1
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Wang Q, Ma L, Wang Z, Chen Q, Wang Q, Qi Q. Construction and yield optimization of a cinnamylamine biosynthesis route in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:100. [PMID: 36175923 PMCID: PMC9524069 DOI: 10.1186/s13068-022-02199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/22/2022] [Indexed: 11/10/2022]
Abstract
Background With the development of metabolic engineering and synthetic biology, the biosynthesis of aromatic compounds has attracted much attention. Cinnamylamine is an aromatic compound derived from l-phenylalanine, which is used in the synthesis of biologically active molecules, including drugs, and energetic materials. Cinnamylamine has been mainly synthesized by chemical methods to date, and few reports have focused on the biosynthesis of cinnamylamine. Therefore, it is desirable to establish an efficient biosynthesis method for cinnamylamine. Results The ω-aminotransferase Cv-ωTA from Chromobacterium violaceum has been demonstrated to have high enzyme activity in the conversion of cinnamaldehyde to cinnamylamine. To prevent the preferable conversion of cinnamaldehyde to cinnamyl alcohol in wild-type Escherichia coli, the E. coli MG1655 strain with reduced aromatic aldehyde reduction (RARE) in which six aldehyde ketone reductase and alcohol dehydrogenase genes have been knocked out was employed. Then, the carboxylic acid reductase from Neurospora crassa (NcCAR) and phosphopantetheinyl transferase (PPTase) from E. coli were screened for a high conversion rate of cinnamic acid to cinnamaldehyde. To shift the equilibrium of the reaction toward cinnamylamine, saturation mutagenesis of Cv-ωTA at key amino acid residues was performed, and Cv-ωTA Y168G had the highest conversion rate with 88.56 mg/L cinnamylamine obtained after 4 h of fermentation. Finally, by optimizing the substrates and the supply of the cofactors, PLP and NADPH, in the fermentation, the yield of cinnamylamine in engineered E. coli reached 523.15 mg/L. Conclusion We achieved the first biosynthesis of cinnamylamine using cinnamic acid as the precursor in E. coli using a combinatorial metabolic engineering strategy. This study provides a reference for the biosynthesis of other amine compounds and lays a foundation for the de novo synthesis of cinnamylamine. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02199-7.
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2
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Dalwadi MP, Orol D, Walter F, Minton NP, King JR, Kovács K. Using singular perturbation theory to determine kinetic parameters in a non-standard coupled enzyme assay. J Math Biol 2020; 81:649-690. [PMID: 32761360 PMCID: PMC7427744 DOI: 10.1007/s00285-020-01524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 06/29/2020] [Indexed: 11/27/2022]
Abstract
We investigate how to characterize the kinetic parameters of an aminotransaminase using a non-standard coupled (or auxiliary) enzyme assay, where the peculiarity arises for two reasons. First, one of the products of the auxiliary enzyme is a substrate for the primary enzyme and, second, we explicitly account for the reversibility of the auxiliary enzyme reaction. Using singular perturbation theory, we characterize the two distinguished asymptotic limits in terms of the strength of the reverse reaction, which allows us to determine how to deduce the kinetic parameters of the primary enzyme for a characterized auxiliary enzyme. This establishes a parameter-estimation algorithm that is applicable more generally to similar reaction networks. We demonstrate the applicability of our theory by performing enzyme assays to characterize a novel putative aminotransaminase enzyme, CnAptA (UniProtKB Q0KEZ8) from Cupriavidus necator H16, for two different omega-amino acid substrates.
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Affiliation(s)
- Mohit P Dalwadi
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Oxford, OX2 6GG, UK.
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Diego Orol
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Frederik Walter
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Nigel P Minton
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - John R King
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Katalin Kovács
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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3
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Hillier HT, Altermark B, Leiros I. The crystal structure of the tetrameric DABA-aminotransferase EctB, a rate-limiting enzyme in the ectoine biosynthesis pathway. FEBS J 2020; 287:4641-4658. [PMID: 32112674 DOI: 10.1111/febs.15265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/30/2020] [Accepted: 02/26/2020] [Indexed: 01/13/2023]
Abstract
l-2,4-diaminobutyric acid (DABA) aminotransferases can catalyze the formation of amines at the distal ω-position of substrates, and is the intial and rate-limiting enzyme in the biosynthesis pathway of the cytoprotecting molecule (S)-2-methyl-1,4,5,6-tetrahydro-4-pyrimidine carboxylic acid (ectoine). Although there is an industrial interest in the biosynthesis of ectoine, the DABA aminotransferases remain poorly characterized. Herein, we present the crystal structure of EctB (2.45 Å), a DABA aminotransferase from Chromohalobacter salexigens DSM 3043, a well-studied organism with respect to osmoadaptation by ectoine biosynthesis. We investigate the enzyme's oligomeric state to show that EctB from C. salexigens is a tetramer of two functional dimers, and suggest conserved recognition sites for dimerization that also includes the characteristic gating loop that helps shape the active site of the neighboring monomer. Although ω-transaminases are known to have two binding pockets to accommodate for their dual substrate specificity, we herein provide the first description of two binding pockets in the active site that may account for the catalytic character of DABA aminotransferases. Furthermore, our biochemical data reveal that the EctB enzyme from C. salexigens is a thermostable, halotolerant enzyme with a broad pH tolerance which may be linked to its tetrameric state. Put together, this study creates a solid foundation for a deeper structural understanding of DABA aminotransferases and opening up for future downstream studies of EctB's catalytic character and its redesign as a better catalyst for ectoine biosynthesis. In summary, we believe that the EctB enzyme from C. salexigens can serve as a benchmark enzyme for characterization of DABA aminotransferases. DATABASE: Structural data are available in PDB database under the accession number 6RL5.
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Affiliation(s)
- Heidi Therese Hillier
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Bjørn Altermark
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Ingar Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
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4
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Using enzyme cascades in biocatalysis: Highlight on transaminases and carboxylic acid reductases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140322. [DOI: 10.1016/j.bbapap.2019.140322] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 12/21/2022]
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5
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Land H, Ruggieri F, Szekrenyi A, Fessner W, Berglund P. Engineering the Active Site of an (
S
)‐Selective Amine Transaminase for Acceptance of Doubly Bulky Primary Amines. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201901252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Henrik Land
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Department of Industrial BiotechnologyAlbaNova University Center SE-106 91 Stockholm Sweden
- Uppsala University, Department of Chemistry-Ångström LaboratoryMolecular Biomimetics Box 523 SE-751 20 Uppsala Sweden
| | - Federica Ruggieri
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Department of Industrial BiotechnologyAlbaNova University Center SE-106 91 Stockholm Sweden
| | - Anna Szekrenyi
- Technische Universität DarmstadtInstitut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Wolf‐Dieter Fessner
- Technische Universität DarmstadtInstitut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Per Berglund
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Department of Industrial BiotechnologyAlbaNova University Center SE-106 91 Stockholm Sweden
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6
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Insight into the dimer dissociation process of the Chromobacterium violaceum (S)-selective amine transaminase. Sci Rep 2019; 9:16946. [PMID: 31740704 PMCID: PMC6861513 DOI: 10.1038/s41598-019-53177-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
One of the main factors hampering the implementation in industry of transaminase-based processes for the synthesis of enantiopure amines is their often low storage and operational stability. Our still limited understanding of the inactivation processes undermining the stability of wild-type transaminases represents an obstacle to improving their stability through enzyme engineering. In this paper we present a model describing the inactivation process of the well-characterized (S)-selective amine transaminase from Chromobacterium violaceum. The cornerstone of the model, supported by structural, computational, mutagenesis and biophysical data, is the central role of the catalytic lysine as a conformational switch. Upon breakage of the lysine-PLP Schiff base, the strain associated with the catalytically active lysine conformation is dissipated in a slow relaxation process capable of triggering the known structural rearrangements occurring in the holo-to-apo transition and ultimately promoting dimer dissociation. Due to the occurrence in the literature of similar PLP-dependent inactivation models valid for other non-transaminase enzymes belonging to the same fold-class, the role of the catalytic lysine as conformational switch might extend beyond the transaminase enzyme group and offer new insight to drive future non-trivial engineering strategies.
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7
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Roura Padrosa D, Alaux R, Smith P, Dreveny I, López-Gallego F, Paradisi F. Enhancing PLP-Binding Capacity of Class-III ω-Transaminase by Single Residue Substitution. Front Bioeng Biotechnol 2019; 7:282. [PMID: 31681755 PMCID: PMC6813460 DOI: 10.3389/fbioe.2019.00282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/04/2019] [Indexed: 11/25/2022] Open
Abstract
Transaminases are pyridoxal-5′-phosphate (PLP) binding enzymes, broadly studied for their potential industrial application. Their affinity for PLP has been related to their performance and operational stability and while significant differences in PLP requirements have been reported, the environment of the PLP-binding pocket is highly conserved. In this study, thorough analysis of the residue interaction network of three homologous transaminases Halomonas elongata (HeTA), Chromobacterium violaceum (CvTA), and Pseudomonas fluorescens (PfTA) revealed a single residue difference in their PLP binding pocket: an asparagine at position 120 in HeTA. N120 is suitably positioned to interact with an aspartic acid known to protonate the PLP pyridinium nitrogen, while the equivalent position is occupied by a valine in the other two enzymes. Three different mutants were constructed (HeTA-N120V, CvTA-V124N, and PfTA-V129N) and functionally analyzed. Notably, in HeTA and CvTA, the asparagine variants, consistently exhibited a higher thermal stability and a significant decrease in the dissociation constant (Kd) for PLP, confirming the important role of N120 in PLP binding. Moreover, the reaction intermediate pyridoxamine-5′-phosphate (PMP) was released more slowly into the bulk, indicating that the mutation also enhances their PMP binding capacity. The crystal structure of PfTA, elucidated in this work, revealed a tetrameric arrangement with the PLP binding sites near the subunit interface. In this case, the V129N mutation had a negligible effect on PLP-binding, but it reduced its temperature stability possibly destabilizing the quaternary structure.
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Affiliation(s)
| | - Raphael Alaux
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Phillip Smith
- Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Ingrid Dreveny
- Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Fernando López-Gallego
- Instituto de Síntesis Química y Catálisis Homogénea, Zaragoza, Spain.,ARAID Foundation, Zaragoza, Spain
| | - Francesca Paradisi
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom.,Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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8
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Márquez SL, Atalah J, Blamey JM. Characterization of a novel thermostable (S)-amine-transaminase from an Antarctic moderately-thermophilic bacterium Albidovulum sp. SLM16. Enzyme Microb Technol 2019; 131:109423. [PMID: 31615676 DOI: 10.1016/j.enzmictec.2019.109423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/26/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022]
Abstract
Amine-transaminases (ATAs) are enzymes that catalyze the reversible transfer of an amino group between primary amines and carbonyl compounds. They have been widely studied in the last decades for their application in stereoselective synthesis of chiral amines, which are one of the most valuable building blocks in pharmaceuticals manufacturing. Their excellent enantioselectivity, use of low-cost substrates and no need for external cofactors has turned these enzymes into a promising alternative to the chemical synthesis of chiral amines. Nevertheless, its application at industrial scale remains limited mainly because most of the available ATAs are scarcely tolerant to harsh reaction conditions such as high temperatures and presence of organic solvents. In this work, a novel (S)-ATA was discovered in a thermophilic bacterium, Albidovulum sp. SLM16, isolated from a geothermal Antarctic environmental sample, more specifically from a shoreline fumarole in Deception Island. The transaminase-coding gene was identified in the genome of the microorganism, cloned and overexpressed in Escherichia coli for biochemical characterization. The activity of the recombinant ATA was optimal at 65 °C and pH 9.5. Molecular mass estimates suggest a 75 kDa homodimeric structure. The enzyme turned out to be highly thermostable, maintaining 80% of its specific activity after 5 days of incubation at 50 °C. These results indicate that ATA_SLM16 is an excellent candidate for potential applications in biocatalytic synthesis. To the best of our knowledge, this would be the first report of the characterization of a thermostable (S)-ATA discovered by means of in vivo screening of thermophilic microorganisms.
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Affiliation(s)
- Sebastián L Márquez
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile; Fundación Científica y Cultural Biociencia, Santiago, Chile
| | - Joaquín Atalah
- Fundación Científica y Cultural Biociencia, Santiago, Chile
| | - Jenny M Blamey
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile; Fundación Científica y Cultural Biociencia, Santiago, Chile.
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9
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Palacio CM, Rozeboom HJ, Lanfranchi E, Meng Q, Otzen M, Janssen DB. Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism. FEBS J 2019; 286:4086-4102. [PMID: 31162815 DOI: 10.1111/febs.14950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/29/2019] [Accepted: 06/01/2019] [Indexed: 01/31/2023]
Abstract
The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest KM values (highest affinity) and highest specificity constant (kcat /KM ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).
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Affiliation(s)
- Cyntia M Palacio
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Henriëtte J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Elisa Lanfranchi
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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10
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Structural basis of substrate recognition by a novel thermostable (S)-enantioselective ω-transaminase from Thermomicrobium roseum. Sci Rep 2019; 9:6958. [PMID: 31061438 PMCID: PMC6502798 DOI: 10.1038/s41598-019-43490-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/24/2019] [Indexed: 01/13/2023] Open
Abstract
Transaminases catalyze the reversible transfer reaction of an amino group between a primary amine and an α-keto acid, utilizing pyridoxal 5'-phosphate as a cofactor. ω-transaminases (ωTAs) recognize an amino group linked to a non-α carbon of amine substrates. Recently, a novel (S)-enantioselective ωTA from Thermomicrobium roseum (Tr-ωTA) was identified and its enzymatic activity reported. However, the detailed mechanism of (S)-enantioselective substrate recognition remained unclear. In this study, we determined the crystal structure of Tr-ωTA at 1.8 Å resolution to elucidate the mechanism underlying Tr-ωTA substrate (S)-enantioselectivity. A structural analysis of Tr-ωTA along with molecular docking simulations revealed that two pockets at the active site tightly restrict the size and orientation of functional groups of substrate candidates. Based on the structural information and docking simulation results, we propose a comprehensive catalytic mechanism of Tr-ωTA. The present study thus provides structural and functional insights into the (S)-enantioselectivity of Tr-ωTA.
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11
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Isupov MN, Boyko KM, Sutter JM, James P, Sayer C, Schmidt M, Schönheit P, Nikolaeva AY, Stekhanova TN, Mardanov AV, Ravin NV, Bezsudnova EY, Popov VO, Littlechild JA. Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization. Front Bioeng Biotechnol 2019; 7:7. [PMID: 30733943 PMCID: PMC6353796 DOI: 10.3389/fbioe.2019.00007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/08/2019] [Indexed: 11/25/2022] Open
Abstract
Two new thermophilic branched chain amino acid transaminases have been identified within the genomes of different hyper-thermophilic archaea, Geoglobus acetivorans, and Archaeoglobus fulgidus. These enzymes belong to the class IV of transaminases as defined by their structural fold. The enzymes have been cloned and over-expressed in Escherichia coli and the recombinant enzymes have been characterized both biochemically and structurally. Both enzymes showed high thermostability with optimal temperature for activity at 80 and 85°C, respectively. They retain good activity after exposure to 50% of the organic solvents, ethanol, methanol, DMSO and acetonitrile. The enzymes show a low activity to (R)-methylbenzylamine but no activity to (S)-methylbenzylamine. Both enzymes have been crystallized and their structures solved in the internal aldimine form, to 1.9 Å resolution for the Geoglobus enzyme and 2.0 Å for the Archaeoglobus enzyme. Also the Geoglobus enzyme structure has been determined in complex with the amino acceptor α-ketoglutarate and the Archaeoglobus enzyme in complex with the inhibitor gabaculine. These two complexes have helped to determine the conformation of the enzymes during enzymatic turnover and have increased understanding of their substrate specificity. A comparison has been made with another (R) selective class IV transaminase from the fungus Nectria haematococca which was previously studied in complex with gabaculine. The subtle structural differences between these enzymes has provided insight regarding their different substrate specificities.
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Affiliation(s)
- Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Konstantin M. Boyko
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Jan-Moritz Sutter
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marcel Schmidt
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Alena Yu. Nikolaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey V. Mardanov
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V. Ravin
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Vladimir O. Popov
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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12
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Bezsudnova EY, Boyko KM, Nikolaeva AY, Zeifman YS, Rakitina TV, Suplatov DA, Popov VO. Biochemical and structural insights into PLP fold type IV transaminase from Thermobaculum terrenum. Biochimie 2018; 158:130-138. [PMID: 30599183 DOI: 10.1016/j.biochi.2018.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/27/2018] [Indexed: 10/27/2022]
Abstract
The high catalytic efficiency of enzymes under reaction conditions is one of the main goals in biocatalysis. Despite the dramatic progress in the development of more efficient biocatalysts by protein design, the search for natural enzymes with useful properties remains a promising strategy. The pyridoxal 5'-phosphate (PLP)-dependent transaminases represent a group of industrially important enzymes due to their ability to stereoselectively transfer amino groups between diverse substrates; however, the complex mechanism of substrate recognition and conversion makes the design of transaminases a challenging task. Here we report a detailed structural and kinetic study of thermostable transaminase from the bacterium Thermobaculum terrenum (TaTT) using the methods of enzyme kinetics, X-ray crystallography and molecular modeling. TaTT can convert L-branched-chain and L-aromatic amino acids as well as (R)-(+)-1-phenylethylamine at a high rate and with high enantioselectivity. The structures of TaTT in complex with the cofactor pyridoxal 5'-phosphate covalently bound to enzyme and in complex with its reduced form, pyridoxamine 5'-phosphate, were determined at resolutions of 2.19 Å and 1.5 Å, and deposited in the Protein Data Bank as entries 6GKR and 6Q8E, respectively. TaTT is a fold type IV PLP-dependent enzyme. In terms of structural similarity, the enzyme is close to known branched-chain amino acid aminotransferases, but differences in characteristic sequence motifs in the active site were observed in TaTT compared to canonical branched-chain amino acid aminotransferases, which can explain the improved binding of aromatic amino acids and (R)-(+)-1-phenylethylamine. This study has shown for the first time that high substrate specificity towards both various l-amino acids and (R)-primary amines can be implemented within one pyridoxal 5'-phosphate-dependent active site of fold type IV. These results complement our knowledge of the catalytic diversity of transaminases and indicate the need for further biochemical and bioinformatic studies to understand the sequence-structure-function relationship in these enzymes.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation.
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
| | - Alena Yu Nikolaeva
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
| | - Yulia S Zeifman
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
| | - Tatiana V Rakitina
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation; Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Str. 16/10, 117997, Moscow, Russian Federation
| | - Dmitry A Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskiye Gory 1-73, Moscow, 119991, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
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13
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Galman JL, Gahloth D, Parmeggiani F, Slabu I, Leys D, Turner NJ. Characterization of a Putrescine Transaminase From Pseudomonas putida and its Application to the Synthesis of Benzylamine Derivatives. Front Bioeng Biotechnol 2018; 6:205. [PMID: 30622946 PMCID: PMC6308316 DOI: 10.3389/fbioe.2018.00205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/12/2018] [Indexed: 01/08/2023] Open
Abstract
The reductive amination of prochiral ketones using biocatalysts has been of great interest to the pharmaceutical industry in the last decade for integrating novel strategies in the production of chiral building blocks with the intent of minimizing impact on the environment. Amongst the enzymes able to catalyze the direct amination of prochiral ketones, pyridoxal 5'-phosphate (PLP) dependent ω-transaminases have shown great promise as versatile industrial biocatalysts with high selectivity, regioselectivity, and broad substrate scope. Herein the biochemical characterization of a putrescine transaminase from Pseudomonas putida (Pp-SpuC) was performed, which showed an optimum pH and temperature of 8.0 and 60°C, respectively. To gain further structural insight of this enzyme, we crystallized the protein in the apo form and determined the structure to 2.1 Å resolution which revealed a dimer that adopts a class I transaminase fold comparable to other class III transaminases. Furthermore we exploited its dual substrate recognition for biogenic diamines (i.e., cadaverine) and readily available monoamines (i.e., isopropylamine) for the synthesis of benzylamine derivatives with excellent product conversions and extremely broad substrate tolerance.
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Affiliation(s)
| | | | | | | | | | - Nicholas J. Turner
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
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14
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Almahboub SA, Narancic T, Fayne D, O'Connor KE. Single point mutations reveal amino acid residues important for Chromobacterium violaceum transaminase activity in the production of unnatural amino acids. Sci Rep 2018; 8:17397. [PMID: 30478262 PMCID: PMC6255834 DOI: 10.1038/s41598-018-35688-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/16/2018] [Indexed: 12/25/2022] Open
Abstract
Unnatural amino acids (UAAs) are chiral amines with high application potential in drug discovery and synthesis of other valuable chemicals. Biocatalysis offers the possibility to synthesise novel optically pure UAAs with different physical and chemical properties. While the biocatalytic potential of transaminases in the synthesis of UAAs has been demonstrated, there is still a need to improve the activity with non-native substrates and to understand which amino acids residues are important for activity with these UAAs. Using a rational design approach, six variants of Chromobacterium violaceum DSM30191 transaminase (CV_TA) carrying a single and one variant carrying two substitutions were generated. Among the variants with a single substitution, CV_Y168F showed a 2 to 2.6-fold increased affinity for 2-oxooctanoic acid (2-OOA) and 3-oxobutyric acid (3-OBA) methyl ester used to synthesise an α- and β-UAA. Analysis of the first half of the transaminase reaction showed no change in the activity with the donor (S)-1-phenylethylamine. The combination of W60C and Y168F substitutions improved the CV_TA affinity for 2-OOA 10-fold compared to the wild type. Other substitutions showed no change, or reduced activity with the tested substrates. Our findings provide structural information on CV_TA and demonstrate the potential of rational design for biosynthesis of UAAs.
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Affiliation(s)
- Sarah A Almahboub
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Tanja Narancic
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland. .,BEACON - Bioeconomy Research Centre, Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Darren Fayne
- Molecular Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Kevin E O'Connor
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.,BEACON - Bioeconomy Research Centre, Ireland, University College Dublin, Belfield, Dublin 4, Ireland
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15
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Voss M, Das D, Genz M, Kumar A, Kulkarni N, Kustosz J, Kumar P, Bornscheuer UT, Höhne M. In Silico Based Engineering Approach to Improve Transaminases for the Conversion of Bulky Substrates. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03900] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Moritz Voss
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Devashish Das
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Maika Genz
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Anurag Kumar
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Naveen Kulkarni
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Jakub Kustosz
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Pravin Kumar
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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16
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Kelly SA, Skvortsov T, Magill D, Quinn DJ, McGrath JW, Allen CCR, Moody TS, Gilmore BF. Characterization of a novel ω-transaminase from a Triassic salt mine metagenome. Biochem Biophys Res Commun 2018; 503:2936-2942. [PMID: 30119883 DOI: 10.1016/j.bbrc.2018.08.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/08/2018] [Indexed: 01/08/2023]
Abstract
Chiral amines are valuable building blocks for the pharmaceutical industry, and are increasingly synthesized by transaminase-mediated (TAm) synthesis. Currently available TAms, primarily isolated from the genomes of cultured mesophilic bacteria, often suffer from a number of drawbacks, including poor substrate range and an inability to tolerate the harsh conditions often demanded by industrial processes. These characteristics have, in part, driven the search for novel biocatalysts from both metagenomic sources and extreme environments. Herein, we report the isolation and characterization of an ω-TAm from a metagenome of a Triassic salt mine in Kilroot, N. Ireland, an extremely hypersaline environment formed circa 220-250 mya. The gene sequence was identified based on homology with existing bacterial TAms, synthesized within a pET28a(+) plasmid and expressed in E. coli BL21 DE3 cells. The resultant 49 kDa protein accepted (S)-methylbenzylamine (MBA) as amino donor and had a specific activity of 0.54 U/mg using α-ketoglutarate (ΑKG) as substrate. Molecular modeling and substrate docking indicated the presence of key residues, conserved in a number of other TAms. Despite the hypersaline environment from which it was isolated, the enzyme displayed low halotolerance, highlighting that not all biocatalysts will demonstrate the extreme characteristics associated with their source environment. This study does however reinforce the viability of mining metagenomic datasets as a means of discovering novel and functional biocatalysts, and adds to a currently scant list of such examples in the field of TAms.
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Affiliation(s)
- Stephen A Kelly
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Timofey Skvortsov
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Damian Magill
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Derek J Quinn
- Almac, Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, N. Ireland, UK
| | - John W McGrath
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Thomas S Moody
- Almac, Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, N. Ireland, UK; Arran Chemical Company Limited, Unit 1 Monksland Industrial Estate, Athlone, Co. Roscommon, Ireland
| | - Brendan F Gilmore
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK.
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17
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Diaminopelargonic acid transaminase from Psychrobacter cryohalolentis is active towards (S)-(-)-1-phenylethylamine, aldehydes and α-diketones. Appl Microbiol Biotechnol 2018; 102:9621-9633. [DOI: 10.1007/s00253-018-9310-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/09/2018] [Accepted: 08/07/2018] [Indexed: 11/25/2022]
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18
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Recent Advances in ω-Transaminase-Mediated Biocatalysis for the Enantioselective Synthesis of Chiral Amines. Catalysts 2018. [DOI: 10.3390/catal8070254] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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19
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Buß O, Buchholz PCF, Gräff M, Klausmann P, Rudat J, Pleiss J. The ω-transaminase engineering database (oTAED): A navigation tool in protein sequence and structure space. Proteins 2018; 86:566-580. [PMID: 29423963 DOI: 10.1002/prot.25477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 01/02/2023]
Abstract
The ω-Transaminase Engineering Database (oTAED) was established as a publicly accessible resource on sequences and structures of the biotechnologically relevant ω-transaminases (ω-TAs) from Fold types I and IV. The oTAED integrates sequence and structure data, provides a classification based on fold type and sequence similarity, and applies a standard numbering scheme to identify equivalent positions in homologous proteins. The oTAED includes 67 210 proteins (114 655 sequences) which are divided into 169 homologous families based on global sequence similarity. The 44 and 39 highly conserved positions which were identified in Fold type I and IV, respectively, include the known catalytic residues and a large fraction of glycines and prolines in loop regions, which might have a role in protein folding and stability. However, for most of the conserved positions the function is still unknown. Literature information on positions that mediate substrate specificity and stereoselectivity was systematically examined. The standard numbering schemes revealed that many positions which have been described in different enzymes are structurally equivalent. For some positions, multiple functional roles have been suggested based on experimental data in different enzymes. The proposed standard numbering schemes for Fold type I and IV ω-TAs assist with analysis of literature data, facilitate annotation of ω-TAs, support prediction of promising mutation sites, and enable navigation in ω-TA sequence space. Thus, it is a useful tool for enzyme engineering and the selection of novel ω-TA candidates with desired biochemical properties.
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Affiliation(s)
- Oliver Buß
- Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Engler-Bunte-Ring 3, Karlsruhe, 76131, Germany
| | - Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, 70569, Germany
| | - Maike Gräff
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, 70569, Germany
| | - Peter Klausmann
- Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Engler-Bunte-Ring 3, Karlsruhe, 76131, Germany
| | - Jens Rudat
- Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Engler-Bunte-Ring 3, Karlsruhe, 76131, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, 70569, Germany
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20
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Chen S, Berglund P, Humble MS. The effect of phosphate group binding cup coordination on the stability of the amine transaminase from Chromobacterium violaceum. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2017.12.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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21
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Abstract
In biocatalysis, structural knowledge regarding an enzyme and its substrate interactions complements and guides experimental investigations. Structural knowledge regarding an enzyme or a biocatalytic reaction system can be generated through computational techniques, such as homology- or molecular modeling. For this type of computational work, a computer program developed for molecular modeling of proteins is required. Here, we describe the use of the program YASARA Structure. Protocols for two specific biocatalytic applications, including both homology modeling and molecular modeling such as energy minimization, molecular docking simulations and molecular dynamics simulations, are shown. The applications are chosen to give realistic examples showing how structural knowledge through homology and molecular modeling is used to guide biocatalytic investigations and protein engineering studies.
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22
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Kelly SA, Megaw J, Caswell J, Scott CJ, Allen CCR, Moody TS, Gilmore BF. Isolation and Characterisation of a Halotolerant ω-Transaminase from a Triassic Period Salt Mine and Its Application to Biocatalysis. ChemistrySelect 2017. [DOI: 10.1002/slct.201701642] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stephen A. Kelly
- School of Pharmacy; Queen's University Belfast; Belfast BT9 7BL, N. Ireland UK
| | - Julianne Megaw
- School of Pharmacy; Queen's University Belfast; Belfast BT9 7BL, N. Ireland UK
| | - Jill Caswell
- Department of Biocatalysis & Isotope Chemistry; Almac; Craigavon BT63 5QD, N. Ireland UK
| | - Christopher J. Scott
- School of Medicine, Dentistry and Biomedical Sciences; Queen's University Belfast; Belfast BT9 7BL, N. Ireland UK
| | | | - Thomas S. Moody
- Department of Biocatalysis & Isotope Chemistry; Almac; Craigavon BT63 5QD, N. Ireland UK
- Arran Chemical Company Limited, Unit 1 Monksland Industrial Estate; Athlone, Co. Roscommon Ireland
| | - Brendan F. Gilmore
- School of Pharmacy; Queen's University Belfast; Belfast BT9 7BL, N. Ireland UK
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23
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Börner T, Rämisch S, Bartsch S, Vogel A, Adlercreutz P, Grey C. Three in One: Temperature, Solvent and Catalytic Stability by Engineering the Cofactor-Binding Element of Amine Transaminase. Chembiochem 2017; 18:1482-1486. [PMID: 28470825 DOI: 10.1002/cbic.201700236] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Indexed: 12/11/2022]
Abstract
Amine transaminase (ATA) catalyse enantioselectively the direct amination of ketones, but insufficient stability during catalysis limits their industrial applicability. Recently, we revealed that ATAs suffer from substrate-induced inactivation mechanism involving dissociation of the enzyme-cofactor intermediate. Here, we report on engineering the cofactor-ring-binding element, which also shapes the active-site entrance. Only two point mutations in this motif improved temperature and catalytic stability in both biphasic media and organic solvent. Thermodynamic analysis revealed a higher melting point for the enzyme-cofactor intermediate. The high cofactor affinity eliminates the need for pyridoxal 5'-phosphate supply, thus making large-scale reactions more cost effective. This is the first report on stabilising a tetrameric ATA by mutating a single structural element. As this structural "hotspot" is a common feature of other transaminases it could serve as a general engineering target.
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Affiliation(s)
- Tim Börner
- Department of Chemistry and Biotechnology, Institute of Materials Science, Nestlé Research Center, Route du Jorat 57, 1000, Lausanne 26, Switzerland
| | - Sebastian Rämisch
- Schief Lab, Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | | | - Andreas Vogel
- c-LEcta GmbH, Perlickstrasse 5, 04103, Leipzig, Germany
| | - Patrick Adlercreutz
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 221 00, Lund, Sweden
| | - Carl Grey
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 221 00, Lund, Sweden
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24
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Han SW, Kim J, Cho HS, Shin JS. Active Site Engineering of ω-Transaminase Guided by Docking Orientation Analysis and Virtual Activity Screening. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03242] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sang-Woo Han
- Department
of Biotechnology and ‡Department of Systems Biology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
| | - Juyeon Kim
- Department
of Biotechnology and ‡Department of Systems Biology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
| | - Hyun-Soo Cho
- Department
of Biotechnology and ‡Department of Systems Biology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
| | - Jong-Shik Shin
- Department
of Biotechnology and ‡Department of Systems Biology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
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25
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Manta B, Cassimjee KE, Himo F. Quantum Chemical Study of Dual-Substrate Recognition in ω-Transaminase. ACS OMEGA 2017; 2:890-898. [PMID: 30023618 PMCID: PMC6044752 DOI: 10.1021/acsomega.6b00376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/20/2017] [Indexed: 05/14/2023]
Abstract
ω-Transaminases are attractive biocatalysts for the production of chiral amines. These enzymes usually have a broad substrate range. Their substrates include hydrophobic amines as well as amino acids, a feature referred to as dual-substrate recognition. In the present study, the reaction mechanism for the half-transamination of l-alanine to pyruvate in (S)-selective Chromobacterium violaceum ω-transaminase is investigated using density functional theory calculations. The role of a flexible arginine residue, Arg416, in the dual-substrate recognition is investigated by employing two active-site models, one including this residue and one lacking it. The results of this study are compared to those of the mechanism of the conversion of (S)-1-phenylethylamine to acetophenone. The calculations suggest that the deaminations of amino acids and hydrophobic amines follow essentially the same mechanism, but the energetics of the reactions differ significantly. It is shown that the amine is kinetically favored in the half-transamination of l-alanine/pyruvate, whereas the ketone is kinetically favored in the half-transamination of (S)-1-phenylethylamine/acetophenone. The calculations further support the proposal that the arginine residue facilitates the dual-substrate recognition by functioning as an arginine switch, where the side chain is positioned inside or outside of the active site depending on the substrate. Arg416 participates in the binding of l-alanine by forming a salt bridge to the carboxylate moiety, whereas the conversion of (S)-1-phenylethylamine is feasible in the absence of Arg416, which here represents the case in which the side chain of Arg416 is positioned outside of the active site.
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26
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Ferrandi EE, Previdi A, Bassanini I, Riva S, Peng X, Monti D. Novel thermostable amine transferases from hot spring metagenomes. Appl Microbiol Biotechnol 2017; 101:4963-4979. [PMID: 28357542 DOI: 10.1007/s00253-017-8228-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/21/2017] [Accepted: 03/05/2017] [Indexed: 01/09/2023]
Abstract
Hot spring metagenomes, prepared from samples collected at temperatures ranging from 55 to 95 °C, were submitted to an in silico screening aimed at the identification of novel amine transaminases (ATAs), valuable biocatalysts for the preparation of optically pure amines. Three novel (S)-selective ATAs, namely Is3-TA, It6-TA, and B3-TA, were discovered in the metagenome of samples collected from hot springs in Iceland and in Italy, cloned from the corresponding metagenomic DNAs and overexpressed in recombinant form in E. coli. Functional characterization of the novel ATAs demonstrated that they all possess a thermophilic character and are capable of performing amine transfer reactions using a broad range of donor and acceptor substrates, thus suggesting a good potential for practical synthetic applications. In particular, the enzyme B3-TA revealed to be exceptionally thermostable, retaining 85% of activity after 5 days of incubation at 80 °C and more than 40% after 2 weeks under the same condition. These results, which were in agreement with the estimation of an apparent melting temperature around 88 °C, make B3-TA, to the best of our knowledge, the most thermostable natural ATA described to date. This biocatalyst showed also a good tolerance toward different water-miscible and water-immiscible organic solvents. A detailed inspection of the homology-based structural model of B3-TA showed that the overall active site architecture of mesophilic (S)-selective ATAs was mainly conserved in this hyperthermophilic homolog. Additionally, a subfamily of B3-TA-like transaminases, mostly uncharacterized and all from thermophilic microorganisms, was identified and analyzed in terms of phylogenetic relationships and sequence conservation.
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Affiliation(s)
- Erica Elisa Ferrandi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R, Via Mario Bianco 9, 20131, Milan, Italy. .,University of Copenhagen, Ole Maaløesvej 5, 2200, Copenhagen N, Denmark.
| | - Alessandra Previdi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R, Via Mario Bianco 9, 20131, Milan, Italy
| | - Ivan Bassanini
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R, Via Mario Bianco 9, 20131, Milan, Italy.,Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy
| | - Sergio Riva
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R, Via Mario Bianco 9, 20131, Milan, Italy
| | - Xu Peng
- University of Copenhagen, Ole Maaløesvej 5, 2200, Copenhagen N, Denmark
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R, Via Mario Bianco 9, 20131, Milan, Italy.
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27
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Börner T, Rämisch S, Reddem ER, Bartsch S, Vogel A, Thunnissen AMWH, Adlercreutz P, Grey C. Explaining Operational Instability of Amine Transaminases: Substrate-Induced Inactivation Mechanism and Influence of Quaternary Structure on Enzyme–Cofactor Intermediate Stability. ACS Catal 2017. [DOI: 10.1021/acscatal.6b02100] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Tim Börner
- Division
of Biotechnology, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Sebastian Rämisch
- Schief
Lab, Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Eswar R. Reddem
- Laboratory
of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | | | - Andy-Mark W. H. Thunnissen
- Laboratory
of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Patrick Adlercreutz
- Division
of Biotechnology, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Carl Grey
- Division
of Biotechnology, Department of Chemistry, Lund University, 221 00 Lund, Sweden
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28
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van Oosterwijk N, Willies S, Hekelaar J, Terwisscha van Scheltinga AC, Turner NJ, Dijkstra BW. Structural Basis of the Substrate Range and Enantioselectivity of Two (S)-Selective ω-Transaminases. Biochemistry 2016; 55:4422-31. [PMID: 27428867 DOI: 10.1021/acs.biochem.6b00370] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ω-Transaminases are enzymes that can introduce an amino group in industrially interesting compounds. We determined crystal structures of two (S)-selective ω-transaminases, one from Arthrobacter sp. (Ars-ωTA) and one from Bacillus megaterium (BM-ωTA), which have 95% identical sequences but somewhat different activity profiles. Substrate profiling measurements using a range of (R)- and (S)-substrates showed that both enzymes have a preference for substrates with large, flat cyclic side groups, for which the activity of BM-ωTA is generally somewhat higher. BM-ωTA has a preference for (S)-3,3-dimethyl-2-butylamine significantly stronger than that of Ars-ωTA, as well as a weaker enantiopreference for 1-cyclopropylethylamine. The crystal structures showed that, as expected for (S)-selective transaminases, both enzymes have the typical transaminase type I fold and have spacious active sites to accommodate largish substrates. A structure of BM-ωTA with bound (R)-α-methylbenzylamine explains the enzymes' preference for (S)-substrates. Site-directed mutagenesis experiments revealed that the presence of a tyrosine, instead of a cysteine, at position 60 increases the relative activities on several small substrates. A structure of Ars-ωTA with bound l-Ala revealed that the Arg442 side chain has been repositioned to bind the l-Ala carboxylate. Compared to the arginine switch residue in other transaminases, Arg442 is shifted by six residues in the amino acid sequence, which appears to be a consequence of extra loops near the active site that narrow the entrance to the active site.
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Affiliation(s)
- Niels van Oosterwijk
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Simon Willies
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Johan Hekelaar
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anke C Terwisscha van Scheltinga
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nicholas J Turner
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Bauke W Dijkstra
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
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29
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A β-Alanine Catabolism Pathway Containing a Highly Promiscuous ω-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas sp. Strain AAC. Appl Environ Microbiol 2016; 82:3846-3856. [PMID: 27107110 PMCID: PMC4907197 DOI: 10.1128/aem.00665-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/12/2016] [Indexed: 11/20/2022] Open
Abstract
We previously isolated the transaminase KES23458 from Pseudomonas sp. strain AAC as a promising biocatalyst for the production of 12-aminododecanoic acid, a constituent building block of nylon-12. Here, we report the subsequent characterization of this transaminase. It exhibits activity with a broad substrate range which includes α-, β-, and ω-amino acids, as well as α,ω-diamines and a number of other industrially relevant compounds. It is therefore a prospective candidate for the biosynthesis of a range of polyamide monomers. The crystal structure of KES23458 revealed that the protein forms a dimer containing a large active site pocket and unusual phosphorylated histidine residues. To infer the physiological role of the transaminase, we expressed, purified, and characterized a dehydrogenase from the same operon, KES23460. Unlike the transaminase, the dehydrogenase was shown to be quite selective, catalyzing the oxidation of malonic acid semialdehyde, formed from β-alanine transamination via KES23458. In keeping with previous reports, the dehydrogenase was shown to catalyze both a coenzyme A (CoA)-dependent reaction to form acetyl-CoA and a significantly slower CoA-independent reaction to form acetate. These findings support the original functional assignment of KES23458 as a β-alanine transaminase. However, a seemingly well-adapted active site and promiscuity toward unnatural compounds, such as 12-aminododecanoic acid, suggest that this enzyme could perform multiple functions for Pseudomonas sp. strain AAC. IMPORTANCE We describe the characterization of an industrially relevant transaminase able to metabolize 12-aminododecanoic acid, a constituent building block of the widely used polymer nylon-12, and we report the biochemical and structural characterization of the transaminase protein. A physiological role for this highly promiscuous enzyme is proposed based on the characterization of a related gene from the host organism. Molecular dynamics simulations were carried out to compare the conformational changes in the transaminase protein to better understand the determinants of specificity in the protein. This study makes a substantial contribution that is of interest to the broad biotechnology and enzymology communities, providing insights into the catalytic activity of an industrially relevant biocatalyst as well as the biological function of this operon.
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Richter N, Simon RC, Lechner H, Kroutil W, Ward JM, Hailes HC. ω-Transaminases for the amination of functionalised cyclic ketones. Org Biomol Chem 2015; 13:8843-51. [PMID: 26194788 DOI: 10.1039/c5ob01204j] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential of a number of enantiocomplementary ω-transaminases (ω-TAms) in the amination of cyclic ketones has been investigated. After a preliminary screening of several compounds with increasing complexity, different approaches to shift the equilibrium of the reaction to the amine products were studied, and reaction conditions (temperature and pH) optimised. Interestingly, 2-propylamine as an amine donor was tolerated by all five selected ω-TAms, and therefore used in further experiments. Due to the higher conversions observed and interest in chiral amines studies then focused on the amination of α-tetralone and 2-methylcyclohexanone. Both ketones were aminated to give the corresponding amine with at least one of the employed enzymes. Moreover, the amination of 2-methylcyclohexanone was investigated in more detail due to the different stereoselectivities observed with TAms used. The highest yields and stereoselectivities were obtained using the ω-TAm from Chromobacterium violaceum (CV-TAm), producing 2-methylcyclohexylamine with complete stereoselectivity at the (1S)-amine position and up to 24 : 1 selectivity for the cis : trans [(1S,2R) : (1S,2S)] isomer.
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Affiliation(s)
- N Richter
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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31
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Börner T, Rehn G, Grey C, Adlercreutz P. A Process Concept for High-Purity Production of Amines by Transaminase-Catalyzed Asymmetric Synthesis: Combining Enzyme Cascade and Membrane-Assisted ISPR. Org Process Res Dev 2015. [DOI: 10.1021/acs.oprd.5b00055] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tim Börner
- Department
of Biotechnology, Lund University, P.O. Box, 221 00 Lund, Sweden
| | - Gustav Rehn
- Department
of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Carl Grey
- Department
of Biotechnology, Lund University, P.O. Box, 221 00 Lund, Sweden
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Guan LJ, Ohtsuka J, Okai M, Miyakawa T, Mase T, Zhi Y, Hou F, Ito N, Iwasaki A, Yasohara Y, Tanokura M. A new target region for changing the substrate specificity of amine transaminases. Sci Rep 2015; 5:10753. [PMID: 26030619 PMCID: PMC5377235 DOI: 10.1038/srep10753] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/27/2015] [Indexed: 11/26/2022] Open
Abstract
(R)-stereospecific amine transaminases (R-ATAs) are important biocatalysts for the production of (R)-amine compounds in a strict stereospecific manner. An improved R-ATA, ATA-117-Rd11, was successfully engineered for the manufacture of sitagliptin, a widely used therapeutic agent for type-2 diabetes. The effects of the individual mutations, however, have not yet been demonstrated due to the lack of experimentally determined structural information. Here we describe three crystal structures of the first isolated R-ATA, its G136F mutant and engineered ATA-117-Rd11, which indicated that the mutation introduced into the 136th residue altered the conformation of a loop next to the active site, resulting in a substrate-binding site with drastically modified volume, shape, and surface properties, to accommodate the large pro-sitagliptin ketone. Our findings provide a detailed explanation of the previously reported molecular engineering of ATA-117-Rd11 and propose that the loop near the active site is a new target for the rational design to change the substrate specificity of ATAs.
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Affiliation(s)
- Li-Jun Guan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Jun Ohtsuka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Masahiko Okai
- 1] Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan [2] Department of Ocean Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Tomoko Mase
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Yuehua Zhi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Feng Hou
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Noriyuki Ito
- Biotechnology Development Laboratories, Kaneka Corporation, 1-8 Miyamae, Takasago, Hyogo 676-8688, Japan
| | - Akira Iwasaki
- Research &Development Group, QOL Division, Kaneka Corporation, 1-8 Miyamae, Takasago, Hyogo 676-8688, Japan
| | - Yoshihiko Yasohara
- Biotechnology Development Laboratories, Kaneka Corporation, 1-8 Miyamae, Takasago, Hyogo 676-8688, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
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33
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Scheidt T, Land H, Anderson M, Chen Y, Berglund P, Yi D, Fessner WD. Fluorescence-Based Kinetic Assay for High-Throughput Discovery and Engineering of Stereoselective ω-Transaminases. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500215] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Deszcz D, Affaticati P, Ladkau N, Gegel A, Ward JM, Hailes HC, Dalby PA. Single active-site mutants are sufficient to enhance serine:pyruvate α-transaminase activity in an ω-transaminase. FEBS J 2015; 282:2512-26. [PMID: 25846556 DOI: 10.1111/febs.13293] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/19/2015] [Accepted: 04/01/2015] [Indexed: 11/28/2022]
Abstract
We have analyzed the natural evolution of transaminase structure and sequence between an α-transaminase serine-pyruvate aminotransferase and an ω-transaminase from Chromobacterium violaceum with < 20% sequence identity, and identified the active-site regions that are least conserved structurally. We also show that these structural changes correlate strongly with transaminase substrate specificity during evolution and therefore might normally be presumed to be essential determinants of substrate specificity. However, key residues are often conserved spatially during evolution and yet originate from within a different region of the sequence via structural reorganizations. In the present study, we also show that α-transaminase-type serine-pyruvate aminotransferase activity can be engineered into the CV2025 ω-transaminase scaffold with any one of many possible single-point mutations at three key positions, without the requirement for significant backbone remodeling, or repositioning of the residue from a different region of sequence. This finding has significant implications for enzyme redesign in which solutions to substrate specificity changes may be found more efficiently than is achieved by engineering in all sequence and structure determinants identified by correlation to substrate specificity.
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Affiliation(s)
- Dawid Deszcz
- Department of Biochemical Engineering, University College London, UK
| | - Pierre Affaticati
- Department of Biochemical Engineering, University College London, UK
| | - Nadine Ladkau
- Department of Chemistry, University College London, UK
| | - Alex Gegel
- Department of Biochemical Engineering, University College London, UK
| | - John M Ward
- Department of Biochemical Engineering, University College London, UK
| | | | - Paul A Dalby
- Department of Biochemical Engineering, University College London, UK
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35
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Schiroli D, Peracchi A. A subfamily of PLP-dependent enzymes specialized in handling terminal amines. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1200-11. [PMID: 25770684 DOI: 10.1016/j.bbapap.2015.02.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/23/2015] [Accepted: 02/26/2015] [Indexed: 01/04/2023]
Abstract
The present review focuses on a subfamily of pyridoxal phosphate (PLP)-dependent enzymes, belonging to the broader fold-type I structural group and whose archetypes can be considered ornithine δ-transaminase and γ-aminobutyrate transaminase. These proteins were originally christened "subgroup-II aminotransferases" (AT-II) but are very often referred to as "class-III aminotransferases". As names suggest, the subgroup includes mainly transaminases, with just a few interesting exceptions. However, at variance with most other PLP-dependent enzymes, catalysts in this subfamily seem specialized at utilizing substrates whose amino function is not adjacent to a carboxylate group. AT-II enzymes are widespread in biology and play mostly catabolic roles. Furthermore, today several transaminases in this group are being used as bioorganic tools for the asymmetric synthesis of chiral amines. We present an overview of the biochemical and structural features of these enzymes, illustrating how they are distinctive and how they compare with those of the other fold-type I enzymes. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
- Davide Schiroli
- Department of Life Sciences, Laboratory of Biochemistry, Molecular Biology and Bioinformatics, University of Parma, 43124 Parma, Italy
| | - Alessio Peracchi
- Department of Life Sciences, Laboratory of Biochemistry, Molecular Biology and Bioinformatics, University of Parma, 43124 Parma, Italy.
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36
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Steffen-Munsberg F, Vickers C, Kohls H, Land H, Mallin H, Nobili A, Skalden L, van den Bergh T, Joosten HJ, Berglund P, Höhne M, Bornscheuer UT. Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications. Biotechnol Adv 2015; 33:566-604. [PMID: 25575689 DOI: 10.1016/j.biotechadv.2014.12.012] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 01/25/2023]
Abstract
In this review we analyse structure/sequence-function relationships for the superfamily of PLP-dependent enzymes with special emphasis on class III transaminases. Amine transaminases are highly important for applications in biocatalysis in the synthesis of chiral amines. In addition, other enzyme activities such as racemases or decarboxylases are also discussed. The substrate scope and the ability to accept chemically different types of substrates are shown to be reflected in conserved patterns of amino acids around the active site. These findings are condensed in a sequence-function matrix, which facilitates annotation and identification of biocatalytically relevant enzymes and protein engineering thereof.
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Affiliation(s)
- Fabian Steffen-Munsberg
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Clare Vickers
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Hannes Kohls
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Henrik Land
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Hendrik Mallin
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Alberto Nobili
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Lilly Skalden
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Tom van den Bergh
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Per Berglund
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Uwe T Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
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37
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Lebedev AA, Isupov MN. Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the program Zanuda. ACTA ACUST UNITED AC 2014; 70:2430-43. [PMID: 25195756 DOI: 10.1107/s1399004714014795] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/23/2014] [Indexed: 11/10/2022]
Abstract
The presence of pseudo-symmetry in a macromolecular crystal and its interplay with twinning may lead to an incorrect space-group (SG) assignment. Moreover, if the pseudo-symmetry is very close to an exact crystallographic symmetry, the structure can be solved and partially refined in the wrong SG. Typically, in such incorrectly determined structures all or some of the pseudo-symmetry operations are, in effect, taken for crystallographic symmetry operations and vice versa. A mistake only becomes apparent when the R(free) ceases to decrease below 0.39 and further model rebuilding and refinement cannot improve the refinement statistics. If pseudo-symmetry includes pseudo-translation, the uncertainty in SG assignment may be associated with an incorrect choice of origin, as demonstrated by the series of examples provided here. The program Zanuda presented in this article was developed for the automation of SG validation. Zanuda runs a series of refinements in SGs compatible with the observed unit-cell parameters and chooses the model with the highest symmetry SG from a subset of models that have the best refinement statistics.
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Affiliation(s)
- Andrey A Lebedev
- CCP4, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
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38
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Recent achievements in developing the biocatalytic toolbox for chiral amine synthesis. Curr Opin Chem Biol 2014; 19:180-92. [PMID: 24721252 DOI: 10.1016/j.cbpa.2014.02.021] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 01/07/2023]
Abstract
Novel enzyme activities and chemoenzymatic reaction concepts have considerably expanded the biocatalytic toolbox for chiral amine synthesis. Creating new activities or extending the scope of existing enzymes by protein engineering is a common trend in biocatalysis and in chiral amine synthesis specifically. For instance, an amine dehydrogenase that allows for the direct asymmetric amination of ketones with ammonia was created by mutagenesis of an l-amino acid dehydrogenase. Another trend in chiral amine chemistry is the development of strategies allowing for the synthesis of secondary amines. For example the smart choice of substrates for amine transaminases provided access to secondary amines by chemoenzymatic reactions. Furthermore novel biocatalysts for the synthesis of secondary amines such as imine reductases and Pictet-Spenglerases have been identified and applied. Recent examples showed that the biocatalytic amine synthesis is emerging from simple model reactions towards industrial scale preparation of pharmaceutical relevant substances, for instance, as shown in the synthesis of a Janus kinase 2 inhibitor using an amine transaminase. A comparison of important process parameters such as turnover number and space-time yield demonstrates that biocatalytic strategies for asymmetric reductive amination are maturing and can already compete with established chemical methods.
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39
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Sayer C, Martinez-Torres RJ, Richter N, Isupov MN, Hailes HC, Littlechild JA, Ward JM. The substrate specificity, enantioselectivity and structure of the (R)-selective amine : pyruvate transaminase from Nectria haematococca. FEBS J 2014; 281:2240-53. [PMID: 24618038 PMCID: PMC4255305 DOI: 10.1111/febs.12778] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/03/2014] [Accepted: 03/05/2014] [Indexed: 11/30/2022]
Abstract
During the last decade the use of transaminases for the production of pharmaceutical and fine chemical intermediates has attracted a great deal of attention. Transaminases are versatile biocatalysts for the efficient production of amine intermediates and many have (S)-enantiospecificity. Transaminases with (R)-specificity are needed to expand the applications of these enzymes in biocatalysis. In this work we have identified a fungal putative (R)-specific transaminase from the Eurotiomycetes Nectria haematococca, cloned a synthetic version of this gene, demonstrated (R)-selective deamination of several substrates including (R)-α-methylbenzylamine, as well as production of (R)-amines, and determined its crystal structure. The crystal structures of the holoenzyme and the complex with an inhibitor gabaculine offer the first detailed insight into the structural basis for substrate specificity and enantioselectivity of the industrially important class of (R)-selective amine : pyruvate transaminases.
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Affiliation(s)
- Christopher Sayer
- Henry Wellcome Building for Biocatalysis, College of Life and Environmental Sciences, University of Exeter, EX4 4QD, UK
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40
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Thomsen M, Skalden L, Palm GJ, Höhne M, Bornscheuer UT, Hinrichs W. Crystallographic characterization of the (R)-selective amine transaminase from Aspergillus fumigatus. ACTA ACUST UNITED AC 2014; 70:1086-93. [PMID: 24699652 DOI: 10.1107/s1399004714001084] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/15/2014] [Indexed: 11/10/2022]
Abstract
The importance of amine transaminases for producing optically pure chiral precursors for pharmaceuticals and chemicals has substantially increased in recent years. The X-ray crystal structure of the (R)-selective amine transaminase from the fungus Aspergillus fumigatus was solved by S-SAD phasing to 1.84 Å resolution. The refined structure at 1.27 Å resolution provides detailed knowledge about the molecular basis of substrate recognition and conversion to facilitate protein-engineering approaches. The protein forms a homodimer and belongs to fold class IV of the pyridoxal-5'-phosphate-dependent enzymes. Both subunits contribute residues to form two active sites. The structure of the holoenzyme shows the catalytically important cofactor pyridoxal-5'-phosphate bound as an internal aldimine with the catalytically responsible amino-acid residue Lys179, as well as in its free form. A long N-terminal helix is an important feature for the stability of this fungal (R)-selective amine transaminase, but is missing in branched-chain amino-acid aminotransferases and D-amino-acid aminotransferases.
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Affiliation(s)
- Maren Thomsen
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Lilly Skalden
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Gottfried J Palm
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Matthias Höhne
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Uwe T Bornscheuer
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Winfried Hinrichs
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
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41
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Łyskowski A, Gruber C, Steinkellner G, Schürmann M, Schwab H, Gruber K, Steiner K. Crystal structure of an (R)-selective ω-transaminase from Aspergillus terreus. PLoS One 2014; 9:e87350. [PMID: 24498081 PMCID: PMC3907554 DOI: 10.1371/journal.pone.0087350] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 12/19/2013] [Indexed: 11/18/2022] Open
Abstract
Chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-Transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5′-phosphate (PLP) as cofactor. In nature, (S)-selective amine transaminases are more abundant than the (R)-selective enzymes, and therefore more information concerning their structures is available. Here, we present the crystal structure of an (R)-ω-transaminase from Aspergillus terreus determined by X-ray crystallography at a resolution of 1.6 Å. The structure of the protein is a homodimer that displays the typical class IV fold of PLP-dependent aminotransferases. The PLP-cofactor observed in the structure is present in two states (i) covalently bound to the active site lysine (the internal aldimine form) and (ii) as substrate/product adduct (the external aldimine form) and free lysine. Docking studies revealed that (R)-transaminases follow a dual binding mode, in which the large binding pocket can harbour the bulky substituent of the amine or ketone substrate and the α-carboxylate of pyruvate or amino acids, and the small binding pocket accommodates the smaller substituent.
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Affiliation(s)
| | | | | | | | - Helmut Schwab
- ACIB GmbH, c/o TU Graz, Graz, Austria
- Institute of Molecular Biotechnology, TU Graz, Graz, Austria
| | - Karl Gruber
- ACIB GmbH, c/o TU Graz, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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42
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Park ES, Park SR, Han SW, Dong JY, Shin JS. Structural Determinants for the Non-Canonical Substrate Specificity of the ω-Transaminase fromParacoccus denitrificans. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300786] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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Investigation of one-enzyme systems in the ω-transaminase-catalyzed synthesis of chiral amines. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.06.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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