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Synthesis of d-Amino Acid-Containing Dipeptides Using the Adenylation Domains of Nonribosomal Peptide Synthetase. Appl Environ Microbiol 2019; 85:AEM.00120-19. [PMID: 31003981 DOI: 10.1128/aem.00120-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/10/2019] [Indexed: 11/20/2022] Open
Abstract
Recent papers have reported dipeptides containing d-amino acids to have novel effects that cannot be observed with ll-dipeptides, and such dipeptides are expected to be novel functional compounds for pharmaceuticals and food additives. Although the functions of d-amino acid-containing dipeptides are gaining more attention, there are few reports on the synthetic enzymes that can accept d-amino acids as substrates, and synthetic methods for d-amino acid-containing dipeptides have not yet been constructed. Previously, we developed a chemoenzymatic system for amide synthesis that comprised enzymatic activation and a subsequent nucleophilic substitution reaction. In this study, we demonstrated the application of the system for d-amino acid-containing-dipeptide synthesis. We chose six adenylation domains as targets according to our newly constructed hypothesis, i.e., an adenylation domain located upstream from the epimerization domain may activate d-amino acid as well as l-amino acid. We successfully synthesized over 40 kinds of d-amino acid-containing dipeptides, including ld-, dl-, and dd-dipeptides, using only two adenylation domains, TycA-A from tyrocidine synthetase and BacB2-A from bacitracin synthetase. Furthermore, this study offered the possibility that the epimerization domain could be a clue to the activity of the adenylation domains toward d-amino acid. This paper provides additional information regarding d-amino acid-containing-dipeptide synthesis through the combination of enzymatic adenylation and chemical nucleophilic reaction, and this system will be a useful tool for dipeptide synthesis.IMPORTANCE Because almost all amino acids in nature are l-amino acids, the functioning of d-amino acids has received little attention. Thus, there is little information available on the activity of enzymes toward d-amino acids or synthetic methods for d-amino acid-containing dipeptides. Recently, d-amino acids and d-amino acid-containing peptides have attracted attention as novel functional compounds, and d-amino acid-activating enzymes and synthetic methods are required for the development of the d-amino acid-containing-peptide industry. This study provides additional knowledge regarding d-amino acid-activating enzymes and proposes a unique synthetic method for d-amino acid-containing peptides, including ld-, dl-, and dd-dipeptides.
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Clark L, Leatherby D, Krilich E, Ropelewski AJ, Perozich J. In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations. PLoS One 2018; 13:e0203218. [PMID: 30180199 PMCID: PMC6122825 DOI: 10.1371/journal.pone.0203218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/16/2018] [Indexed: 12/24/2022] Open
Abstract
Luciferases, aryl- and fatty-acyl CoA synthetases, and non-ribosomal peptide synthetase proteins belong to the class I adenylate-forming enzyme superfamily. The reaction catalyzed by the adenylate-forming enzymes is categorized by a two-step process of adenylation and thioesterification. Although all of these proteins perform a similar two-step process, each family may perform the process to yield completely different results. For example, luciferase proteins perform adenylation and oxidation to produce the green fluorescent light found in fireflies, while fatty-acyl CoA synthetases perform adenylation and thioesterification with coenzyme A to assist in metabolic processes involving fatty acids. This study aligned a total of 374 sequences belonging to the adenylate-forming superfamily. Analysis of the sequences revealed five fully conserved residues throughout all sequences, as well as 78 more residues conserved in at least 60% of sequences aligned. Conserved positions are involved in magnesium and AMP binding and maintaining enzyme structure. Also, ten conserved sequence motifs that included most of the conserved residues were identified. A phylogenetic tree was used to assign sequences into nine different groups. Finally, group entropy analysis identified novel conservations unique to each enzyme group. Common group-specific positions identified in multiple groups include positions critical to coordinating AMP and the CoA-bound product, a position that governs active site shape, and positions that help to maintain enzyme structure through hydrogen bonds and hydrophobic interactions. These positions could serve as excellent targets for future research.
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Affiliation(s)
- Louis Clark
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
| | - Danielle Leatherby
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
| | - Elizabeth Krilich
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
| | - Alexander J Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - John Perozich
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
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Hara R, Hirai K, Suzuki S, Kino K. A chemoenzymatic process for amide bond formation by an adenylating enzyme-mediated mechanism. Sci Rep 2018; 8:2950. [PMID: 29440726 PMCID: PMC5811625 DOI: 10.1038/s41598-018-21408-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 02/02/2018] [Indexed: 12/13/2022] Open
Abstract
Amide bond formation serves as a fundamental reaction in chemistry, and is practically useful for the synthesis of peptides, food additives, and polymers. However, current methods for amide bond formation essentially generate wastes and suffer from poor atom economy under harsh conditions. To solve these issues, we demonstrated an alternative synthesis method for diverse tryptophyl-N-alkylamides by the combination of the first adenylation domain of tyrocidine synthetase 1 with primary or secondary amines as nucleophiles. Moreover, the physiological role of this domain is l-phenylalanine adenylation; however, we revealed that it displayed broad substrate flexibility from mono-substituted tryptophan analogues to even d-tryptophan. To the best of our knowledge, this is the first evidence for an adenylating enzyme-mediated direct amide bond formation via a sequential enzymatic activation of amino acids followed by nucleophilic substitution by general amines. These findings facilitate the design of a promising tool for biocatalytic straightforward amide bond formation with less side products.
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Affiliation(s)
- Ryotaro Hara
- Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Kengo Hirai
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Shin Suzuki
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Kuniki Kino
- Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555, Japan. .,Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555, Japan.
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Suzuki S, Hara R, Kino K. Production of aminoacyl prolines using the adenylation domain of nonribosomal peptide synthetase with class III polyphosphate kinase 2-mediated ATP regeneration. J Biosci Bioeng 2018; 125:644-648. [PMID: 29366718 DOI: 10.1016/j.jbiosc.2017.12.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/25/2017] [Accepted: 12/26/2017] [Indexed: 11/19/2022]
Abstract
An ATP regeneration system is advantageous for industrial processes that are coupled with ATP-dependent enzymes. For ATP regeneration from AMP, a few methods have been reported; however, these methods employ multiple enzymes. To establish an ATP regeneration system using a single enzyme, we focused on class III polyphosphate kinase 2 (class III PPK2) that can synthesize ATP from AMP and polyphosphate. We constructed an ATP regeneration system from AMP using Deipr_1912, a class III PPK2 from Deinococcus proteolyticus NBRC 101906T, coupled with aminoacyl proline (Xaa-Pro) synthesis catalyzed by the adenylation domain of tyrocidine synthetase A (TycA-A). Using this system, 0.87 mM of l-Trp-l-Pro was successfully synthesized from AMP after 72 h. Farther, addition of inorganic pyrophosphatase from Escherichia coli to the coupling reaction increased the reaction rate by 14-fold to yield 6.2 mM l-Trp-l-Pro. When the coupling reaction was applied to whole-cell reactions in E. coli BL21(DE3) pepQ-putA-, ATP was successfully regenerated from AMP by Deipr_1912, and 6.7 mM of l-Trp-l-Pro was produced after 24 h with the supplementation of 10 mM AMP. In addition, by altering the substrate amino acid of TycA-A, not only l-Trp-l-Pro, but also various other l-Xaa-l-Pro (Xaa = Val, Leu, Met, or Tyr) were produced using the whole-cell reaction incorporating ATP regeneration. Therefore, a production method for Xaa-Pro employing the adenylation domain of a nonribosomal peptide synthetase was established by introducing an ATP regeneration system that utilizes class III PPK2 with pyrophosphatase.
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Affiliation(s)
- Shin Suzuki
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Ryotaro Hara
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kuniki Kino
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan; Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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Wood AJL, Weise NJ, Frampton JD, Dunstan MS, Hollas MA, Derrington SR, Lloyd RC, Quaglia D, Parmeggiani F, Leys D, Turner NJ, Flitsch SL. Adenylation Activity of Carboxylic Acid Reductases Enables the Synthesis of Amides. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707918] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alexander J. L. Wood
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Nicholas J. Weise
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Joseph D. Frampton
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Mark S. Dunstan
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM); Manchester Institute of Biotechnology; The University of Manchester; Manchester M1 7DN UK
| | - Michael A. Hollas
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Sasha R. Derrington
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Richard C. Lloyd
- Dr. Reddy's Laboratories (EU) Ltd.; 410 Cambridge Science Park, Milton Road Cambridge CB4 0PE UK
| | - Daniela Quaglia
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
- Chemistry Department; Université de Montréal; 2900, Edouard-Montpetit H3C 3J7 Montréal Canada
| | - Fabio Parmeggiani
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - David Leys
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Nicholas J. Turner
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Sabine L. Flitsch
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
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Wood AJL, Weise NJ, Frampton JD, Dunstan MS, Hollas MA, Derrington SR, Lloyd RC, Quaglia D, Parmeggiani F, Leys D, Turner NJ, Flitsch SL. Adenylation Activity of Carboxylic Acid Reductases Enables the Synthesis of Amides. Angew Chem Int Ed Engl 2017; 56:14498-14501. [DOI: 10.1002/anie.201707918] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/05/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Alexander J. L. Wood
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Nicholas J. Weise
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Joseph D. Frampton
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Mark S. Dunstan
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM); Manchester Institute of Biotechnology; The University of Manchester; Manchester M1 7DN UK
| | - Michael A. Hollas
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Sasha R. Derrington
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Richard C. Lloyd
- Dr. Reddy's Laboratories (EU) Ltd.; 410 Cambridge Science Park, Milton Road Cambridge CB4 0PE UK
| | - Daniela Quaglia
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
- Chemistry Department; Université de Montréal; 2900, Edouard-Montpetit H3C 3J7 Montréal Canada
| | - Fabio Parmeggiani
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - David Leys
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Nicholas J. Turner
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
| | - Sabine L. Flitsch
- School of Chemistry & Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street M1 7DN Manchester UK
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Hara R, Suzuki R, Kino K. Hydroxamate-based colorimetric assay to assess amide bond formation by adenylation domain of nonribosomal peptide synthetases. Anal Biochem 2015; 477:89-91. [PMID: 25615416 DOI: 10.1016/j.ab.2015.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/26/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022]
Abstract
We demonstrated the usefulness of a hydroxamate-based colorimetric assay for predicting amide bond formation (through an aminoacyl-AMP intermediate) by the adenylation domain of nonribosomal peptide synthetases. By using a typical adenylation domain of tyrocidine synthetase (involved in tyrocidine biosynthesis), we confirmed the correlation between the absorbance at 490 nm of the l-Trp-hydroxamate-Fe(3+) complex and the formation of l-Trp-l-Pro, where l-Pro was used instead of hydroxylamine. Furthermore, this assay was adapted to the adenylation domains of surfactin synthetase (involved in surfactin biosynthesis) and bacitracin synthetase (involved in bacitracin biosynthesis). Consequently, the formation of various aminoacyl l-Pro formations was observed.
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Affiliation(s)
- Ryotaro Hara
- Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Ryohei Suzuki
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Kuniki Kino
- Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan; Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan.
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Usuki H, Yamamoto Y, Arima J, Iwabuchi M, Miyoshi S, Nitoda T, Hatanaka T. Peptide bond formation by aminolysin-A catalysis: a simple approach to enzymatic synthesis of diverse short oligopeptides and biologically active puromycins. Org Biomol Chem 2011; 9:2327-35. [PMID: 21321761 DOI: 10.1039/c0ob00403k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new S9 family aminopeptidase derived from the actinobacterial thermophile Acidothermus cellulolyticus was cloned and engineered into a transaminopeptidase by site-directed mutagenesis of catalytic Ser(491) into Cys. The engineered biocatalyst, designated aminolysin-A, can catalyze the formation of peptide bonds to give linear homo-oligopeptides, hetero-dipeptides, and cyclic dipeptides using cost-effective substrates in a one-pot reaction. Aminolysin-A can recognize several C-terminal-modified amino acids, including the l- and d-forms, as acyl donors as well as free amines, including amino acids and puromycin aminonucleoside, as acyl acceptors. The absence of amino acid esters prevents the formation of peptides; therefore, the reaction mechanism involves aminolysis and not a reverse reaction of hydrolysis. The aminolysin system will be a beneficial tool for the preparation of structurally diverse peptide mimetics by a simple approach.
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Affiliation(s)
- Hirokazu Usuki
- Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences (RIBS), 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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Usuki H, Uesugi Y, Arima J, Yamamoto Y, Iwabuchi M, Hatanaka T. Engineered transaminopeptidase, aminolysin-S for catalysis of peptide bond formation to give linear and cyclic dipeptides by one-pot reaction. Chem Commun (Camb) 2010; 46:580-2. [DOI: 10.1039/b914320c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Synthesis and application of dipeptides; current status and perspectives. Appl Microbiol Biotechnol 2008; 81:13-22. [DOI: 10.1007/s00253-008-1590-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/22/2008] [Accepted: 06/23/2008] [Indexed: 10/21/2022]
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