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Kawakami R, Takami N, Hayashi J, Yoneda K, Ohmori T, Ohshima T, Sakuraba H. First crystal structure of an NADP +-dependent l-arginine dehydrogenase belonging to the μ-crystallin family. Int J Biol Macromol 2023; 249:126070. [PMID: 37524275 DOI: 10.1016/j.ijbiomac.2023.126070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
Crystal structures of Pseudomonas veroniil-arginine dehydrogenase (l-ArgDH), belonging to the μ-crystallin/ornithine cyclodeaminase family, were determined for the enzyme in complex with l-lysine and NADP+ and with l-arginine and NADPH. The main chain coordinates of the P. veroniil-ArgDH monomer showed notable similarity to those of Archaeoglobus fulgidusl-AlaDH, belonging to the same family, and pro-R specificity similar to l-AlaDH for hydride transfer to NADP+ was postulated. However, the residues recognizing the α-amino group of the substrates differed between the two enzymes. Based on a substrate modeling study, it was proposed that in A. fulgidusl-AlaDH, the amino group of l-alanine interacts via a water molecule (W510) with the side chains of Lys41 and Arg52. By contrast, the α-amino group of l-arginine formed hydrogen bonds with the side chains of Thr224 and Asn225 in P. veroniil-ArgDH. Moreover, the guanidino group of l-arginine was fixed into the active site via hydrogen bonds with the side chain of Asp54. Site-directed mutagenesis suggested that Asp54 plays an important role in maintaining high reactivity against the substrate and that Tyr58 and Lys71 play critical roles in enzyme catalysis.
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Affiliation(s)
- Ryushi Kawakami
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1, Minamijosanjima-cho, Tokushima 770-8513, Tokushima, Japan
| | - Naoki Takami
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Junji Hayashi
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1, Minamijosanjima-cho, Tokushima 770-8513, Tokushima, Japan
| | - Kazunari Yoneda
- Department of Food and Life Sciences, School of Agriculture, Tokai University, 871-12 Sugido, Mashiki-machi, Kamimashiki-gun, Kumamoto 861-2205, Japan
| | - Taketo Ohmori
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka 535-8585, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka 535-8585, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan.
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Wu T, Wang Y, Zhang N, Yin D, Xu Y, Nie Y, Mu X. Reshaping Substrate-Binding Pocket of Leucine Dehydrogenase for Bidirectionally Accessing Structurally Diverse Substrates. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tao Wu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
- Suqian Jiangnan University Institute of Industrial Technology, Suqian223800, China
| | - Yinmiao Wang
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Ningxin Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Dejing Yin
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Xiaoqing Mu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
- Suqian Jiangnan University Institute of Industrial Technology, Suqian223800, China
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Ohshima T, Tanaka M, Ohmori T. NADP +-dependent l-arginine dehydrogenase from Pseudomonas velonii: Purification, characterization and application to an l-arginine assay. Protein Expr Purif 2022; 199:106135. [PMID: 35760253 DOI: 10.1016/j.pep.2022.106135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 10/31/2022]
Abstract
l-Arginine dehydrogenase (L-ArgDH) is an amino acid dehydrogenase which catalyzes the reversible oxidative deamination of l-arginine to the oxo analog in the presence of NAD(P)+. We here found the gene homolog of L-ArgDH in genome data of Pseudomonas veronii and succeeded in expression of P. veronii JCM11942 gene in E. coli. The gene product exhibited strong NADP + -dependent L-ArgDH activity. The enzyme was unstable, but markedly stabilized by the addition of 10% glycerol. The enzyme first purified to homogeneity consisted of a homodimeric protein with a molecular mass of about 65 kDa. The enzyme selectively catalyzed NADP+-dependent l-arginine oxidation with maximal activity at pH 9.5. The apparent Km values for l-arginine and NADP+ were 2.5 and 0.21 mM, respectively. The nucleotide sequence coding the enzyme gene was determined and the amino acid sequence was deduced from the nucleotide sequence. The simple colorimetric microassay for l-arginine using the enzyme was achieved.
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Affiliation(s)
- Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka, 535-8585, Japan.
| | - Masaki Tanaka
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka, 535-8585, Japan.
| | - Taketo Ohmori
- 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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Substrate-Specific Engineering of Amino Acid Dehydrogenase Superfamily for Synthesis of a Variety of Chiral Amines and Amino Acids. Catalysts 2022. [DOI: 10.3390/catal12040380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Amino acid dehydrogenases (AADHs) are a group of enzymes that catalyze the reversible reductive amination of keto acids with ammonia to produce chiral amino acids using either nicotinamide adenine dinucleotide (NAD+) or nicotinamide adenine dinucleotide phosphate (NADP+) as cofactors. Among them, glutamate dehydrogenase, valine dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and tryptophan dehydrogenase have been classified as a superfamily of amino acid dehydrogenases (s-AADHs) by previous researchers because of their conserved structures and catalytic mechanisms. Owing to their excellent stereoselectivity, high atom economy, and low environmental impact of the reaction pathway, these enzymes have been extensively engineered to break strict substrate specificities for the synthesis of high value-added chiral compounds (chiral amino acids, chiral amines, and chiral amino alcohols). Substrate specificity engineering of s-AADHs mainly focuses on recognition engineering of the substrate side chain R group and substrate backbone carboxyl group. This review summarizes the reported studies on substrate specificity engineering of s-AADHs and reports that this superfamily of enzymes shares substrate specificity engineering hotspots (the inside of the pocket, substrate backbone carboxyl anchor sites, substrate entrance tunnel, and hinge region), which sheds light on the substrate-specific tailoring of these enzymes.
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Yoneda K, Sakuraba H, Araki T, Ohshima T. Stereospecificity of hydride transfer and molecular docking in FMN-dependent NADH-indigo reductase of Bacillus smithii. FEBS Open Bio 2021; 11:1981-1986. [PMID: 34043290 PMCID: PMC8255831 DOI: 10.1002/2211-5463.13200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/20/2022] Open
Abstract
In this study, we investigated the stereospecificity of hydride transfer from NADH to flavin mononucleotide (FMN) in reactions catalyzed by the FMN‐dependent NADH‐indigo reductase expressed by thermophilic Bacillus smithii. We performed 1H‐NMR spectroscopy using deuterium‐labeled NADH (4R‐2H‐NADH) and molecular docking simulations to reveal that the pro‐S hydrogen at the C4 position of the nicotinamide moiety in NADH was specifically transferred to the flavin‐N5 atom of FNM. Altogether, our findings may aid in the improvement of the indigo dyeing (Aizome) process.
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Affiliation(s)
- Kazunari Yoneda
- Department of Bioscience, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kita-gun, Japan
| | - Tomohiro Araki
- Department of Bioscience, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, Japan
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Matsui D, Asano Y. Creation of thermostable l-tryptophan dehydrogenase by protein engineering and its application for l-tryptophan quantification. Anal Biochem 2019; 579:57-63. [DOI: 10.1016/j.ab.2019.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 02/08/2023]
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Structural Insights into l-Tryptophan Dehydrogenase from a Photoautotrophic Cyanobacterium, Nostoc punctiforme. Appl Environ Microbiol 2017; 83:AEM.02710-16. [PMID: 27815281 DOI: 10.1128/aem.02710-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 10/31/2016] [Indexed: 01/08/2023] Open
Abstract
l-Tryptophan dehydrogenase from Nostoc punctiforme NIES-2108 (NpTrpDH), despite exhibiting high amino acid sequence identity (>30%)/homology (>50%) with NAD(P)+-dependent l-Glu/l-Leu/l-Phe/l-Val dehydrogenases, exclusively catalyzes reversible oxidative deamination of l-Trp to 3-indolepyruvate in the presence of NAD+ Here, we determined the crystal structure of the apo form of NpTrpDH. The structure of the NpTrpDH monomer, which exhibited high similarity to that of l-Glu/l-Leu/l-Phe dehydrogenases, consisted of a substrate-binding domain (domain I, residues 3 to 133 and 328 to 343) and an NAD+/NADH-binding domain (domain II, residues 142 to 327) separated by a deep cleft. The apo-NpTrpDH existed in an open conformation, where domains I and II were apart from each other. The subunits dimerized themselves mainly through interactions between amino acid residues around the β-1 strand of each subunit, as was observed in the case of l-Phe dehydrogenase. The binding site for the substrate l-Trp was predicted by a molecular docking simulation and validated by site-directed mutagenesis. Several hydrophobic residues, which were located in the active site of NpTrpDH and possibly interacted with the side chain of the substrate l-Trp, were arranged similarly to that found in l-Leu/l-Phe dehydrogenases but fairly different from that of an l-Glu dehydrogenase. Our crystal structure revealed that Met-40, Ala-69, Ile-74, Ile-110, Leu-288, Ile-289, and Tyr-292 formed a hydrophobic cluster around the active site. The results of the site-directed mutagenesis experiments suggested that the hydrophobic cluster plays critical roles in protein folding, l-Trp recognition, and catalysis. Our results provide critical information for further characterization and engineering of this enzyme. IMPORTANCE In this study, we determined the three-dimensional structure of l-Trp dehydrogenase, analyzed its various site-directed substitution mutants at residues located in the active site, and obtained the following informative results. Several residues in the active site form a hydrophobic cluster, which may be a part of the hydrophobic core essential for protein folding. To our knowledge, there is no previous report demonstrating that a hydrophobic cluster in the active site of any l-amino acid dehydrogenase may have a critical impact on protein folding. Furthermore, our results suggest that this hydrophobic cluster could strictly accommodate l-Trp. These studies show the structural characteristics of l-Trp dehydrogenase and hence would facilitate novel applications of l-Trp dehydrogenase.
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Enhancement of stability of l-tryptophan dehydrogenase from Nostoc punctiforme ATCC29133 and its application to l-tryptophan assay. J Biotechnol 2015; 196-197:27-32. [DOI: 10.1016/j.jbiotec.2015.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 01/04/2015] [Accepted: 01/12/2015] [Indexed: 11/20/2022]
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