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Naeem M, Hao S, Chu M, Zhang X, Huang X, Wang J, He G, Zhao B, Ju J. Efficient biosynthesis of D/L-alanine in the recombinant Escherichia coli BL21(DE3) by biobrick approach. Front Bioeng Biotechnol 2024; 12:1421167. [PMID: 39188373 PMCID: PMC11345225 DOI: 10.3389/fbioe.2024.1421167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/26/2024] [Indexed: 08/28/2024] Open
Abstract
Alanine is the most abundant chiral amino acid that exists into the D-alanine or L-alanine forms with diverse applications in the biomedical, pharmaceutical, plastics, and food industries. D/L-alanine production can be carried out through chemical, microbial fermentation, and biocatalytic methods and not much effective due to complicated processes or purification issues and is still challenging to achieve a higher yield. In the present study, biobrick method was utilized for efficient production of D/L-alanine in the recombinant Escherichia coli BL21(DE3) with tandem three-gene co-expression plasmid. Firstly, the co-expression plasmid pET-22bNS-DadX-Ald-Gdh containing three genes, alanine dehydrogenase (ald), alanine racemase (dadX), and glucose dehydrogenase (gdh) from Bacillus pseudofirmus OF4 were successfully constructed and introduced into the E. coli BL21(DE3) strain. Then, under optimized conditions in the whole-cell biocatalytic reaction [20 mM Na2CO3-NaHCO3 (pH 10.1), 200 mM D-glucose, 200 mM sodium pyruvate, and 200 mM ammonium chloride], the concentration of D-alanine and L-alanine reached the maximum value (6.48 g/L and 7.05 g/L) after 3.0 h reaction time at 37°C under 180 rpm rotation. Meanwhile, promoter replacement experiments and Western blot analysis revealed that the expression level of protein OF4Ald had a significant effect on the production of D/L-alanine, indicating that alanine dehydrogenase might be the rate-limiting enzyme for D/L-alanine synthesis. This study provides a simple, feasible, and efficient biosynthesis process of D/L-alanine, which could explore emerging applications for large-scale production of industrial bioproducts.
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Affiliation(s)
- Muhammad Naeem
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Shimiao Hao
- College of Life Science, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Shijiazhuang, China
| | - Mengqiu Chu
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xuan Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xinyan Huang
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jiaying Wang
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Guangzheng He
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Shijiazhuang, China
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2
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A bi-enzymatic cascade to yield pyruvate as co-substrate for l-tyrosine production. Appl Microbiol Biotechnol 2020; 104:10005-10018. [DOI: 10.1007/s00253-020-10975-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/07/2020] [Accepted: 10/25/2020] [Indexed: 11/25/2022]
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3
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Muhammad M, Li Y, Gong S, Shi Y, Ju J, Zhao B, Liu D. Purification, Characterization and Inhibition of Alanine Racemase from a Pathogenic Strain of Streptococcus iniae. Pol J Microbiol 2019; 68:331-341. [PMID: 31880879 PMCID: PMC7256847 DOI: 10.33073/pjm-2019-036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 01/25/2023] Open
Abstract
Streptococcus iniae is a pathogenic and zoonotic bacteria that impacted high mortality to many fish species as well as capable of causing serious disease to humans. Alanine racemase (Alr, EC 5.1.1.1) is a pyridoxal-5’-phosphate (PLP)-containing homodimeric enzyme that catalyzes the racemization of L-alanine and D-alanine. In this study, we purified alanine racemase from S. iniae that was isolated from an infected Chinese sturgeon (Acipenser sinensis), as well as determined its biochemical characteristics and inhibitors. The alr gene has an open reading frame (ORF) of 1107 bp, encoding a protein of 369 amino acids, which has a molecular mass of 40 kDa. The enzyme has optimal activity at a temperature of 35°C and a pH of 9.5. It belongs to the PLP-dependent enzymes family and is highly specific to L-alanine. S. iniae Alr (SiAlr) could be inhibited by some metal ions, hydroxylamine and dithiothreitol (DTT). The kinetic parameters Km and Vmax of the enzyme were 33.11 mM, 2426 units/mg for L-alanine, and 14.36 mM, 963.6 units/mg for D-alanine. Finally, the 50% inhibitory concentrations (IC50) values and antibiotic activity of two alanine racemase inhibitors (homogentisic acid and hydroquinone), were determined and found to be effective against both Gram-positive and Gram-negative bacteria employed in this study.
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Affiliation(s)
- Murtala Muhammad
- College of Life Science, Hebei Normal University , Shijiazhuang , China
| | - Yangyang Li
- College of Life Science, Hebei Normal University , Shijiazhuang , China
| | - Siyu Gong
- College of Life Science, Hebei Normal University , Shijiazhuang , China
| | - Yanmin Shi
- College of Life Science, Hebei Normal University , Shijiazhuang , China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University , Shijiazhuang , China
| | - Baohua Zhao
- College of Life Science, Hebei Normal University , Shijiazhuang , China
| | - Dong Liu
- College of Life Science, Hebei Normal University , Shijiazhuang , China
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4
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Biochemical characterization and mutational analysis of alanine racemase from Clostridium perfringens. J Biosci Bioeng 2019; 128:149-155. [DOI: 10.1016/j.jbiosc.2019.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 11/24/2022]
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5
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Dong H, Han Q, Guo Y, Ju J, Wang S, Yuan C, Long W, He X, Xu S, Li S. Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1. Biochem Biophys Res Commun 2018; 503:2319-2325. [PMID: 29964014 DOI: 10.1016/j.bbrc.2018.06.155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 06/27/2018] [Indexed: 02/02/2023]
Abstract
Alanine racemase is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l-alanine to d-alanine. d-alanine is an essential constituent in many prokaryotic cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.
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Affiliation(s)
- Hui Dong
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Qingqing Han
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yu Guo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Shanshan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Chao Yuan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wei Long
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Xin He
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Shujing Xu
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Sheng Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
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6
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He G, Xu S, Wang S, Zhang Q, Liu D, Chen Y, Ju J, Zhao B. A conserved residue of l -alanine dehydrogenase from Bacillus pseudofirmus , Lys-73, participates in the catalytic reaction through hydrogen bonding. Enzyme Microb Technol 2018; 110:61-68. [DOI: 10.1016/j.enzmictec.2017.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/25/2017] [Accepted: 10/10/2017] [Indexed: 11/30/2022]
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7
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Structural features and kinetic characterization of alanine racemase from Bacillus pseudofirmus OF4. Biochem Biophys Res Commun 2018; 497:139-145. [DOI: 10.1016/j.bbrc.2018.02.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 02/05/2018] [Indexed: 02/02/2023]
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8
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Matsukawa T, Hasegawa H, Goto H, Shinohara Y, Shinohara A, Omori Y, Ichida K, Yokoyama K. Evaluation of the metabolic chiral inversion of d-selenomethionine in rats by stable isotope dilution gas chromatography–mass spectrometry. J Pharm Biomed Anal 2015; 116:59-64. [DOI: 10.1016/j.jpba.2015.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/19/2015] [Accepted: 04/08/2015] [Indexed: 11/26/2022]
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9
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Kobayashi J, Yukimoto J, Shimizu Y, Ohmori T, Suzuki H, Doi K, Ohshima T. Characterization of Lactobacillus salivarius alanine racemase: short-chain carboxylate-activation and the role of A131. SPRINGERPLUS 2015; 4:639. [PMID: 26543773 PMCID: PMC4628008 DOI: 10.1186/s40064-015-1335-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 12/24/2014] [Indexed: 11/10/2022]
Abstract
Many strains of lactic acid bacteria produce high concentrations of d-amino acids. Among them, Lactobacillus salivarius UCC 118 produces d-alanine at a relative concentration much greater than 50 % of the total d, l-alanine (100d/d, l-alanine). We characterized the L. salivarius alanine racemase (ALR) likely responsible for this d-alanine production and found that the enzyme was activated by carboxylates, which is an unique characteristic among ALRs. In addition, alignment of the amino acid sequences of several ALRs revealed that A131 of L. salivarius ALR is likely involved in the activation. To confirm that finding, an L. salivarius ALR variant with an A131K (ALR(A131K)) substitution was prepared, and its properties were compared with those of ALR. The activity of ALR(A131K) was about three times greater than that of ALR. In addition, whereas L. salivarius ALR was strongly activated by low concentrations (e.g., 1 mM) of short chain carboxylates, and was inhibited at higher concentrations (e.g., 10 mM), ALR(A131K) was clearly inhibited at all carboxylate concentrations tested (1-40 mM). Acetate also increased the stability of ALR such that maximum activity was observed at 35 °C and pH 8.0 without acetate, but at 50 °C in the presence of 1 mM acetate. On the other hand, maximum ALR(A131K) activity was observed at 45 °C and around pH 9.0 with or without acetate. It thus appears that A131 mediates the activation and stabilization of L. salivarius ALR by short chain carboxylates.
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Affiliation(s)
- Jyumpei Kobayashi
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Jotaro Yukimoto
- Applied Molecular Microbiology and Biomass Chemistry Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Yasuhiro Shimizu
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Taketo Ohmori
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka, 535-8585 Japan
| | - Hirokazu Suzuki
- Functional Genomics of Extremophiles, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581 Japan
| | - Katsumi Doi
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka, 535-8585 Japan
| | - Toshihisa Ohshima
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan ; Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka, 535-8585 Japan
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10
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Sun X, He G, Wang X, Xu S, Ju J, Xu X. Crystal Structure of a Thermostable Alanine Racemase from Thermoanaerobacter tengcongensis MB4 Reveals the Role of Gln360 in Substrate Selection. PLoS One 2015. [PMID: 26218070 PMCID: PMC4517790 DOI: 10.1371/journal.pone.0133516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Pyridoxal 5’-phosphate (PLP) dependent alanine racemase catalyzes racemization of L-Ala to D-Ala, a key component of the peptidoglycan network in bacterial cell wall. It has been extensively studied as an important antimicrobial drug target due to its restriction in eukaryotes. However, many marketed alanine racemase inhibitors also act on eukaryotic PLP-dependent enzymes and cause side effects. A thermostable alanine racemase (AlrTt) from Thermoanaerobacter tengcongensis MB4 contains an evolutionarily non-conserved residue Gln360 in inner layer of the substrate entryway, which is supposed to be a key determinant in substrate specificity. Here we determined the crystal structure of AlrTt in complex with L-Ala at 2.7 Å resolution, and investigated the role of Gln360 by saturation mutagenesis and kinetic analysis. Compared to typical bacterial alanine racemase, presence of Gln360 and conformational changes of active site residues disrupted the hydrogen bonding interactions necessary for proper PLP immobilization, and decreased both the substrate affinity and turnover number of AlrTt. However, it could be complemented by introduction of hydrophobic amino acids at Gln360, through steric blocking and interactions with a hydrophobic patch near active site pocket. These observations explained the low racemase activity of AlrTt, revealed the essential role of Gln360 in substrate selection, and its preference for hydrophobic amino acids especially Tyr in bacterial alanine racemization. Our work will contribute new insights into the alanine racemization mechanism for antimicrobial drug development.
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Affiliation(s)
- Xiaoliang Sun
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Guangzheng He
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xiaoyan Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Shujing Xu
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, China
- * E-mail: (JSJ); (XLX)
| | - Xiaoling Xu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
- * E-mail: (JSJ); (XLX)
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Wen J, Li Z, He G, Xu S, Zhao B, Zhu X, Dong H, Ju J. Crystallization and preliminary X-ray study of alanine dehydrogenase from Bacillus pseudofirmus OF4. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1227-30. [PMID: 24192355 DOI: 10.1107/s1744309113025426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/13/2013] [Indexed: 11/11/2022]
Abstract
Alanine dehydrogenase (OF4Ald) from the alkaliphilic Bacillus pseudofirmus OF4 was expressed and purified with a His6 tag in a form suitable for X-ray crystallographic analysis. Crystals were grown by the hanging-drop vapour-diffusion method at 289 K using a solution consisting of 0.1 M Tris-HCl pH 8.0, 0.2 M LiSO4, 22%(w/v) PEG 3350. X-ray diffraction data were collected to 2.8 Å resolution. The crystal belonged to the triclinic space group P1, with unit-cell parameters a = 88.04, b = 105.59, c = 120.53 Å, α = 88.37, β = 78.77, γ = 82.65°.
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Affiliation(s)
- Jinjin Wen
- Tianjin University of Science and Technology, Tianjin 300222, People's Republic of China
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12
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Identification, purification, and characterization of a novel amino acid racemase, isoleucine 2-epimerase, from Lactobacillus species. J Bacteriol 2013; 195:5207-15. [PMID: 24039265 DOI: 10.1128/jb.00709-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Accumulation of d-leucine, d-allo-isoleucine, and d-valine was observed in the growth medium of a lactic acid bacterium, Lactobacillus otakiensis JCM 15040, and the racemase responsible was purified from the cells and identified. The N-terminal amino acid sequence of the purified enzyme was GKLDKASKLI, which is consistent with that of a putative γ-aminobutyrate aminotransferase from Lactobacillus buchneri. The putative γ-aminobutyrate aminotransferase gene from L. buchneri JCM 1115 was expressed in recombinant Escherichia coli and then purified to homogeneity. The enzyme catalyzed the racemization of a broad spectrum of nonpolar amino acids. In particular, it catalyzed at high rates the epimerization of l-isoleucine to d-allo-isoleucine and d-allo-isoleucine to l-isoleucine. In contrast, the enzyme showed no γ-aminobutyrate aminotransferase activity. The relative molecular masses of the subunit and native enzyme were estimated to be about 49 kDa and 200 kDa, respectively, indicating that the enzyme was composed of four subunits of equal molecular masses. The Km and Vmax values of the enzyme for l-isoleucine were 5.00 mM and 153 μmol·min(-1)·mg(-1), respectively, and those for d-allo-isoleucine were 13.2 mM and 286 μmol·min(-1)·mg(-1), respectively. Hydroxylamine and other inhibitors of pyridoxal 5'-phosphate-dependent enzymes completely blocked the enzyme activity, indicating the enzyme requires pyridoxal 5'-phosphate as a coenzyme. This is the first evidence of an amino acid racemase that specifically catalyzes racemization of nonpolar amino acids at the C-2 position.
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Xue Z, Hu Y, Xu S, Ohnishi K, Ma Y, Ju J, Zhao B. Characterization and preliminary mutation analysis of a thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4. Extremophiles 2013; 17:611-21. [PMID: 23703245 DOI: 10.1007/s00792-013-0545-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 05/12/2013] [Indexed: 10/26/2022]
Abstract
A thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4 was successfully expressed in Escherichia coli and characterized. The full-length gene MBalr2 (1164 bp) encodes 388 amino acid residues including 6 out of 8 highly conserved amino acid residues at the entryway to the active site of alanine racemase. Recombinant MBAlr2 and three mutants (S171A, H359Y and double mutation S171A/H359Y) of MBAlr2 were purified by His6-tag affinity column and gel filtration chromatography. The purified protein MBAlr2 was a dimeric PLP-dependent enzyme with broad substrate specificity. The optimal racemization temperature and pH were 70-75 °C and 11.0, respectively. The kinetic parameters K m and V max of MBAlr2 at 70 °C, determined by HPLC, were 20.16 mM and 1414 μmol min(-1) for L-alanine, and 9.95 mM and 702.6 μmol min(-1) for D-alanine, respectively. Enzymatic assays showed that the activity of both mutants (S171A and H359Y) was lost, but the activity of mutant S171A/H359Y was recovered to 69.8 % of wild type, which suggested that residues Ser171 and His359 might be the important residues for catalytic mechanisms of MBAlr2.
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Affiliation(s)
- Zhangwei Xue
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
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Conti P, Tamborini L, Pinto A, Blondel A, Minoprio P, Mozzarelli A, De Micheli C. Drug Discovery Targeting Amino Acid Racemases. Chem Rev 2011; 111:6919-46. [DOI: 10.1021/cr2000702] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Paola Conti
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Lucia Tamborini
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Pinto
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Arnaud Blondel
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS-URA 2185, Département de Biologie Structurale et Chimie, 25 rue du Dr. Roux, 75724 Paris, France
| | - Paola Minoprio
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosoma; Département d’Infection et Epidémiologie; 25 rue du Dr. Roux, 75724 Paris, France
| | - Andrea Mozzarelli
- Dipartimento di Biochimica e Biologia Molecolare, via G. P. Usberti 23/A, 43100 Parma, Italy
- Istituto di Biostrutture e Biosistemi, viale Medaglie d’oro, Roma, Italy
| | - Carlo De Micheli
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
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15
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Liu JL, Liu XQ, Shi YW. Expression, purification, and characterization of alanine racemase from Pseudomonas putida YZ-26. World J Microbiol Biotechnol 2011; 28:267-74. [PMID: 22806802 DOI: 10.1007/s11274-011-0816-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 06/07/2011] [Indexed: 12/26/2022]
Abstract
Alanine racemase catalyzes the interconversion of D: - and L: -alanine and plays an important role in supplying D: -alanine, a component of peptidoglycan biosynthesis, to most bacteria. Alanine racemase exists mostly in prokaryotes and is generally absent in higher eukaryotes; this makes it an attractive target for the design of new antibacterial drugs. Here, we present the cloning and characterization of a new gene-encoding alanine racemase from Pseudomonas putida YZ-26. An open reading frame (ORF) of 1,230 bp, encoding a protein of 410 amino acids with a calculated molecular weight of 44,217.3 Da, was cloned into modified vector pET32M to form the recombinant plasmid pET-alr. After introduction into E.coli BL21, the strain pET-alr/E.coli BL21 expressed His(6)-tagged alanine racemase. The recombinant alanine racemase was efficiently purified to homogeneity using Ni(2+)-NTA and a gel filtration column, with 82.5% activity recovery. The amino acid sequence deduced from the alanine racemase gene revealed identity similarities of 97.0, 93, 23, and 22.0% with from P. putida F1, P. putida200, P. aeruginosa, and Salmonella typhimurium, respectively. The recombinant alanine racemase is a monomeric protein with a molecular mass of 43 kDa. The enzyme exhibited activity with L: -alanine and L: -isoleucine, and showed higher specificity for the former compared with the latter. The enzyme was stable from pH 7.0-11.0; its optimum pH was at 9.0. The optimum temperature for the enzyme was 37°C, and its activity was rapidly lost at temperatures above 40°C. Divalent metals, including Sr(2+), Mn(2+), Co(2+), and Ni(2+) obviously enhanced enzymatic activity, while the Cu(2+) ion showed inhibitory effects.
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Affiliation(s)
- Jun-Lin Liu
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, 92 Wucheng Road, Taiyuan, People's Republic of China
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Ju J, Xu S, Furukawa Y, Zhang Y, Misono H, Minamino T, Namba K, Zhao B, Ohnishi K. Correlation between catalytic activity and monomer-dimer equilibrium of bacterial alanine racemases. J Biochem 2010; 149:83-9. [PMID: 20971724 DOI: 10.1093/jb/mvq120] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
From the reaction mechanism and crystal structure analysis, a bacterial alanine racemase is believed to work as a homodimer with a substrate, l-alanine or d-alanine. We analysed oligomerization states of seven alanine racemases, biosynthetic and catabolic, from Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa, P. putida and P. fluorescens, with three different methods, gel filtration chromatography, native PAGE and analytical ultracentrifugation. All alanine racemases were proved to be in a dynamic equilibrium between monomeric and dimeric form with every methods used in this study. In both biosynthetic and catabolic alanine racemases, association constants for dimerization were high for the enzymes with high V(max) values. The enzymes with low V(max) values gave the low association constants. We proposed that alanine racemases are classified into two types; the enzymes with low and high-equilibrium association constants for dimerization.
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Affiliation(s)
- Jiansong Ju
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050016, Japan
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Ju J, Qi J, Xu S, Ohnishi K, Benedik MJ, Xue Y, Ma Y. Crystallization and preliminary X-ray study of alkaline alanine racemase from Bacillus pseudofirmus OF4. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:166-8. [PMID: 19194012 PMCID: PMC2635857 DOI: 10.1107/s174430910900013x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 01/03/2009] [Indexed: 11/10/2022]
Abstract
Alanine racemase (DadX(OF4)), a dimeric endogenous PLP-dependent alkaline enzyme from alkaliphilic Bacillus pseudofirmus OF4, was expressed in Escherichia coli and purified with a His(6) tag in a form suitable for X-ray crystallographic analysis. Crystals were grown by the hanging-drop vapour-diffusion method at 291 K using a solution containing 1.4 M sodium/potassium phosphate pH 8.2. The protein crystallized in space group P2(1)2(1)2(1), with two protein molecules in the asymmetric unit.
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Affiliation(s)
- Jiansong Ju
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Jianxun Qi
- Institute of Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Shujing Xu
- Life College of Science and Engineering, Shaanxi University of Science and Technology, Xi’an 710021, People’s Republic of China
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Michael J. Benedik
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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