliation(s)
- Qihang Chen
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian 710119, P.R. China
| | - Yaqin Jiang
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian 710119, P.R. China
| | - Zhengzhong Kang
- AutoDrug Biotech Co. Ltd, No. 58 XiangKe Rd, Pudong New Area, Shanghai 201210, China
| | - Jie Cheng
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, P.R. China
| | - Xiaochao Xiong
- Biological Systems Engineering, Washington State University, Pullman, Washington 99163, United States
| | - Ching Yuan Hu
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian 710119, P.R. China
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, 1955 East-West Road, AgSci. 415J, Honolulu, Hawaii 96822, United States
| | - Yonghong Meng
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian 710119, P.R. China
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4
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Lee JA, Stolyar S, Marx CJ. Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae. Front Microbiol 2022; 13:849573. [PMID: 35359736 PMCID: PMC8963497 DOI: 10.3389/fmicb.2022.849573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/16/2022] [Indexed: 11/18/2022] Open
Abstract
Pink-pigmented facultative methylotrophs have long been studied for their ability to grow on reduced single-carbon (C1) compounds. The C1 groups that support methylotrophic growth may come from a variety of sources. Here, we describe a group of Methylobacterium strains that can engage in methoxydotrophy: they can metabolize the methoxy groups from several aromatic compounds that are commonly the product of lignin depolymerization. Furthermore, these organisms can utilize the full aromatic ring as a growth substrate, a phenotype that has rarely been described in Methylobacterium. We demonstrated growth on p-hydroxybenzoate, protocatechuate, vanillate, and ferulate in laboratory culture conditions. We also used comparative genomics to explore the evolutionary history of this trait, finding that the capacity for aromatic catabolism is likely ancestral to two clades of Methylobacterium, but has also been acquired horizontally by closely related organisms. In addition, we surveyed the published metagenome data to find that the most abundant group of aromatic-degrading Methylobacterium in the environment is likely the group related to Methylobacterium nodulans, and they are especially common in soil and root environments. The demethoxylation of lignin-derived aromatic monomers in aerobic environments releases formaldehyde, a metabolite that is a potent cellular toxin but that is also a growth substrate for methylotrophs. We found that, whereas some known lignin-degrading organisms excrete formaldehyde as a byproduct during growth on vanillate, Methylobacterium do not. This observation is especially relevant to our understanding of the ecology and the bioengineering of lignin degradation.
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Affiliation(s)
- Jessica A. Lee
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, United States
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, United States
- *Correspondence: Jessica A. Lee,
| | - Sergey Stolyar
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, United States
| | - Christopher J. Marx
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, United States
- Christopher J. Marx,
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5
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Padavattan S, Jos S, Gogoi H, Bagautdinov B. Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2021; 77:148-155. [PMID: 33949975 DOI: 10.1107/s2053230x21004593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/30/2021] [Indexed: 11/11/2022]
Abstract
Fatty-acid degradation is an oxidative process that involves four enzymatic steps and is referred to as the β-oxidation pathway. During this process, long-chain acyl-CoAs are broken down into acetyl-CoA, which enters the mitochondrial tricarboxylic acid (TCA) cycle, resulting in the production of energy in the form of ATP. Enoyl-CoA hydratase (ECH) catalyzes the second step of the β-oxidation pathway by the syn addition of water to the double bond between C2 and C3 of a 2-trans-enoyl-CoA, resulting in the formation of a 3-hydroxyacyl CoA. Here, the crystal structure of ECH from Thermus thermophilus HB8 (TtECH) is reported at 2.85 Å resolution. TtECH forms a hexamer as a dimer of trimers, and wide clefts are uniquely formed between the two trimers. Although the overall structure of TtECH is similar to that of a hexameric ECH from Rattus norvegicus (RnECH), there is a significant shift in the positions of the helices and loops around the active-site region, which includes the replacement of a longer α3 helix with a shorter α-helix and 310-helix in RnECH. Additionally, one of the catalytic residues of RnECH, Glu144 (numbering based on the RnECH enzyme), is replaced by a glycine in TtECH, while the other catalytic residue Glu164, as well as Ala98 and Gly141 that stabilize the enolate intermediate, is conserved. Their putative ligand-binding sites and active-site residue compositions are dissimilar.
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Affiliation(s)
- Sivaraman Padavattan
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560 029, India
| | - Sneha Jos
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560 029, India
| | - Hemanga Gogoi
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560 029, India
| | - Bagautdin Bagautdinov
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
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6
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Ortega P, Zanchet A, Sanz-Sanz C, Gómez-Carrasco S, González-Sánchez L, Jambrina PG. DpgC-Catalyzed Peroxidation of 3,5-Dihydroxyphenylacetyl-CoA (DPA-CoA): Insights into the Spin-Forbidden Transition and Charge Transfer Mechanisms*. Chemistry 2020; 27:1700-1712. [PMID: 32975323 DOI: 10.1002/chem.202002993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Indexed: 11/06/2022]
Abstract
Despite being a very strong oxidizing agent, most organic molecules are not oxidized in the presence of O2 at room temperature because O2 is a diradical whereas most organic molecules are closed-shell. Oxidation then requires a change in the spin state of the system, which is forbidden according to non-relativistic quantum theory. To overcome this limitation, oxygenases usually rely on metal or redox cofactors to catalyze the incorporation of, at least, one oxygen atom into an organic substrate. However, some oxygenases do not require any cofactor, and the detailed mechanism followed by these enzymes remains elusive. To fill this gap, here the mechanism for the enzymatic cofactor-independent oxidation of 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) is studied by combining multireference calculations on a model system with QM/MM calculations. Our results reveal that intersystem crossing takes place without requiring the previous protonation of molecular oxygen. The characterization of the electronic states reveals that electron transfer is concomitant with the triplet-singlet transition. The enzyme plays a passive role in promoting the intersystem crossing, although spontaneous reorganization of the water wire connecting the active site with the bulk presets the substrate for subsequent chemical transformations. The results show that the stabilization of the singlet radical-pair between dioxygen and enolate is enough to promote spin-forbidden reaction without the need for neither metal cofactors nor basic residues in the active site.
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Affiliation(s)
- Pablo Ortega
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain
| | - Alexandre Zanchet
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain.,Instituto de Física Fundamental (CSIC), Madrid, 28006, Spain
| | - Cristina Sanz-Sanz
- Departamento de Química Física Aplicada, University Autónoma de Madrid, Madrid, 28049, Spain
| | | | | | - Pablo G Jambrina
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain
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7
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Zhao NL, Zhang QQ, Zhao C, Liu L, Li T, Li CC, He LH, Zhu YB, Song YJ, Liu HX, Bao R. Structural and molecular dynamic studies of Pseudomonas aeruginosa OdaA reveal the regulation role of a C-terminal hinge element. Biochim Biophys Acta Gen Subj 2020; 1865:129756. [PMID: 33010351 DOI: 10.1016/j.bbagen.2020.129756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/18/2020] [Accepted: 09/27/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Crotonase superfamily members exhibit great catalytic diversity towards various acyl-CoA substrates. A common CoA moiety binding pattern is usually observed in this family, understanding the substrate-binding mechanism would facilitate the rational engineering of crotonases for improved properties. METHODS We applied X-ray crystallography to investigate a putative enoyl-CoA hydratase/isomerase OdaA in Pseudomonas aeruginosa. Thermal shift assay (TSA) were performed to explore the binding of OdaA with CoA thioester substrates. Furthermore, we performed molecular dynamics (MD) simulations to elucidate the dynamics of its CoA-binding site. RESULTS We solved the crystal structures of the apo and CoA-bound OdaA. Thermal shift assay (TSA) showed that CoA thioester substrates bind to OdaA with a different degree. MD simulations demonstrated that the C-terminal alpha helix underwent a structural transition and a hinge region would associate with this conformational change. CONCLUSIONS TSA in combination with MD simulations elucidate that the dynamics of C-terminal alpha helix in CoA-binding, and a hinge region play an important role in conformational change. GENERAL SIGNIFICANCE Those results help to extend our knowledge about the nature of crotonases and would be informative for future mechanistic studies and industry applications.
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Affiliation(s)
- Ning-Lin Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qian-Qian Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Chang Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Li Liu
- Department of dermatology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Tao Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chang-Cheng Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Li-Hui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Yi-Bo Zhu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ying-Jie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Huan-Xiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.
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8
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Johnston JM, Bulloch EM. Advances in menaquinone biosynthesis: sublocalisation and allosteric regulation. Curr Opin Struct Biol 2020; 65:33-41. [PMID: 32634692 DOI: 10.1016/j.sbi.2020.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/31/2022]
Abstract
Menaquinones (vitamin K2) are a family of redox-active small molecules with critical functions across all domains of life, including energy generation in bacteria and bone health in humans. The enzymes involved in menaquinone biosynthesis also have bioengineering applications and are potential antimicrobial drug targets. New insights into the essential roles of menaquinones, and their potential to cause redox-related toxicity, have highlighted the need for this pathway to be tightly controlled. Here, we provide an overview of our current understanding of the classical menaquinone biosynthesis pathway in bacteria. We also review recent discoveries on protein-level allostery and sublocalisation of membrane-bound enzymes that have provided insight into the regulation of flux through this biosynthetic pathway.
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Affiliation(s)
- Jodie M Johnston
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre, and Maurice Wilkins Centre for MolecularBiodiscovery, University of Canterbury, Christchurch 8041, New Zealand.
| | - Esther Mm Bulloch
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for MolecularBiodiscovery, University of Auckland, Private Bag 92019, Auckland, New Zealand
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9
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Walker PD, Williams C, Weir ANM, Wang L, Crosby J, Race PR, Simpson TJ, Willis CL, Crump MP. Control of β‐Branching in Kalimantacin Biosynthesis: Application of13C NMR to Polyketide Programming. Angew Chem Int Ed Engl 2019; 58:12446-12450. [DOI: 10.1002/anie.201905482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/12/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Paul D. Walker
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Angus N. M. Weir
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Luoyi Wang
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - John Crosby
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Paul R. Race
- School of BiochemistryUniversity of Bristol University Walk Bristol BS8 1TD UK
| | - Thomas J. Simpson
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Matthew P. Crump
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
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10
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Walker PD, Williams C, Weir ANM, Wang L, Crosby J, Race PR, Simpson TJ, Willis CL, Crump MP. Control of β‐Branching in Kalimantacin Biosynthesis: Application of13C NMR to Polyketide Programming. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Paul D. Walker
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Angus N. M. Weir
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Luoyi Wang
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - John Crosby
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Paul R. Race
- School of BiochemistryUniversity of Bristol University Walk Bristol BS8 1TD UK
| | - Thomas J. Simpson
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Matthew P. Crump
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
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11
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Das S, Batra S, Gupta PP, Kumar M, Srivastava VK, Jyoti A, Singh N, Kaushik S. Identification and evaluation of quercetin as a potential inhibitor of naphthoate synthase from Enterococcus faecalis. J Mol Recognit 2019; 32:e2802. [PMID: 31353747 DOI: 10.1002/jmr.2802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/29/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022]
Abstract
Enterococcus faecalis is a gram-positive, rod-shape bacteria responsible for around 65% to 80% of all enterococcal nosocomial infections. It is multidrug resistant (MDR) bacterium resistant to most of the first-line antibiotics. Due to the emergence of MDR strains, there is an urgent need to find novel targets to develop new antibacterial drugs against E. faecalis. In this regard, we have identified naphthoate synthase (1,4-dihydroxy-2-naphthoyl-CoA synthase, EC: 4.1.3.36; DHNS) as an anti-E. faecalis target, as it is an essential enzyme for menaquinone (vitamin K2 ) synthetic pathway in the bacterium. Thus, inhibiting naphtholate synthase may consequently inhibit the bacteria's growth. In this regard, we report here cloning, expression, purification, and preliminary structural studies of naphthoate synthase along with in silico modeling, molecular dynamic simulation of the model and docking studies of naphthoate synthase with quercetin, a plant alkaloid. Biochemical studies have indicated quercetin, a plant flavonoid as the potential lead compound to inhibit catalytic activity of EfDHNS. Quercetin binding has also been validated by spectrofluorimetric studies in order to confirm the bindings of the ligand compound with EfDHNS at ultralow concentrations. Reported studies may provide a base for structure-based drug development of antimicrobial compounds against E. faecalis.
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Affiliation(s)
- Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sagar Batra
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Pramodkumar P Gupta
- School of Biotechnology and Bioinformatics, DY Patil Deemed to be University, Navi Mumbai, India
| | - Mukesh Kumar
- School of Medicine, Case Western reserve University, Cleveland, Ohio
| | | | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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12
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Hamed RB, Gomez-Castellanos JR, Henry L, Warhaut S, Claridge TDW, Schofield CJ. Biocatalytic production of bicyclic β-lactams with three contiguous chiral centres using engineered crotonases. Commun Chem 2019; 2. [PMID: 31157308 PMCID: PMC6542682 DOI: 10.1038/s42004-018-0106-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
There is a need to develop asymmetric routes to functionalised β-lactams, which remain the most important group of antibacterials. Here we describe biocatalytic and protein engineering studies concerning carbapenem biosynthesis enzymes, aiming to enable stereoselective production of functionalised carbapenams with three contiguous chiral centres. Structurally-guided substitutions of wildtype carboxymethylproline synthases enable tuning of their C-N and C-C bond forming capacity to produce 5-carboxymethylproline derivatives substituted at C-4 and C-6, from amino acid aldehyde and malonyl-CoA derivatives. Use of tandem enzyme incubations comprising an engineered carboxymethylproline synthase and an alkylmalonyl-CoA forming enzyme (i.e. malonyl-CoA synthetase or crotonyl-CoA carboxylase reductase) can improve stereocontrol and expand the product range. Some of the prepared 4,6-disubstituted-5-carboxymethylproline derivatives are converted to bicyclic β-lactams by carbapenam synthetase catalysis. The results illustrate the utility of tandem enzyme systems involving engineered crotonases for asymmetric bicyclic β-lactam synthesis. Beta-lactams are important antiobiotics but synthesising functionalised derivatives in high enantiomeric purity can be challenging. Here malonyl-CoA derivatives are applied in an enantioselective multi-enzyme cascade, yielding beta-lactams bearing three contiguous chiral centres in high diastereomeric purity.
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Affiliation(s)
- Refaat B Hamed
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - J Ruben Gomez-Castellanos
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Luc Henry
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Sven Warhaut
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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