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Gong R, Yao P, Chen X, Feng J, Wu Q, Lau PCK, Zhu D. Accessing d
-Valine Synthesis by Improved Variants of Bacterial Cyclohexylamine Oxidase. ChemCatChem 2017. [DOI: 10.1002/cctc.201701229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rui Gong
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P.R. China
- University of Chinese Academy of Sciences; No.19(A) Yuquan Road, Shijingshan District Beijing 100049 P.R. China
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P.R. China
| | - Xi Chen
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P.R. China
| | - Jinhui Feng
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P.R. China
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P.R. China
| | - Peter C. K. Lau
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P.R. China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P.R. China
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Aranaz I, Acosta N, Heras A. Enzymatic d-p-hydrophenyl glycine synthesis using chitin and chitosan as supports for biocatalyst immobilization. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1366991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- I. Aranaz
- Departamento de Química Física II, Instituto de Estudios Biofuncionales, Universidad Complutense de Madrid, Madrid, Spain
| | - N. Acosta
- Departamento de Química Física II, Instituto de Estudios Biofuncionales, Universidad Complutense de Madrid, Madrid, Spain
| | - A. Heras
- Departamento de Química Física II, Instituto de Estudios Biofuncionales, Universidad Complutense de Madrid, Madrid, Spain
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Translational fidelity and mistranslation in the cellular response to stress. Nat Microbiol 2017; 2:17117. [PMID: 28836574 DOI: 10.1038/nmicrobiol.2017.117] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/20/2017] [Indexed: 11/08/2022]
Abstract
Faithful translation of mRNA into the corresponding polypeptide is a complex multistep process, requiring accurate amino acid selection, transfer RNA (tRNA) charging and mRNA decoding on the ribosome. Key players in this process are aminoacyl-tRNA synthetases (aaRSs), which not only catalyse the attachment of cognate amino acids to their respective tRNAs, but also selectively hydrolyse incorrectly activated non-cognate amino acids and/or misaminoacylated tRNAs. This aaRS proofreading provides quality control checkpoints that exclude non-cognate amino acids during translation, and in so doing helps to prevent the formation of an aberrant proteome. However, despite the intrinsic need for high accuracy during translation, and the widespread evolutionary conservation of aaRS proofreading pathways, requirements for translation quality control vary depending on cellular physiology and changes in growth conditions, and translation errors are not always detrimental. Recent work has demonstrated that mistranslation can also be beneficial to cells, and some organisms have selected for a higher degree of mistranslation than others. The aims of this Review Article are to summarize the known mechanisms of protein translational fidelity and explore the diversity and impact of mistranslation events as a potentially beneficial response to environmental and cellular stress.
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de Souza ROMA, Miranda LSM, Bornscheuer UT. A Retrosynthesis Approach for Biocatalysis in Organic Synthesis. Chemistry 2017; 23:12040-12063. [DOI: 10.1002/chem.201702235] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Rodrigo O. M. A. de Souza
- Biocatalysis and Organic Synthesis Group; Federal University of Rio de Janeiro, Chemistry Institute; 21941909 Rio de Janeiro Brazil
| | - Leandro S. M. Miranda
- Biocatalysis and Organic Synthesis Group; Federal University of Rio de Janeiro, Chemistry Institute; 21941909 Rio de Janeiro Brazil
| | - Uwe T. Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 17487 Greifswald Germany
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Structure-Based Engineering of an Artificially Generated NADP +-Dependent d-Amino Acid Dehydrogenase. Appl Environ Microbiol 2017; 83:AEM.00491-17. [PMID: 28363957 DOI: 10.1128/aem.00491-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/22/2017] [Indexed: 01/13/2023] Open
Abstract
A stable NADP+-dependent d-amino acid dehydrogenase (DAADH) was recently created from Ureibacillus thermosphaericusmeso-diaminopimelate dehydrogenase through site-directed mutagenesis. To produce a novel DAADH mutant with different substrate specificity, the crystal structure of apo-DAADH was determined at a resolution of 1.78 Å, and the amino acid residues responsible for the substrate specificity were evaluated using additional site-directed mutagenesis. By introducing a single D94A mutation, the enzyme's substrate specificity was dramatically altered; the mutant utilized d-phenylalanine as the most preferable substrate for oxidative deamination and had a specific activity of 5.33 μmol/min/mg at 50°C, which was 54-fold higher than that of the parent DAADH. In addition, the specific activities of the mutant toward d-leucine, d-norleucine, d-methionine, d-isoleucine, and d-tryptophan were much higher (6 to 25 times) than those of the parent enzyme. For reductive amination, the D94A mutant exhibited extremely high specific activity with phenylpyruvate (16.1 μmol/min/mg at 50°C). The structures of the D94A-Y224F double mutant in complex with NADP+ and in complex with both NADPH and 2-keto-6-aminocapronic acid (lysine oxo-analogue) were then determined at resolutions of 1.59 Å and 1.74 Å, respectively. The phenylpyruvate-binding model suggests that the D94A mutation prevents the substrate phenyl group from sterically clashing with the side chain of Asp94. A structural comparison suggests that both the enlarged substrate-binding pocket and enhanced hydrophobicity of the pocket are mainly responsible for the high reactivity of the D94A mutant toward the hydrophobic d-amino acids with bulky side chains.IMPORTANCE In recent years, the potential uses for d-amino acids as source materials for the industrial production of medicines, seasonings, and agrochemicals have been growing. To date, several methods have been used for the production of d-amino acids, but all include tedious steps. The use of NAD(P)+-dependent d-amino acid dehydrogenase (DAADH) makes single-step production of d-amino acids from oxo-acid analogs and ammonia possible. We recently succeeded in creating a stable DAADH and demonstrated that it is applicable for one-step synthesis of d-amino acids, such as d-leucine and d-isoleucine. As the next step, the creation of an enzyme exhibiting different substrate specificity and higher catalytic efficiency is a key to the further development of d-amino acid production. In this study, we succeeded in creating a novel mutant exhibiting extremely high catalytic activity for phenylpyruvate amination. Structural insight into the mutant will be useful for further improvement of DAADHs.
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A Newly Determined Member of the meso-Diaminopimelate Dehydrogenase Family with a Broad Substrate Spectrum. Appl Environ Microbiol 2017; 83:AEM.00476-17. [PMID: 28341677 DOI: 10.1128/aem.00476-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 03/16/2017] [Indexed: 01/07/2023] Open
Abstract
meso-Diaminopimelate dehydrogenase (meso-DAPDH) from Symbiobacterium thermophilum (StDAPDH) is the first member of the meso-DAPDH family known to catalyze the asymmetric reductive amination of 2-keto acids to produce d-amino acids. It is important to understand the catalytic mechanisms of StDAPDH and other enzymes in this family. In this study, based on an evolutionary analysis and examination of catalytic activity, the meso-DAPDH enzymes can be divided into two types. Type I showed highly preferable activity toward meso-diaminopimelate (meso-DAP), and type II exhibited obviously reversible amination activity with a broad substrate spectrum. StDAPDH belongs to type II. A quaternary structure analysis revealed that insertions/deletions (indels) and a loss of quaternary structure resulted in divergence among members of the meso-DAPDH family. A structure alignment of StDAPDH with a representative of type I, the meso-DAPDH from Corynebacterium glutamicum (CgDAPDH), indicated that they had the same folding. Based on sequence and conservation analyses, two amino acid residues of StDAPDH, R35 and R71, were found to be highly conserved within type II while also distinct from each other between the subtypes. Site mutagenesis studies identified R71 as a substrate preference-related residue of StDAPDH, which may serve as an indicator of the amination preference of type II. These results deepen the present understanding of the meso-DAPDH family and provide a solid foundation for the discovery and engineering of meso-DAPDH for d-amino acid biosynthesis.IMPORTANCE The l-form of amino acids is typically more abundant than the d-form. However, the d-form has many important pharmaceutical applications. meso-Diaminopimelate dehydrogenase (meso-DAPDH) from Symbiobacterium thermophilum (StDAPDH) was the first member of meso-DAPDH known to catalyze the amination of 2-keto acids to produce d-amino acids. Accordingly, we analyzed the evolution of meso-DAPDH proteins and found that they form two groups, i.e., type I proteins, which show high preference toward meso-diaminopimelate (meso-DAP), and type II proteins, which show a broad substrate spectrum. We examined the differences in sequence, ternary structure, and quaternary structure to determine the mechanisms underlying the functional differences between the type I and type II lineages. These results will facilitate the identification of additional meso-DAPDHs and may provide guidance to protein engineering studies for d-amino acid biosynthesis.
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Kawakami R, Sakuraba H, Ohmori T, Ohshima T. First characterization of an archaeal amino acid racemase with broad substrate specificity from the hyperthermophile Pyrococcus horikoshii OT-3. J Biosci Bioeng 2017; 124:23-27. [PMID: 28343923 DOI: 10.1016/j.jbiosc.2017.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/26/2017] [Accepted: 02/05/2017] [Indexed: 01/22/2023]
Abstract
A novel amino acid racemase with broad substrate specificity (BAR) was recently isolated from the hyperthermophilic archaeon Pyrococcus horikoshii OT-3. Characterization of this enzyme has been difficult, however, because the recombinant enzyme is produced mainly as an inclusion body in Escherichia coli. In this study, expression of the recombinant protein into the soluble fraction was markedly improved by co-expression with chaperone molecules. The purified enzyme retained its full activity after incubation at 80°C for at least 2 h in buffer (pH 7-10), making this enzyme the most thermostable amino acid racemase so far known. Besides the nine amino acids containing hydrophobic and aromatic amino acids previously reported (Kawakami et al., Amino Acids, 47, 1579-1587, 2015), the enzyme exhibited substantial activity toward Thr (about 42% of relative activity toward Phe) and showed no activity toward Arg, His, Gln, and Asn. The substrate specificity of this enzyme thus differs markedly from those of other known amino acid racemases. In particular, the high reaction rate with Trp and Tyr, in addition to Leu, Met and Phe as substrates is a noteworthy feature of this enzyme. The high reactivity toward Trp and Tyr, as well as extremely high thermostability, is likely a major advantage of using BAR for biochemical conversion of these aromatic amino acids.
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Affiliation(s)
- Ryushi Kawakami
- Graduate School of Bioscience and Bioindustry, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, Tokushima 770-8513, Japan.
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2392 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Taketo Ohmori
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka 535-8585, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka 535-8585, Japan
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Manig F, Kuhne K, von Neubeck C, Schwarzenbolz U, Yu Z, Kessler BM, Pietzsch J, Kunz-Schughart LA. The why and how of amino acid analytics in cancer diagnostics and therapy. J Biotechnol 2017; 242:30-54. [DOI: 10.1016/j.jbiotec.2016.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 12/11/2022]
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59
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Efficient Production of Enantiopure d-Lysine from l-Lysine by a Two-Enzyme Cascade System. Catalysts 2016. [DOI: 10.3390/catal6110168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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60
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Chen M, Shi C, Zhao J, Gao Z, Zhang C. Application and microbial preparation of D-valine. World J Microbiol Biotechnol 2016; 32:171. [PMID: 27565781 DOI: 10.1007/s11274-016-2119-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/04/2016] [Indexed: 11/28/2022]
Abstract
D-Valine is an important organic chiral source and has extensive industrial application, which is used as intermediate for the synthesis of agricultural pesticides, semi-synthetic veterinary antibiotics and pharmaceutical drugs. Its derivatives have shown great activity in clinical use, such as penicillamine for the treatment of immune-deficiency diseases, and actinomycin D for antitumor therapy. Fluvalinate, a pyrethroid pesticide made from D-valine, is a broad-spectrum insecticide with low mammalian toxicity. Valnemulin, a semi-synthetic pleuromutilin derivative synthesized from D-valine, is an antibiotic for animals. Moreover, D-valine is also used in cell culture for selectively inhibiting fibroblasts proliferation. Due to its widespread application, D-valine is gaining more and more attention and some approaches for D-valine preparation have been investigated. In comparison with other approaches, microbial preparation of D-valine is more competitive and promising because of its high stereo selectivity, mild reaction conditions and environmental friendly process. So far, microbial preparation of D-valine can be mainly classified into three categories: microbial asymmetric degradation of DL-valine, microbial stereoselective hydrolysis of N-acyl-DL-valine by D-aminoacylase, and microbial specific hydrolysis of DL-5-isopropylhydantoin by D-hydantoinase coupled with D-carbamoylase. In this paper, the industrial application of D-valine and its microbial preparation are reviewed.
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Affiliation(s)
- Ming Chen
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
| | - Chao Shi
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
| | - Jing Zhao
- College of Life Science, Dalian Nationalities University, Dalian, 116600, People's Republic of China
| | - Ziqing Gao
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
| | - Chunzhi Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China.
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61
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Femmer C, Bechtold M, Roberts TM, Panke S. Exploiting racemases. Appl Microbiol Biotechnol 2016; 100:7423-36. [DOI: 10.1007/s00253-016-7729-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/03/2016] [Accepted: 07/04/2016] [Indexed: 01/11/2023]
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Roles of d-Amino Acids on the Bioactivity of Host Defense Peptides. Int J Mol Sci 2016; 17:ijms17071023. [PMID: 27376281 PMCID: PMC4964399 DOI: 10.3390/ijms17071023] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 12/15/2022] Open
Abstract
Host defense peptides (HDPs) are positively-charged and amphipathic components of the innate immune system that have demonstrated great potential to become the next generation of broad spectrum therapeutic agents effective against a vast array of pathogens and tumor. As such, many approaches have been taken to improve the therapeutic efficacy of HDPs. Amongst these methods, the incorporation of d-amino acids (d-AA) is an approach that has demonstrated consistent success in improving HDPs. Although, virtually all HDP review articles briefly mentioned about the role of d-AA, however it is rather surprising that no systematic review specifically dedicated to this topic exists. Given the impact that d-AA incorporation has on HDPs, this review aims to fill that void with a systematic discussion of the impact of d-AA on HDPs.
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Characterization and Soluble Expression of D-Hydantoinase from Pseudomonas fluorescens for the Synthesis of D-Amino Acids. Appl Biochem Biotechnol 2016; 179:1-15. [PMID: 26821258 DOI: 10.1007/s12010-015-1975-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/29/2015] [Indexed: 10/22/2022]
Abstract
An active D-hydantoinase from Pseudomonas fluorescens was heterogeneously overexpressed in Escherichia coli BL21(DE3) and designated as D-PfHYD. Sequence and consensus analysis suggests that D-PfHYD belongs to the dihydropyrimidinase/hydantoinase family and possesses catalytic residues for metal ion and hydantoin binding. D-PfHYD was purified to homogeneity by nickel affinity chromatography for characterization. D-PfHYD is a homotetramer with molecular weight of 215 kDa and specific activity of 20.9 U mg(-1). D-PfHYD showed the highest activity at pH 9.0 and 60 °C. Metal ions such as Mn(2+), Fe(2+), and Fe(3+) could activate D-PfHYD with 20 % improvement. Substrate specificity analysis revealed that purified D-PfHYD preferred aliphatic to aromatic 5'-monosubstituted hydantoins. Among various strategies tested, chaperone GroES-GroEL was efficient in improving the soluble expression of D-PfHYD. Employing 1.0 g L(-1) recombinant E. coli BL21(DE3)-pET28-hyd/pGRO7 dry cells, 100 mM isobutyl hydantoin was converted into D-isoleucine with 98.7 % enantiomeric excess (ee), isolation yield of 78.3 %, and substrate to biocatalyst ratio of 15.6. Our results suggest that recombinant D-PfHYD could be potentially applied in the synthesis of D-amino acids.
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Winkelblech J, Xie X, Li SM. Characterisation of 6-DMATSMo from Micromonospora olivasterospora leading to identification of the divergence in enantioselectivity, regioselectivity and multiple prenylation of tryptophan prenyltransferases. Org Biomol Chem 2016; 14:9883-9895. [DOI: 10.1039/c6ob01803c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Identification of a new tryptophan prenyltransferase 6-DMATSMo and different behaviours of DMATS enzymes for regiospecific mono- and diprenylations of l- and d-tryptophan as well as methylated derivatives.
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Affiliation(s)
- Julia Winkelblech
- Philipps-Universität Marburg
- Institut für Pharmazeutische Biologie und Biotechnologie
- 35037 Marburg
- Germany
- Zentrum für Synthetische Mikrobiologie
| | - Xiulan Xie
- Philipps-Universität Marburg
- Fachbereich Chemie
- 35032 Marburg
- Germany
| | - Shu-Ming Li
- Philipps-Universität Marburg
- Institut für Pharmazeutische Biologie und Biotechnologie
- 35037 Marburg
- Germany
- Zentrum für Synthetische Mikrobiologie
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65
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Hernández SB, Cava F. Environmental roles of microbial amino acid racemases. Environ Microbiol 2015; 18:1673-85. [DOI: 10.1111/1462-2920.13072] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/15/2015] [Accepted: 09/27/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Sara B. Hernández
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
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