1
|
Brack Y, Sun C, Yi D, Bornscheuer UT. Systematic Analysis of the MIO-forming Residues of Aromatic Ammonia Lyases. Chembiochem 2024; 25:e202400016. [PMID: 38323706 DOI: 10.1002/cbic.202400016] [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: 01/05/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024]
Abstract
Aromatic ammonia lyases (AALs) and tyrosine/phenylalanine ammonia mutases (TAM/PAM) are 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO)-dependent enzymes. Usually, the MIO moiety is autocatalytically formed from the tripeptide Ala-Ser-Gly (ASG) and acts as an electrophile during the enzymatic reaction. However, the MIO-forming residues (ASG) have some diversity in this enzyme class. In this work, a systematic investigation on the variety of MIO-forming residues was carried out using in-depth sequence analyses. Several protein clusters of AAL-like enzymes with unusual MIO-forming residues such as ACG, TSG, SSG, and CSG were identified, including two novel histidine ammonia lyases and one PAM with CSG and TSG residues, respectively, as well as three novel ergothioneine trimethylammonia lyases without MIO motif. The mutagenesis of common MIO-groups confirmed the function of these MIO variants, which provides good starting points for future functional prediction and mutagenesis research of AALs.
Collapse
Affiliation(s)
- Yannik Brack
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
| | - Chenghai Sun
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
| | - Dong Yi
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
- National Key Laboratory of Lead Druggability Research, Research Center for Systems Biosynthesis, China State Institute of Pharmaceutical Industry, Gebaini Road 285, 201203, Shanghai, China
| | - Uwe T Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
| |
Collapse
|
2
|
Liu N, Feng J, Chen X, Luo Y, Lv T, Wu Q, Zhu D. Reshaping the Substrate Binding Pocket of β-Amino Acid Dehydrogenase for the Synthesis of Aromatic β-Amino Acids. Org Lett 2023; 25:8469-8473. [PMID: 37972311 DOI: 10.1021/acs.orglett.3c03366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
By reshaping the substrate-binding pocket of β-amino acid dehydrogenase (β-AADH), some variants were obtained with up to 2560-fold enhanced activity toward the model substrates (S)-β-homophenylalanine and (R)-β-phenylalanine. A few aromatic β-amino acids were prepared with >99% ee and high isolated yields via either kinetic resolution of racemates or reductive amination of the corresponding β-keto acids. This work expands the catalytic capability of β-AADHs and highlights their practical application in the synthesis of pharmaceutically relevant β-amino acids.
Collapse
Affiliation(s)
- Na Liu
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jinhui Feng
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xi Chen
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yuyang Luo
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- School of Biotechnology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tong Lv
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qiaqing Wu
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dunming Zhu
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| |
Collapse
|
3
|
Genchi G, Lauria G, Catalano A, Carocci A, Sinicropi MS. Prevalence of Cobalt in the Environment and Its Role in Biological Processes. BIOLOGY 2023; 12:1335. [PMID: 37887045 PMCID: PMC10604320 DOI: 10.3390/biology12101335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/08/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023]
Abstract
Cobalt (Co) is an essential trace element for humans and other animals, but high doses can be harmful to human health. It is present in some foods such as green vegetables, various spices, meat, milk products, seafood, and eggs, and in drinking water. Co is necessary for the metabolism of human beings and animals due to its key role in the formation of vitamin B12, also known as cobalamin, the biological reservoir of Co. In high concentrations, Co may cause some health issues such as vomiting, nausea, diarrhea, bleeding, low blood pressure, heart diseases, thyroid damage, hair loss, bone defects, and the inhibition of some enzyme activities. Conversely, Co deficiency can lead to anorexia, chronic swelling, and detrimental anemia. Co nanoparticles have different and various biomedical applications thanks to their antioxidant, antimicrobial, anticancer, and antidiabetic properties. In addition, Co and cobalt oxide nanoparticles can be used in lithium-ion batteries, as a catalyst, a carrier for targeted drug delivery, a gas sensor, an electronic thin film, and in energy storage. Accumulation of Co in agriculture and humans, due to natural and anthropogenic factors, represents a global problem affecting water quality and human and animal health. Besides the common chelating agents used for Co intoxication, phytoremediation is an interesting environmental technology for cleaning up soil contaminated with Co. The occurrence of Co in the environment is discussed and its involvement in biological processes is underlined. Toxicological aspects related to Co are also examined in this review.
Collapse
Affiliation(s)
- Giuseppe Genchi
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria, Arcavacata di Rende, 87036 Cosenza, Italy; (G.G.); (G.L.); (M.S.S.)
| | - Graziantonio Lauria
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria, Arcavacata di Rende, 87036 Cosenza, Italy; (G.G.); (G.L.); (M.S.S.)
| | - Alessia Catalano
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “A. Moro”, 70125 Bari, Italy;
| | - Alessia Carocci
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “A. Moro”, 70125 Bari, Italy;
| | - Maria Stefania Sinicropi
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria, Arcavacata di Rende, 87036 Cosenza, Italy; (G.G.); (G.L.); (M.S.S.)
| |
Collapse
|
4
|
Adak S, Ye N, Calderone LA, Schäfer RJB, Lukowski AL, Pandelia ME, Drennan CL, Moore BS. Oxidative rearrangement of tryptophan to indole nitrile by a single diiron enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551874. [PMID: 37577561 PMCID: PMC10418191 DOI: 10.1101/2023.08.03.551874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Nitriles are uncommon in nature and are typically constructed from oximes via the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third strategy of nitrile biosynthesis featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the 'eagle-killing' neurotoxin, aetokthonotoxin, AetD converts the alanyl side chain of 5,7-dibromo-L-tryptophan to a nitrile. Employing a combination of structural, biochemical, and biophysical techniques, we characterized AetD as a non-heme diiron enzyme that belongs to the emerging Heme Oxygenase-like Diiron Oxidase and Oxygenase (HDO) superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation that we propose proceeds via an aziridine intermediate. Our work presents a new paradigm for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other HDO enzymes.
Collapse
Affiliation(s)
- Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Naike Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Logan A. Calderone
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Rebecca J. B. Schäfer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - April L. Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, United States
| |
Collapse
|
5
|
Chen K, Zeng Q, Xie L, Xue Z, Wang J, Xu Y. Functional-group translocation of cyano groups by reversible C-H sampling. Nature 2023; 620:1007-1012. [PMID: 37364765 DOI: 10.1038/s41586-023-06347-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Chemical transformations that introduce, remove or manipulate functional groups are ubiquitous in synthetic chemistry1. Unlike conventional functional-group interconversion reactions that swap one functionality for another, transformations that alter solely the location of functional groups are far less explored. Here, by photocatalytic, reversible C-H sampling, we report a functional-group translocation reaction of cyano (CN) groups in common nitriles, allowing for the direct positional exchange between a CN group and an unactivated C-H bond. The reaction shows high fidelity for 1,4-CN translocation, frequently contrary to inherent site selectivity in conventional C-H functionalizations. We also report the direct transannular CN translocation of cyclic systems, providing access to valuable structures that are non-trivial to obtain by other methods. Making use of the synthetic versatility of CN and a key CN translocation step, we showcase concise syntheses of building blocks of bioactive molecules. Furthermore, the combination of C-H cyanation and CN translocation allows access to unconventional C-H derivatives. Overall, the reported reaction represents a way to achieve site-selective C-H transformation reactions without requiring a site-selective C-H cleavage step.
Collapse
Affiliation(s)
- Ken Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Qingrui Zeng
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Longhuan Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Zisheng Xue
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jianbo Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yan Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| |
Collapse
|
6
|
Kim W, Kim M, Park W. Unlocking the mystery of lysine toxicity on Microcystis aeruginosa. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130932. [PMID: 36860069 DOI: 10.1016/j.jhazmat.2023.130932] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Lysine toxicity on certain groups of bacterial cells has been recognized for many years, but the detailed molecular mechanisms that drive this phenomenon have not been elucidated. Many cyanobacteria including Microcystis aeruginosa cannot efficiently export and degrade lysine, although they have evolved to maintain a single copy of the lysine uptake system through which arginine or ornithine can also be transported into the cytoplasm. Autoradiographic analysis using 14C-l-lysine confirmed that lysine was competitively uptaken into cells with arginine or ornithine, which explained the arginine or ornithine-mediated alleviation of lysine toxicity in M. aeruginosa. A relatively non-specific MurE amino acid ligase could incorporate l-lysine into the 3rd position of UDP-N-acetylmuramyl-tripeptide by replacing meso-diaminopimelic acid during the stepwise addition of amino acids on peptidoglycan (PG) biosynthesis. However, further transpeptidation was blocked because lysine substitution at the pentapeptide of the cell wall inhibited the activity of transpeptidases. The leaky PG structure caused irreversible damage to the photosynthetic system and membrane integrity. Collectively, our results suggest that a lysine-mediated coarse-grained PG network and the absence of concrete septal PG lead to the death of slow-growing cyanobacteria.
Collapse
Affiliation(s)
- Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea.
| |
Collapse
|
7
|
Luo X, Wang X, Zhang L, Du A, Deng Z, Jiang M, He X. Importance of aspartic acid side chain carboxylate-arginine interaction in substrate selection of arginine 2,3-aminomutase BlsG. Protein Sci 2023; 32:e4584. [PMID: 36721314 PMCID: PMC9926467 DOI: 10.1002/pro.4584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/02/2023]
Abstract
The fungicide nucleoside blasticidin S features a β-arginine, a moiety seldom revealed in the structure of natural products. BlsG, a radical SAM arginine-2,3-aminomutase from the blasticidin S biosynthetic pathway, displayed promiscuous activity to three basic amino acids. Here in this study, we demonstrated that BlsG showed high preference toward its natural substrate arginine. The combined structural modeling, steady-state kinetics, and mutational analyses lead to the detailed understanding of the substrate recognition of BlsG. A single mutation of T340D changed the substrate preference of BlsG leading to a little more preference to lysine than arginine. On the basis of our understanding of the substrate selection of BlsG and bioinformatic analysis, we propose that the D…D motif locationally corresponding to D293 and D330 of KAM is characteristic of lysine 2,3-aminomutase while the corresponding D…T motif is characteristic of arginine 2,3-aminomutase. The study may provide a simple way to discern the arginine 2,3-aminomutase and thus lead to the discovery of new natural compounds with β-arginine moiety.
Collapse
Affiliation(s)
- Xiangkun Luo
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xiankun Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Lina Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Aiqin Du
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| |
Collapse
|
8
|
Li Y, Handunneththige S, Xiong J, Guo Y, Talipov MR, Wang D. Direct Activation of the C(sp 3)-NH 2 Bond of Primary Aliphatic Alkylamines by a High-Valent Co III,IV2(μ-O) 2 Diamond Core Complex. J Am Chem Soc 2023; 145:2690-2697. [PMID: 36689463 PMCID: PMC9976198 DOI: 10.1021/jacs.2c13199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Aliphatic alkylamines are abundant feedstock and versatile building blocks for many organic transformations. While remarkable progress has been made to construct C-N bonds on aliphatic and aromatic carbon centers, the activation and functionalization of C(sp3)-NH2 bonds in primary alkylamines remain a challenging process. In the present work, we discovered an unprecedented method to directly activate the C(sp3)-NH2 bond of primary alkylamines by a high-valent dinuclear CoIII,IV2(μ-O)2 diamond core complex. This reaction results in the installation of other functional groups such as halides and alkenes onto the α-carbon center concomitant with the 2-e- oxidation of the nitrogen atom on the amino group to form NH2OH. These results shed light on future development enabling versatile functionalization of primary alkylamines based on the dinuclear cobalt system. Moreover, our work suggests that a related high-valent copper-oxo intermediate is likely generated in the ammonia monooxygenase catalytic cycle to affect the oxidation of NH3 to NH2OH.
Collapse
Affiliation(s)
- Yan Li
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana; Missoula, MT 59812, United States
| | - Suhashini Handunneththige
- Department of Chemistry and Biochemistry, New Mexico State University; Las Cruces, NM 88003, United States
| | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University; Pittsburgh, PA 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University; Pittsburgh, PA 15213, United States,Corresponding Author:; ;
| | - Marat R. Talipov
- Department of Chemistry and Biochemistry, New Mexico State University; Las Cruces, NM 88003, United States,Corresponding Author:; ;
| | - Dong Wang
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana; Missoula, MT 59812, United States,Corresponding Author:; ;
| |
Collapse
|
9
|
Merging enzymatic and synthetic chemistry with computational synthesis planning. Nat Commun 2022; 13:7747. [PMID: 36517480 PMCID: PMC9750992 DOI: 10.1038/s41467-022-35422-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
Synthesis planning programs trained on chemical reaction data can design efficient routes to new molecules of interest, but are limited in their ability to leverage rare chemical transformations. This challenge is acute for enzymatic reactions, which are valuable due to their selectivity and sustainability but are few in number. We report a retrosynthetic search algorithm using two neural network models for retrosynthesis-one covering 7984 enzymatic transformations and one 163,723 synthetic transformations-that balances the exploration of enzymatic and synthetic reactions to identify hybrid synthesis plans. This approach extends the space of retrosynthetic moves by thousands of uniquely enzymatic one-step transformations, discovers routes to molecules for which synthetic or enzymatic searches find none, and designs shorter routes for others. Application to (-)-Δ9 tetrahydrocannabinol (THC) (dronabinol) and R,R-formoterol (arformoterol) illustrates how our strategy facilitates the replacement of metal catalysis, high step counts, or costly enantiomeric resolution with more elegant hybrid proposals.
Collapse
|
10
|
Niehs SP, Scherlach K, Dose B, Uzum Z, Stinear TP, Pidot SJ, Hertweck C. A highly conserved gene locus in endofungal bacteria codes for the biosynthesis of symbiosis-specific cyclopeptides. PNAS NEXUS 2022; 1:pgac152. [PMID: 36714835 PMCID: PMC9802438 DOI: 10.1093/pnasnexus/pgac152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/30/2022] [Accepted: 08/03/2022] [Indexed: 02/01/2023]
Abstract
The tight association of the pathogenic fungus Rhizopus microsporus and its toxin-producing, bacterial endosymbionts (Mycetohabitans spp.) is distributed worldwide and has significance for agriculture, food production, and human health. Intriguingly, the endofungal bacteria are essential for the propagation of the fungal host. Yet, little is known about chemical mediators fostering the symbiosis, and universal metabolites that support the mutualistic relationship have remained elusive. Here, we describe the discovery of a complex of specialized metabolites produced by endofungal bacteria under symbiotic conditions. Through full genome sequencing and comparative genomics of eight endofungal symbiont strains from geographically distant regions, we discovered a conserved gene locus (hab) for a nonribosomal peptide synthetase as a unifying trait. Bioinformatics analyses, targeted gene deletions, and chemical profiling uncovered unprecedented depsipeptides (habitasporins) whose structures were fully elucidated. Computational network analysis and labeling experiments granted insight into the biosynthesis of their nonproteinogenic building blocks (pipecolic acid and β-phenylalanine). Deletion of the hab gene locus was shown to impair the ability of the bacteria to enter their fungal host. Our study unveils a common principle of the endosymbiotic lifestyle of Mycetohabitans species and expands the repertoire of characterized chemical mediators of a globally occurring mutualistic association.
Collapse
Affiliation(s)
| | | | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, 3000, Australia
| | | |
Collapse
|
11
|
Tunçkanat T, Gendron A, Sadler Z, Neitz A, Byquist S, Lie TJ, Allen KD. Lysine 2,3-Aminomutase and a Newly Discovered Glutamate 2,3-Aminomutase Produce β-Amino Acids Involved in Salt Tolerance in Methanogenic Archaea. Biochemistry 2022; 61:1077-1090. [PMID: 35544775 DOI: 10.1021/acs.biochem.2c00014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many methanogenic archaea synthesize β-amino acids as osmolytes that allow survival in high salinity environments. Here, we investigated the radical S-adenosylmethionine (SAM) aminomutases involved in the biosynthesis of Nε-acetyl-β-lysine and β-glutamate in Methanococcus maripaludis C7. Lysine 2,3-aminomutase (KAM), encoded by MmarC7_0106, was overexpressed and purified from Escherichia coli, followed by biochemical characterization. In the presence of l-lysine, SAM, and dithionite, this archaeal KAM had a kcat = 14.3 s-1 and a Km = 19.2 mM. The product was shown to be 3(S)-β-lysine, which is like the well-characterized Clostridium KAM as opposed to the E. coli KAM that produces 3(R)-β-lysine. We further describe the function of MmarC7_1783, a putative radical SAM aminomutase with a ∼160 amino acid extension at its N-terminus. Bioinformatic analysis of the possible substrate-binding residues suggested a function as glutamate 2,3-aminomutase, which was confirmed here through heterologous expression in a methanogen followed by detection of β-glutamate in cell extracts. β-Glutamate has been known to serve as an osmolyte in select methanogens for a long time, but its biosynthetic origin remained unknown until now. Thus, this study defines the biosynthetic routes for β-lysine and β-glutamate in M. maripaludis and expands the importance and diversity of radical SAM enzymes in all domains of life.
Collapse
Affiliation(s)
- Taylan Tunçkanat
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Aleksei Gendron
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Zoie Sadler
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Alex Neitz
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, United States
| | - Sarah Byquist
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, United States
| | - Thomas J Lie
- Department of Microbiology, University of Washington, Seattle, Washington 98195, United States
| | - Kylie D Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| |
Collapse
|
12
|
Chen JR, Ke TX, Frey PA, Ke SC. Electron Spin Echo Envelope Modulation Spectroscopy Reveals How Adenosylcobalamin-Dependent Lysine 5,6-Aminomutase Positions the Radical Pair Intermediates and Modulates Their Stabilities for Efficient Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun-Ru Chen
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Ting-Xi Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Perry A. Frey
- Department of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53726, United States
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| |
Collapse
|
13
|
Hall M. Enzymatic strategies for asymmetric synthesis. RSC Chem Biol 2021; 2:958-989. [PMID: 34458820 PMCID: PMC8341948 DOI: 10.1039/d1cb00080b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Enzymes, at the turn of the 21st century, are gaining a momentum. Especially in the field of synthetic organic chemistry, a broad variety of biocatalysts are being applied in an increasing number of processes running at up to industrial scale. In addition to the advantages of employing enzymes under environmentally friendly reaction conditions, synthetic chemists are recognizing the value of enzymes connected to the exquisite selectivity of these natural (or engineered) catalysts. The use of hydrolases in enantioselective protocols paved the way to the application of enzymes in asymmetric synthesis, in particular in the context of biocatalytic (dynamic) kinetic resolutions. After two decades of impressive development, the field is now mature to propose a panel of catalytically diverse enzymes for (i) stereoselective reactions with prochiral compounds, such as double bond reduction and bond forming reactions, (ii) formal enantioselective replacement of one of two enantiotopic groups of prochiral substrates, as well as (iii) atroposelective reactions with noncentrally chiral compounds. In this review, the major enzymatic strategies broadly applicable in the asymmetric synthesis of optically pure chiral compounds are presented, with a focus on the reactions developed within the past decade.
Collapse
Affiliation(s)
- Mélanie Hall
- Institute of Chemistry, University of Graz Heinrichstrasse 28 8010 Graz Austria
- Field of Excellence BioHealth - University of Graz Austria
| |
Collapse
|
14
|
Varga A, Csuka P, Sonesouphap O, Bánóczi G, Toşa MI, Katona G, Molnár Z, Bencze LC, Poppe L, Paizs C. A novel phenylalanine ammonia-lyase from Pseudozyma antarctica for stereoselective biotransformations of unnatural amino acids. Catal Today 2021. [DOI: 10.1016/j.cattod.2020.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
15
|
Groß S, Schnell B, Haack PA, Auerbach D, Müller R. In vivo and in vitro reconstitution of unique key steps in cystobactamid antibiotic biosynthesis. Nat Commun 2021; 12:1696. [PMID: 33727542 PMCID: PMC7966384 DOI: 10.1038/s41467-021-21848-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/13/2021] [Indexed: 01/31/2023] Open
Abstract
Cystobactamids are myxobacteria-derived topoisomerase inhibitors with potent anti-Gram-negative activity. They are formed by a non-ribosomal peptide synthetase (NRPS) and consist of tailored para-aminobenzoic acids, connected by a unique α-methoxy-L-isoasparagine or a β-methoxy-L-asparagine linker moiety. We describe the heterologous expression of the cystobactamid biosynthetic gene cluster (BGC) in Myxococcus xanthus. Targeted gene deletions produce several unnatural cystobactamids. Using in vitro experiments, we reconstitute the key biosynthetic steps of linker formation and shuttling via CysB to the NRPS. The biosynthetic logic involves a previously uncharacterized bifunctional domain found in the stand-alone NRPS module CysH, albicidin biosynthesis and numerous BGCs of unknown natural products. This domain performs either an aminomutase (AM) or an amide dehydratase (DH) type of reaction, depending on the activity of CysJ which hydroxylates CysH-bound L-asparagine. Furthermore, CysQ O-methylates hydroxyl-L-(iso)asparagine only in the presence of the AMDH domain. Taken together, these findings provide direct evidence for unique steps in cystobactamid biosynthesis.
Collapse
Affiliation(s)
- Sebastian Groß
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Bastien Schnell
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Patrick A. Haack
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - David Auerbach
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| |
Collapse
|
16
|
Mays ZJS, Nair NU. A quantitative model for metabolic intervention using gut microbes. Biotechnol Prog 2021; 37:e3125. [PMID: 33426814 DOI: 10.1002/btpr.3125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/08/2022]
Abstract
As medicine shifts toward precision-based and personalized therapeutics, utilizing more complex biomolecules to treat increasingly difficult and rare conditions, microorganisms provide an avenue for realizing the production and processing necessary for novel drug pipelines. More so, probiotic microbes can be co-opted to deliver therapeutics by oral administration as living drugs, able to survive and safely transit the digestive tract. As living therapeutics are in their nascency, traditional pharmacokinetic-pharmacodynamic (PK-PD) models for evaluating drug candidates are not appropriate for this novel platform. Using a living therapeutic in late-stage clinical development for phenylketonuria (PKU) as a case study, we adapt traditional oral drug delivery models to properly evaluate and inform the engineering of living therapeutics. We develop the adapted for living therapeutics compartmental absorption and transit (ALT-CAT) model to provide metrics for drug efficacy across nine age groups of PKU patients and evaluate model parameters that are influenced by patient physiology, microbe selection and therapeutic production, and dosing formulations. In particular, the ALT-CAT model describes the mathematical framework to model the behavior of orally delivered engineered bacteria that act as living therapeutics by adapting similar methods that have been developed and widely-used for small molecular drug delivery and absorption.
Collapse
Affiliation(s)
- Zachary J S Mays
- Department of Chemical & Biological Engineering, Tufts University, Medford, Massachusetts, USA
| | - Nikhil U Nair
- Department of Chemical & Biological Engineering, Tufts University, Medford, Massachusetts, USA
| |
Collapse
|
17
|
Chen M, Liu CT, Tang Y. Discovery and Biocatalytic Application of a PLP-Dependent Amino Acid γ-Substitution Enzyme That Catalyzes C-C Bond Formation. J Am Chem Soc 2020; 142:10506-10515. [PMID: 32434326 DOI: 10.1021/jacs.0c03535] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes can catalyze transformations of l-amino acids at α, β, and γ positions. These enzymes are frequently involved in the biosynthesis of nonproteinogenic amino acids as building blocks of natural products and are attractive biocatalysts. Here, we report the discovery of a two-step enzymatic synthesis of (2S,6S)-6-methyl pipecolate 1, from the biosynthetic pathway of citrinadin. The key enzyme CndF is PLP-dependent and catalyzes the synthesis of (S)-2-amino-6-oxoheptanoate 3 that is in equilibrium with the cyclic Schiff base. The second enzyme CndE is a stereoselective imine reductase that gives 1. Biochemical characterization of CndF showed this enzyme performs γ-elimination of O-acetyl-l-homoserine to generate the vinylglycine ketimine, which is subjected to nucleophilic attack by acetoacetate to form the new Cγ-Cδ bond in 3 and complete the γ-substitution reaction. CndF displays promiscuity toward different β-keto carboxylate and esters. With use of an Aspergillus strain expressing CndF and CndE, feeding various alkyl-β-keto esters led to the biosynthesis of 6-substituted l-pipecolates. The discovery of CndF expands the repertoire of reactions that can be catalyzed by PLP-dependent enzymes.
Collapse
Affiliation(s)
- Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Chun-Ting Liu
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| |
Collapse
|
18
|
Song W, Chen X, Wu J, Xu J, Zhang W, Liu J, Chen J, Liu L. Biocatalytic derivatization of proteinogenic amino acids for fine chemicals. Biotechnol Adv 2020; 40:107496. [DOI: 10.1016/j.biotechadv.2019.107496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 01/09/2023]
|
19
|
The production of L- and D-phenylalanines using engineered phenylalanine ammonia lyases from Petroselinum crispum. Sci Rep 2019; 9:20123. [PMID: 31882791 PMCID: PMC6934771 DOI: 10.1038/s41598-019-56554-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022] Open
Abstract
The biocatalytic synthesis of l- and d-phenylalanine analogues of high synthetic value have been developed using as biocatalysts mutant variants of phenylalanine ammonia lyase from Petroselinum crispum (PcPAL), specifically tailored towards mono-substituted phenylalanine and cinnamic acid substrates. The catalytic performance of the engineered PcPAL variants was optimized within the ammonia elimination and ammonia addition reactions, focusing on the effect of substrate concentration, biocatalyst:substrate ratio, reaction buffer and reaction time, on the conversion and enantiomeric excess values. The optimal conditions provided an efficient preparative scale biocatalytic procedure of valuable phenylalanines, such as (S)-m-methoxyphenylalanine (Y = 40%, ee > 99%), (S)-p-bromophenylalanine (Y = 82%, ee > 99%), (S)-m-(trifluoromethyl)phenylalanine (Y = 26%, ee > 99%), (R)-p-methylphenylalanine, (Y = 49%, ee = 95%) and (R)-m-(trifluoromethyl)phenylalanine (Y = 34%, ee = 93%).
Collapse
|
20
|
Investigation into isomerization reaction of phenylalanine aminomutase from Pantoea agglomerans. Enzyme Microb Technol 2019; 132:109428. [PMID: 31731949 DOI: 10.1016/j.enzmictec.2019.109428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/30/2019] [Accepted: 09/10/2019] [Indexed: 11/23/2022]
Abstract
Phenylalanine aminomutase (PaPAM) from Pantoea agglomerans is a member of the MIO (4-methylene-imidazol-5-one) family of enzymes, which isomerizes α-phenylalanine to β-phenylalanine, and could be used to synthesize unnatural β-arylalanine. However, the mechanism of isomerization reaction is not clear. To investigate the mechanism, the gene (pam), which encodes PaPAM, was first expressed in E.coli, and recombinant PaPAM was prepared using affinity chromatography. Then, 15N-(2S)-α-phenylalanine, (2S)-(3-2H2)-α-phenylalanine and (2S,3S)-[2,3-2H2]-α-phenylalanine were used as substrates to analyze the mechanism of isomerization reaction. The results of MS and NMR showed that the isomerization reaction was performed through the intramolecular exchange of NH2 with pro-3R hydrogen of α-phenylalanine. The PaPAM shuttles the α-NH2 of α-phenylalanine to β site to replace the pro-3R hydrogen. Simultaneously, the pro-3R hydrogen is shifted to α site to produce β-phenylalanine. Furthermore, a key residue, Phe at position 455 in the active site, was determined to control the exchange way using molecular docking and sequence alignment of MIO family enzymes. The results indicated that the key 455 Phe residue is involved in changing the binding orientation of the carboxyl group of the intermediate trans-cinnamic acid to control the NH2-H pair exchange.
Collapse
|
21
|
Shee PK, Ratnayake ND, Walter T, Goethe O, Onyeozili EN, Walker KD. Exploring the Scope of an α/β-Aminomutase for the Amination of Cinnamate Epoxides to Arylserines and Arylisoserines. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01557] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | | | | | - Edith Ndubuaku Onyeozili
- Department of Chemistry, Florida Agricultural & Mechanical University, Tallahassee, Florida 32307, United States
| | | |
Collapse
|
22
|
Sheldon RA, Brady D. Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis. CHEMSUSCHEM 2019; 12:2859-2881. [PMID: 30938093 DOI: 10.1002/cssc.201900351] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 05/21/2023]
Abstract
This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new-to-nature biocatalytic reactions.
Collapse
Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
| |
Collapse
|
23
|
Bogart JW, Bowers AA. Dehydroamino acids: chemical multi-tools for late-stage diversification. Org Biomol Chem 2019; 17:3653-3669. [PMID: 30849157 PMCID: PMC6637761 DOI: 10.1039/c8ob03155j] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
α,β-Dehydroamino acids (dhAAs) are noncanonical amino acids that are found in a wide array of natural products and can be easily installed into peptides and proteins. dhAAs exhibit remarkable synthetic flexibility, readily undergoing a number of reactions, such as polar and single-electron additions, transition metal catalyzed cross-couplings, and cycloadditions. Because of the relatively mild conditions required for many of these reactions, dhAAs are increasingly being used as orthogonal chemical handles for late-stage modification of biomolecules. Still, only a fraction of the chemical reactivity of dhAAs has been exploited in such biorthogonal applications. Herein, we provide an overview of the broad spectrum of chemical reactivity of dhAAs, with special emphasis on recent efforts to adapt such transformations for biomolecules such as natural products, peptides, and proteins. We also discuss examples of enzymes from natural product biosynthetic pathways that have been found to catalyze many similar reactions; these enzymes provide mild, regio- and stereoselective, biocatalytic alternatives for future development. We anticipate that the continued investigation of the innate reactivity of dhAAs will furnish a diverse portfolio dhAA-based chemistries for use in chemical biology and drug discovery.
Collapse
Affiliation(s)
- Jonathan W Bogart
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | | |
Collapse
|
24
|
Attanayake G, Walter T, Walker KD. Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define Its Mutase and Lyase Activities. Biochemistry 2018; 57:3503-3514. [PMID: 29757631 DOI: 10.1021/acs.biochem.8b00269] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-directed mutations and substrate analogues were used to gain insights into the branch-point reaction of the 3,5-dihydro-5-methylidene-4 H-imidazol-4-one (MIO)-tyrosine aminomutase from Oryza sativa ( OsTAM). Exchanging the active residues of OsTAM (Y125C/N446K) for those in a phenylalanine aminomutase TcPAM altered its substrate specificity from tyrosine to phenylalanine. The aminomutase mechanism of OsTAM surprisingly changed almost exclusively to that of an ammonia lyase making cinnamic acid (>95%) over β-phenylalanine [Walter, T., et al. (2016) Biochemistry 55, 3497-3503]. We hypothesized that the missing electronics or sterics on the aryl ring of the phenylalanine substrate, compared with the sizable electron-donating hydroxyl of the natural tyrosine substrate, influenced the unexpected lyase reactivity of the OsTAM mutant. The double mutant was incubated with 16 α-phenylalanine substituent analogues of varying electronic strengths and sterics. The mutant converted each analogue principally to its acrylate with ∼50% conversion of the p-Br substrate, making only a small amount of the β-amino acid. The inner loop structure over the entrance to the active site was also mutated to assess how the lyase and mutase activities are affected. An OsTAM loop mutant, matching the loop residues of TcPAM, still chiefly made >95% of the acrylate from each substrate. A combined active site:loop mutant was most reactive but remained a lyase, making 10-fold more acrylates than other mutants did. While mutations within the active site changed the substrate specificity of OsTAM, continued exploration is needed to fully understand the interplay among the inner loop, the substrate, and the active site in defining the mutase and lyase activities.
Collapse
Affiliation(s)
- Gayanthi Attanayake
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Tyler Walter
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Kevin D Walker
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States.,Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| |
Collapse
|
25
|
Zhu L, Ge F, Li W, Song P, Tang H, Tao Y, Liu Y, Du G. One step synthesis of unnatural β-arylalanines using mutant phenylalanine aminomutase from Taxus chinensis with high β-regioselectivity. Enzyme Microb Technol 2018; 114:22-28. [PMID: 29685349 DOI: 10.1016/j.enzmictec.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/18/2018] [Accepted: 03/20/2018] [Indexed: 11/30/2022]
Abstract
Phenylalanine aminomutase (TcPAM) from Taxus chinensis catalyzes the regioselective hydroamination of trans-cinnamic acid (t-CA) to yield β-phe. However, the final product mixture consists of both α- and β-phe owing to low regioselectivity, which is still a challenge to synthesize highly pure β-phe. Therefore, a modified TcPAM with high β-selectivity is expected. Based on the catalytic mechanism and structure, two amino acid residues (Asn458 and Leu108) in active sites were identified as the key residues for controlling the regioselective hydroamination of t-CA and as promising candidates for mutagenesis to enhance β-selectivity and decrease α-selectivity. The Asn458 and Leu108 residues were mutated to yield variant TcPAM-Asn458Phe/Leu108Glu, and the β-selectivity was approximately 5.2-fold higher than that of wild-type TcPAM, while α-selectivity decreased to 68%, and the percentage of β-phe in the product mixture increased from 42% to 83%. In addition, the mutant was applied to synthesize β-arylalanines using substituent t-CA as a substrate. The regioselectivity was also affected by the substituent groups at the phenyl ring of t-CA with respect to their electronic properties and position, and the 4-methoxy and methyl substituent t-CA were transferred into β-arylalanines. The conversion rate also exceeded 90%. In summary, the engineered TcPAM proved to be useful for one-step asymmetric amination of t-CA and its derivatives to synthesize highly pure β-arylalanines.
Collapse
Affiliation(s)
- Longbao Zhu
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Fei Ge
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Wanzhen Li
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Ping Song
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Hongjin Tang
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Yugui Tao
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China.
| | - Yi Liu
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, People's Republic of China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| |
Collapse
|
26
|
Csuka P, Juhász V, Kohári S, Filip A, Varga A, Sátorhelyi P, Bencze LC, Barton H, Paizs C, Poppe L. Pseudomonas fluorescensStrain R124 Encodes Three Different MIO Enzymes. Chembiochem 2018; 19:411-418. [DOI: 10.1002/cbic.201700530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Pál Csuka
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - Vivien Juhász
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - Szabolcs Kohári
- Fermentia Microbiological Ltd; Berlini út 47-49 1049 Budapest Hungary
| | - Alina Filip
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Andrea Varga
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Péter Sátorhelyi
- Fermentia Microbiological Ltd; Berlini út 47-49 1049 Budapest Hungary
| | - László Csaba Bencze
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Hazel Barton
- Department of Biology; The University of Akron; ASEC West Tower 178 Akron OH 44325 USA
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - László Poppe
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
- SynBiocat Ltd; Szilasliget u. 3 1172 Budapest Hungary
| |
Collapse
|
27
|
Xue YP, Cao CH, Zheng YG. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev 2018; 47:1516-1561. [DOI: 10.1039/c7cs00253j] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.
Collapse
Affiliation(s)
- Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Cheng-Hao Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| |
Collapse
|
28
|
Parmeggiani F, Weise NJ, Ahmed ST, Turner NJ. Synthetic and Therapeutic Applications of Ammonia-lyases and Aminomutases. Chem Rev 2017; 118:73-118. [DOI: 10.1021/acs.chemrev.6b00824] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fabio Parmeggiani
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Weise
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Syed T. Ahmed
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| |
Collapse
|
29
|
Lo HH, Lin HH, Maity AN, Ke SC. The molecular mechanism of the open–closed protein conformational cycle transitions and coupled substrate binding, activation and product release events in lysine 5,6-aminomutase. Chem Commun (Camb) 2016; 52:6399-402. [DOI: 10.1039/c6cc01888b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The contributions of Lys370α and Asp298α to the critical Co–C bond cleavage trigger and open–closed cycle transitions of lysine 5,6-aminomutase.
Collapse
Affiliation(s)
- Hsin-Hsi Lo
- Physics Department
- National Dong Hwa University
- Hualien
- Taiwan 97401
| | - Hsin-Hua Lin
- Physics Department
- National Dong Hwa University
- Hualien
- Taiwan 97401
| | | | - Shyue-Chu Ke
- Physics Department
- National Dong Hwa University
- Hualien
- Taiwan 97401
| |
Collapse
|
30
|
Otzen M, Crismaru CG, Postema CP, Wijma HJ, Heberling MM, Szymanski W, de Wildeman S, Janssen DB. Metabolism of β-valine via a CoA-dependent ammonia lyase pathway. Appl Microbiol Biotechnol 2015; 99:8987-98. [PMID: 26004802 PMCID: PMC4619459 DOI: 10.1007/s00253-015-6551-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/24/2015] [Accepted: 03/17/2015] [Indexed: 11/30/2022]
Abstract
Pseudomonas species strain SBV1 can rapidly grow on medium containing β-valine as a sole nitrogen source. The tertiary amine feature of β-valine prevents direct deamination reactions catalyzed by aminotransferases, amino acid dehydrogenases, and amino acid oxidases. However, lyase- or aminomutase-mediated conversions would be possible. To identify enzymes involved in the degradation of β-valine, a PsSBV1 gene library was prepared and used to complement the β-valine growth deficiency of a closely related Pseudomonas strain. This resulted in the identification of a gene encoding β-valinyl-coenzyme A ligase (BvaA) and two genes encoding β-valinyl-CoA ammonia lyases (BvaB1 and BvaB2). The BvaA protein demonstrated high sequence identity to several known phenylacetate CoA ligases. Purified BvaA enzyme did not convert phenyl acetic acid but was able to activate β-valine in an adenosine triphosphate (ATP)- and CoA-dependent manner. The substrate range of the enzyme appears to be narrow, converting only β-valine and to a lesser extent, 3-aminobutyrate and β-alanine. Characterization of BvaB1 and BvaB2 revealed that both enzymes were able to deaminate β-valinyl-CoA to produce 3-methylcrotonyl-CoA, a common intermediate in the leucine degradation pathway. Interestingly, BvaB1 and BvaB2 demonstrated no significant sequence identity to known CoA-dependent ammonia lyases, suggesting they belong to a new family of enzymes. BLAST searches revealed that BvaB1 and BvaB2 show high sequence identity to each other and to several enoyl-CoA hydratases, a class of enzymes that catalyze a similar reaction with water instead of amine as the leaving group.
Collapse
Affiliation(s)
- Marleen Otzen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Ciprian G Crismaru
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Christiaan P Postema
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Hein J Wijma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Matthew M Heberling
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Wiktor Szymanski
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Stefaan de Wildeman
- DSM Pharmaceutical Products, Geleen, The Netherlands.,BioBased Materials, Faculty of Humanities and Sciences, Maastricht University, Chemelot, The Netherlands
| | - Dick B Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
31
|
Maity AN, Lin HH, Chiang HS, Lo HH, Ke SC. Reaction of Pyridoxal-5′-phosphate-N-oxide with Lysine 5,6-Aminomutase: Enzyme Flexibility toward Cofactor Analog. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00671] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Hsin-Hua Lin
- Department
of Physics, National Dong Hwa University, Hualien, Taiwan 97401
| | | | - Hsin-Hsi Lo
- Department
of Physics, National Dong Hwa University, Hualien, Taiwan 97401
| | - Shyue-Chu Ke
- Department
of Physics, National Dong Hwa University, Hualien, Taiwan 97401
| |
Collapse
|
32
|
Zhang D, Chen X, Zhang R, Yao P, Wu Q, Zhu D. Development of β-Amino Acid Dehydrogenase for the Synthesis of β-Amino Acids via Reductive Amination of β-Keto Acids. ACS Catal 2015. [DOI: 10.1021/cs5017358] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dalong Zhang
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Xi Chen
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Rui Zhang
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| |
Collapse
|
33
|
Menon BRK, Menon N, Fisher K, Rigby SEJ, Leys D, Scrutton NS. Glutamate 338 is an electrostatic facilitator of C-Co bond breakage in a dynamic/electrostatic model of catalysis by ornithine aminomutase. FEBS J 2015; 282:1242-55. [PMID: 25627283 PMCID: PMC4413051 DOI: 10.1111/febs.13215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 01/04/2023]
Abstract
How cobalamin-dependent enzymes promote C–Co homolysis to initiate radical catalysis has been debated extensively. For the pyridoxal 5′-phosphate and cobalamin-dependent enzymes lysine 5,6-aminomutase and ornithine 4,5-aminomutase (OAM), large-scale re-orientation of the cobalamin-binding domain linked to C–Co bond breakage has been proposed. In these models, substrate binding triggers dynamic sampling of the B12-binding Rossmann domain to achieve a catalytically competent ‘closed’ conformational state. In ‘closed’ conformations of OAM, Glu338 is thought to facilitate C–Co bond breakage by close association with the cobalamin adenosyl group. We investigated this using stopped-flow continuous-wave photolysis, viscosity dependence kinetic measurements, and electron paramagnetic resonance spectroscopy of a series of Glu338 variants. We found that substrate-induced C–Co bond homolysis is compromised in Glu388 variant forms of OAM, although photolysis of the C–Co bond is not affected by the identity of residue 338. Electrostatic interactions of Glu338 with the 5′-deoxyadenosyl group of B12 potentiate C–Co bond homolysis in ‘closed’ conformations only; these conformations are unlocked by substrate binding. Our studies extend earlier models that identified a requirement for large-scale motion of the cobalamin domain. Our findings indicate that large-scale motion is required to pre-organize the active site by enabling transient formation of ‘closed’ conformations of OAM. In ‘closed’ conformations, Glu338 interacts with the 5′-deoxyadenosyl group of cobalamin. This interaction is required to potentiate C–Co homolysis, and is a crucial component of the approximately 1012 rate enhancement achieved by cobalamin-dependent enzymes for C–Co bond homolysis.
Collapse
Affiliation(s)
- Binuraj R K Menon
- Biotechnology and Biological Sciences Research Council/Engineering and Physical Sciences Research Council Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, UK
| | | | | | | | | | | |
Collapse
|
34
|
Maity AN, Chen YH, Ke SC. Large-scale domain motions and pyridoxal-5'-phosphate assisted radical catalysis in coenzyme B12-dependent aminomutases. Int J Mol Sci 2014; 15:3064-87. [PMID: 24562332 PMCID: PMC3958899 DOI: 10.3390/ijms15023064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/25/2013] [Accepted: 01/22/2014] [Indexed: 12/31/2022] Open
Abstract
Lysine 5,6-aminomutase (5,6-LAM) and ornithine 4,5-aminomutase (4,5-OAM) are two of the rare enzymes that use assistance of two vitamins as cofactors. These enzymes employ radical generating capability of coenzyme B12 (5'-deoxyadenosylcobalamin, dAdoCbl) and ability of pyridoxal-5'-phosphate (PLP, vitamin B6) to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form. In spite of all the similarities, these enzymes differ in substrate specificities. 4,5-OAM is highly specific for D-ornithine as a substrate while 5,6-LAM can accept D-lysine and L-β-lysine. This review focuses on recent computational, spectroscopic and structural studies of these enzymes and their implications on the related enzymes. Additionally, we also discuss the potential biosynthetic application of 5,6-LAM.
Collapse
Affiliation(s)
| | - Yung-Han Chen
- Physics Department, National Dong Hwa University, Hualien 97401, Taiwan.
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien 97401, Taiwan.
| |
Collapse
|
35
|
Walsh CT, O'Brien RV, Khosla C. Nonproteinogenic amino acid building blocks for nonribosomal peptide and hybrid polyketide scaffolds. Angew Chem Int Ed Engl 2013; 52:7098-124. [PMID: 23729217 PMCID: PMC4634941 DOI: 10.1002/anie.201208344] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Indexed: 12/24/2022]
Abstract
Freestanding nonproteinogenic amino acids have long been recognized for their antimetabolite properties and tendency to be uncovered to reactive functionalities by the catalytic action of target enzymes. By installing them regiospecifically into biogenic peptides and proteins, it may be possible to usher a new era at the interface between small molecule and large molecule medicinal chemistry. Site-selective protein functionalization offers uniquely attractive strategies for posttranslational modification of proteins. Last, but not least, many of the amino acids not selected by nature for protein incorporation offer rich architectural possibilities in the context of ribosomally derived polypeptides. This Review summarizes the biosynthetic routes to and metabolic logic for the major classes of the noncanonical amino acid building blocks that end up in both nonribosomal peptide frameworks and in hybrid nonribosomal peptide-polyketide scaffolds.
Collapse
Affiliation(s)
- Christopher T Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | | |
Collapse
|
36
|
Walsh CT, O'Brien RV, Khosla C. Nichtproteinogene Aminosäurebausteine für Peptidgerüste aus nichtribosomalen Peptiden und hybriden Polyketiden. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208344] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
37
|
Bartsch S, Wybenga GG, Jansen M, Heberling MM, Wu B, Dijkstra BW, Janssen DB. Redesign of a Phenylalanine Aminomutase into a Phenylalanine Ammonia Lyase. ChemCatChem 2013. [DOI: 10.1002/cctc.201200871] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
38
|
Heberling MM, Wu B, Bartsch S, Janssen DB. Priming ammonia lyases and aminomutases for industrial and therapeutic applications. Curr Opin Chem Biol 2013; 17:250-60. [PMID: 23557642 DOI: 10.1016/j.cbpa.2013.02.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/05/2013] [Indexed: 01/17/2023]
Abstract
Ammonia lyases (AL) and aminomutases (AM) are emerging in green synthetic routes to chiral amines and an AL is being explored as an enzyme therapeutic for treating phenylketonuria and cancer. Although the restricted substrate range of the wild-type enzymes limits their widespread application, the non-reliance on external cofactors and direct functionalization of an olefinic bond make ammonia lyases attractive biocatalysts for use in the synthesis of natural and non-natural amino acids, including β-amino acids. The approach of combining structure-guided enzyme engineering with efficient mutant library screening has extended the synthetic scope of these enzymes in recent years and has resolved important mechanistic issues for AMs and ALs, including those containing the MIO (4-methylideneimidazole-5-one) internal cofactor.
Collapse
Affiliation(s)
- Matthew M Heberling
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | | | | |
Collapse
|
39
|
New biocatalytic route for the production of enantioenriched β-alanine derivatives starting from 5- and 6-monosubstituted dihydrouracils. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.07.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
40
|
Biochemical properties and crystal structure of a β-phenylalanine aminotransferase from Variovorax paradoxus. Appl Environ Microbiol 2012; 79:185-95. [PMID: 23087034 DOI: 10.1128/aem.02525-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By selective enrichment, we isolated a bacterium that can use β-phenylalanine as a sole nitrogen source. It was identified by 16S rRNA gene sequencing as a strain of Variovorax paradoxus. Enzyme assays revealed an aminotransferase activity. Partial genome sequencing and screening of a cosmid DNA library resulted in the identification of a 1,302-bp aminotransferase gene, which encodes a 46,416-Da protein. The gene was cloned and overexpressed in Escherichia coli. The recombinant enzyme was purified and showed a specific activity of 17.5 U mg(-1) for (S)-β-phenylalanine at 30°C and 33 U mg(-1) at the optimum temperature of 55°C. The β-specific aminotransferase exhibits a broad substrate range, accepting ortho-, meta-, and para-substituted β-phenylalanine derivatives as amino donors and 2-oxoglutarate and pyruvate as amino acceptors. The enzyme is highly enantioselective toward (S)-β-phenylalanine (enantioselectivity [E], >100) and derivatives thereof with different substituents on the phenyl ring, allowing the kinetic resolution of various racemic β-amino acids to yield (R)-β-amino acids with >95% enantiomeric excess (ee). The crystal structures of the holoenzyme and of the enzyme in complex with the inhibitor 2-aminooxyacetate revealed structural similarity to the β-phenylalanine aminotransferase from Mesorhizobium sp. strain LUK. The crystal structure was used to rationalize the stereo- and regioselectivity of V. paradoxus aminotransferase and to define a sequence motif with which new aromatic β-amino acid-converting aminotransferases may be identified.
Collapse
|
41
|
Rudat J, Brucher BR, Syldatk C. Transaminases for the synthesis of enantiopure beta-amino acids. AMB Express 2012; 2:11. [PMID: 22293122 PMCID: PMC3281772 DOI: 10.1186/2191-0855-2-11] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 01/31/2012] [Indexed: 11/29/2022] Open
Abstract
Optically pure β-amino acids constitute interesting building blocks for peptidomimetics and a great variety of pharmaceutically important compounds. Their efficient synthesis still poses a major challenge. Transaminases (also known as aminotransferases) possess a great potential for the synthesis of optically pure β-amino acids. These pyridoxal 5'-dependent enzymes catalyze the transfer of an amino group from a donor substrate to an acceptor, thus enabling the synthesis of a wide variety of chiral amines and amino acids. Transaminases can be applied either for the kinetic resolution of racemic compounds or the asymmetric synthesis starting from a prochiral substrate. This review gives an overview over microbial transaminases with activity towards β-amino acids and their substrate spectra. It also outlines current strategies for the screening of new biocatalysts. Particular emphasis is placed on activity assays which are applicable to high-throughput screening.
Collapse
|
42
|
Wu B, Szymański W, Wybenga GG, Heberling MM, Bartsch S, de Wildeman S, Poelarends GJ, Feringa BL, Dijkstra BW, Janssen DB. Mechanism-Inspired Engineering of Phenylalanine Aminomutase for Enhanced β-Regioselective Asymmetric Amination of Cinnamates. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106372] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
43
|
Wu B, Szymański W, Wybenga GG, Heberling MM, Bartsch S, de Wildeman S, Poelarends GJ, Feringa BL, Dijkstra BW, Janssen DB. Mechanism-Inspired Engineering of Phenylalanine Aminomutase for Enhanced β-Regioselective Asymmetric Amination of Cinnamates. Angew Chem Int Ed Engl 2011; 51:482-6. [DOI: 10.1002/anie.201106372] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/12/2011] [Indexed: 11/11/2022]
|