1
|
Demir Ğ, Valjakka J, Turunen O, Aktaş F, Binay B. Cloning and expression heterologous alanine dehydrogenase genes: Investigation of reductive amination potential of L-alanine dehydrogenases for green synthesis of alanine derivatives. Heliyon 2024; 10:e26899. [PMID: 38463761 PMCID: PMC10923667 DOI: 10.1016/j.heliyon.2024.e26899] [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: 12/29/2023] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Unnatural amino acids (UAAs) offer significant promise in a wide range of applications, including drug discovery, the custom design of peptides and proteins, and their utility and use as markers for monitoring molecular interactions in biological research. The synthesis of UAAs presents a formidable challenge and can be classified into two primary categories: enzymatic and chemical synthesis. Notably, the enzymatic route, specifically asymmetric synthesis, emerges as a an attractive method for procuring enantiopure UAAs with high efficiency, owing to its streamlined and concise reaction mechanism. The current study investigated the reductive amination activity mechanisms of alanine dehydrogenase (L-AlaDH), sourced from a combination of newly and previously characterized microorganisms. Our principal aim was to evaluate the catalytic efficiency of these L-AlaDH enzymes concerning a range of specific ketoacids and pyruvate to ascertain their capability for facilitating the production of both natural and unnatural amino acids. After the characterization processes, mutation points for TtAlaDH were determined and as a result of the mutations, mutants that could use ketocaproate and ketovalerate more effectively than the wild type were obtained. Among the enzymes studied, MetAlaDH exhibited the highest specific activity against pyruvate, 173 U/mg, and a KM value of 1.3 mM. VlAlaDH displayed the most favourable catalytic efficiency with a rate constant of 170 s-1mM-1. On the other hand, AfAlaDH demonstrated the highest catalytic efficiency against α-ketobutyrate (34.0 s-1mM-1) and α-ketovalerate (2.7 s-1mM-1). Of the enzymes investigated in the study, TtAlaDH exhibited the highest effectiveness among bacterial enzymes in catalyzing ketocaproate with a measured catalytic efficiency of about 0.6 s-1mM-1 and a KM value of approximately 0.3 mM. These findings provide valuable insights into the substrate specificity and catalytic performance of L-AlaDHs, enhancing our understanding of their potential applications in various biocatalytic processes.
Collapse
Affiliation(s)
- Ğarip Demir
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Jarkko Valjakka
- Faculty of Medicine and Health Technology, Tampere University, FI-33100, Tampere, Finland
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland
| | - Fatih Aktaş
- Faculty of Engineering, Düzce University, 81600, Düzce, Turkey
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
- BAUZYME Biotechnology Co., Gebze Technical University Technopark, 41400, Gebze, Kocaeli, Turkey
| |
Collapse
|
2
|
Gu P, Ma Q, Zhao S, Li Q, Gao J. Alanine dehydrogenases from four different microorganisms: characterization and their application in L-alanine production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:123. [PMID: 37537629 PMCID: PMC10401832 DOI: 10.1186/s13068-023-02373-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Alanine dehydrogenase (AlaDH) belongs to oxidoreductases, and it exists in several different bacteria species and plays a key role in microbial carbon and nitrogen metabolism, spore formation and photosynthesis. In addition, AlaDH can also be applied in biosynthesis of L-alanine from cheap carbon source, such as glucose. RESULTS To achieve a better performance of L-alanine accumulation, system evaluation and comparison of different AlaDH with potential application value are essential. In this study, enzymatic properties of AlaDH from Bacillus subtilis 168 (BsAlaDH), Bacillus cereus (BcAlaDH), Mycobacterium smegmatis MC2 155 (MsAlaDH) and Geobacillus stearothermophilus (GsAlaDH) were firstly carefully investigated. Four different AlaDHs have few similarities in optimum temperature and optimum pH, while they also exhibited significant differences in enzyme activity, substrate affinity and enzymatic reaction rate. The wild E. coli BL21 with these four AlaDHs could produce 7.19 g/L, 7.81 g/L, 6.39 g/L and 6.52 g/L of L-alanine from 20 g/L glucose, respectively. To further increase the L-alanine titer, competitive pathways for L-alanine synthesis were completely blocked in E. coli. The final strain M-6 could produce 80.46 g/L of L-alanine with a yield of 1.02 g/g glucose after 63 h fed-batch fermentation, representing the highest yield for microbial L-alanine production. CONCLUSIONS Enzyme assay, biochemical characterization and structure analysis of BsAlaDH, BcAlaDH, MsAlaDH and GsAlaDH were carried out. In addition, application potential of these four AlaDHs in L-alanine productions were explored. The strategies here can be applied for developing L-alanine producing strains with high titers.
Collapse
Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Qianqian Ma
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Shuo Zhao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Juan Gao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
| |
Collapse
|
3
|
Maeno M, Ohmori T, Nukada D, Sakuraba H, Satomura T, Ohshima T. Two different alanine dehydrogenases from Geobacillus kaustophilus: Their biochemical characteristics and differential expression in vegetative cells and spores. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140904. [PMID: 36918121 DOI: 10.1016/j.bbapap.2023.140904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/25/2023] [Accepted: 02/26/2023] [Indexed: 03/14/2023]
Abstract
Two putative alanine dehydrogenase (AlaDH) genes (GK2752 and GK3448) were found in the genome of a thermophilic spore-forming bacterium, Geobacillus kaustophilus. The amino acid sequences deduced from the two genes showed mutually high homology (71%), and the phylogenetic tree based on the amino acid sequences of the two putative AlaDHs and the homologous proteins showed that the two putative AlaDH genes (GK2752 and GK3448) belong to different groups. Both of the recombinant gene products exhibited high NAD+-dependent AlaDH activity and were purified to homogeneity and characterized in detail. Both enzymes showed high stability against low and high pHs and high temperatures (70 °C). Kinetic analyses showed that the activities of both enzymes proceeded according to the same sequentially ordered Bi-Ter mechanism. X-ray crystallographic analysis showed the two AlaDHs to have similar homohexameric structures. Notably, GK3448-AlaDH was detected in vegetative cells of G. kaustophilus but not spores, while GK2752-AlaDH was present only in the spores. This is the first report showing the presence of two AlaDHs separately expressed in vegetative cells and spores.
Collapse
Affiliation(s)
- Miku Maeno
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan
| | - Taketo Ohmori
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan
| | - Daiki Nukada
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
| | - Takenori Satomura
- Division of Engineering, Faculty of Engineering, University of Fukui, Fukui 910-8507, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan.
| |
Collapse
|
4
|
Kollipara M, Matzel P, Bornscheuer U, Höhne M. Activity Levels of Amine Transaminases Correlate with Active Site Hydrophobicity. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manideep Kollipara
- University of Greifswald Institute of Biochemistry, Protein Biochemistry Felix-Hausdorff-Straße 4 17489 Greifswald Germany
| | - Philipp Matzel
- University of Greifswald Institute of Biochemistry, Protein Biochemistry Felix-Hausdorff-Straße 4 17489 Greifswald Germany
| | - Uwe Bornscheuer
- University of Greifswald Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis Felix-Hausdorff-Straße 4 17489 Greifswald Germany
| | - Matthias Höhne
- University of Greifswald Institute of Biochemistry, Protein Biochemistry Felix-Hausdorff-Straße 4 17489 Greifswald Germany
| |
Collapse
|
5
|
Characterization of proteins from the 3N5M family reveals an operationally stable amine transaminase. Appl Microbiol Biotechnol 2022; 106:5563-5574. [PMID: 35932295 PMCID: PMC9418295 DOI: 10.1007/s00253-022-12071-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/22/2022] [Accepted: 07/05/2022] [Indexed: 01/24/2023]
Abstract
Abstract Amine transaminases (ATA) convert ketones into optically active amines and are used to prepare active pharmaceutical ingredients and building blocks. Novel ATA can be identified in protein databases due to the extensive knowledge of sequence-function relationships. However, predicting thermo- and operational stability from the amino acid sequence is a persisting challenge and a vital step towards identifying efficient ATA biocatalysts for industrial applications. In this study, we performed a database mining and characterized selected putative enzymes of the β-alanine:pyruvate transaminase cluster (3N5M) — a subfamily with so far only a few described members, whose tetrameric structure was suggested to positively affect operational stability. Four putative transaminases (TA-1: Bilophilia wadsworthia, TA-5: Halomonas elongata, TA-9: Burkholderia cepacia, and TA-10: Burkholderia multivorans) were obtained in a soluble form as tetramers in E. coli. During comparison of these tetrameric with known dimeric transaminases we found that indeed novel ATA with high operational stabilities can be identified in this protein subfamily, but we also found exceptions to the hypothesized correlation that a tetrameric assembly leads to increased stability. The discovered ATA from Burkholderia multivorans features a broad substrate specificity, including isopropylamine acceptance, is highly active (6 U/mg) in the conversion of 1-phenylethylamine with pyruvate and shows a thermostability of up to 70 °C under both, storage and operating conditions. In addition, 50% (v/v) of isopropanol or DMSO can be employed as co-solvents without a destabilizing effect on the enzyme during an incubation time of 16 h at 30 °C. Key points • Database mining identified a thermostable amine transaminase in the β-alanine:pyruvate transaminase subfamily. • The tetrameric transaminase tolerates 50% DMSO and isopropanol under operating conditions at 30 °C. • A tetrameric structure is not necessarily associated with a higher operational stability Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12071-1.
Collapse
|
6
|
Aktaş F. Heterologous Expression and Partial Characterization of a New Alanine Dehydrogenase from Amycolatopsis sulphurea. Protein J 2021; 40:342-347. [PMID: 33818657 DOI: 10.1007/s10930-021-09982-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2021] [Indexed: 10/21/2022]
Abstract
A novel alanine dehydrogenase (AlaDH; EC.1.4.1.1) was isolated from Amycolatopsis sulphurea and the AlaDH gene was cloned into a pET28a(+) plasmid and expressed in E. coli BL21 (DE3). The molecular mass of this enzyme was calculated as 41.09 kDa and the amino acid residues of the pure protein indicated the presence of N terminus polyhistidine tags. Its enzyme kinetic values were Km 2.03 mM, kcat 13.24 (s-1), and kcat/Km 6.53 (s-1 mM-1). AlaDH catalyzes the reversible conversion of L-alanine and pyruvate, which has an important role in the TCA energy cycle. Maximum AlaDH activity occurred at about pH 10.5 and 25 °C for the oxidative deamination of L-alanine. AlaDH retained about 10% of its relative activity at 55 °C and it remained about 90% active at 50 °C. These findings show that the AsAlaDH from A. sulphurea has the ability to produce valuable molecules for various industrial purposes and could represent a new potential biocatalyst for biotechnological applications after further characterization and improvement of its catalytic properties.
Collapse
Affiliation(s)
- Fatih Aktaş
- Faculty of Engineering, Düzce University, 81600, Düzce, Turkey.
| |
Collapse
|
7
|
Phogosee S, Hibino T, Kageyama H, Waditee-Sirisattha R. Bifunctional alanine dehydrogenase from the halotolerant cyanobacterium Aphanothece halophytica: characterization and molecular properties. Arch Microbiol 2018; 200:719-727. [DOI: 10.1007/s00203-018-1481-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/11/2018] [Accepted: 01/18/2018] [Indexed: 11/28/2022]
|
8
|
Steffen-Munsberg F, Matzel P, Sowa MA, Berglund P, Bornscheuer UT, Höhne M. Bacillus anthracis ω-amino acid:pyruvate transaminase employs a different mechanism for dual substrate recognition than other amine transaminases. Appl Microbiol Biotechnol 2016; 100:4511-21. [DOI: 10.1007/s00253-015-7275-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/17/2015] [Accepted: 12/23/2015] [Indexed: 11/25/2022]
|
9
|
Last D, Müller J, Dawood AWH, Moldenhauer EJ, Pavlidis IV, Bornscheuer UT. Highly efficient and easy protease-mediated protein purification. Appl Microbiol Biotechnol 2015; 100:1945-1953. [DOI: 10.1007/s00253-015-7206-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/25/2015] [Accepted: 11/28/2015] [Indexed: 11/29/2022]
|
10
|
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°.
Collapse
Affiliation(s)
- Jinjin Wen
- Tianjin University of Science and Technology, Tianjin 300222, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Hayes D, Izzard L, Seviour R. Microbial ecology of autothermal thermophilic aerobic digester (ATAD) systems for treating waste activated sludge. Syst Appl Microbiol 2011; 34:127-38. [DOI: 10.1016/j.syapm.2010.11.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/13/2010] [Accepted: 11/02/2010] [Indexed: 11/29/2022]
|
12
|
Coolbear T, Daniel RM, Morgan HW. The enzymes from extreme thermophiles: bacterial sources, thermostabilities and industrial relevance. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 45:57-98. [PMID: 1605092 DOI: 10.1007/bfb0008756] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review on enzymes from extreme thermophiles (optimum growth temperature greater than 65 degrees C) concentrates on their characteristics, especially thermostabilities, and their commercial applicability. The enzymes are considered in general terms first, with comments on denaturation, stabilization and industrial processes. Discussion of the enzymes subsequently proceeds in order of their E.C. classification: oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases. The ramifications of cloned enzymes from extreme thermophiles are also discussed.
Collapse
Affiliation(s)
- T Coolbear
- University of Waikato, Hamilton, New Zealand
| | | | | |
Collapse
|
13
|
Ohshima T, Soda K. Biochemistry and biotechnology of amino acid dehydrogenases. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 42:187-209. [PMID: 2291437 DOI: 10.1007/bfb0000734] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the last decade, amino acid dehydrogenases such as alanine dehydrogenase (Ala DH), leucine dehydrogenase (Leu DH), and phenylalanine dehydrogenase (Phe DH) have been applied to the enantiomer-specific synthesis and analysis of various amino acids. In perticular, amino acid dehydrogenases from thermophiles have received much attention because of their high stability. Their productivity was enhanced and the purification facilitated by the gene cloning. The advances in biotechnological applications of these enzymes are based on fundamental studies concerning characteristics of the enzymes and reaction mechanism as described in this chapter. Further elucidation of the structure and function of these enzymes based on genetic engineering and protein engineering may enable their properties to be improved for their future uses in biotechnology.
Collapse
Affiliation(s)
- T Ohshima
- Department of Chemistry, Kyoto University of Education, Japan
| | | |
Collapse
|
14
|
Schröder I, Vadas A, Johnson E, Lim S, Monbouquette HG. A novel archaeal alanine dehydrogenase homologous to ornithine cyclodeaminase and mu-crystallin. J Bacteriol 2004; 186:7680-9. [PMID: 15516582 PMCID: PMC524889 DOI: 10.1128/jb.186.22.7680-7689.2004] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel alanine dehydrogenase (AlaDH) showing no significant amino acid sequence homology with previously known bacterial AlaDHs was purified to homogeneity from the soluble fraction of the hyperthermophilic archaeon Archaeoglobus fulgidus. AlaDH catalyzed the reversible, NAD+-dependent deamination of L-alanine to pyruvate and NH4+. NADP(H) did not serve as a coenzyme. The enzyme is a homodimer of 35 kDa per subunit. The Km values for L-alanine, NAD+, pyruvate, NADH, and NH4+ were estimated at 0.71, 0.60, 0.16, 0.02, and 17.3 mM, respectively. The A. fulgidus enzyme exhibited its highest activity at about 82 degrees C (203 U/mg for reductive amination of pyruvate) yet still retained 30% of its maximum activity at 25 degrees C. The thermostability of A. fulgidus AlaDH was increased by more than 10-fold by 1.5 M KCl to a half-life of 55 h at 90 degrees C. At 25 degrees C in the presence of this salt solution, the enzyme was approximately 100% stable for more than 3 months. Closely related A. fulgidus AlaDH homologues were found in other archaea. On the basis of its amino acid sequence, A. fulgidus AlaDH is a member of the ornithine cyclodeaminase-mu-crystallin family of enzymes. Similar to the mu-crystallins, A. fulgidus AlaDH did not exhibit any ornithine cyclodeaminase activity. The recombinant human mu-crystallin was assayed for AlaDH activity, but no activity was detected. The novel A. fulgidus gene encoding AlaDH, AF1665, is designated ala.
Collapse
Affiliation(s)
- Imke Schröder
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, USA.
| | | | | | | | | |
Collapse
|
15
|
Conversion of cofactor specificities of alanine dehydrogenases by site-directed mutagenesis. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2004.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
16
|
Nagata S, Kobayashi Y, Shinkawa S, Katoh R, Ohshima T, Misono H. Novel halophilic 2-aminobutyrate dehydrogenase from Halobacterium saccahrovorum DSM 1137. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1381-1177(03)00084-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
17
|
Jala VR, Prakash V, Rao NA, Savithri HS. Overexpression and characterization of dimeric and tetrameric forms of recombinant serine hydroxymethyltransferase from Bacillus stearothermophilus. J Biosci 2002; 27:233-42. [PMID: 12089472 DOI: 10.1007/bf02704912] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Serine hydroxymethyltransferase (SHMT), a pyridoxal-5' -phosphate (PLP) dependent enzyme catalyzes the interconversion of L-Ser and Gly using tetrahydrofolate as a substrate. The gene encoding for SHMT was amplified by PCR from genomic DNA of Bacillus stearothermophilus and the PCR product was cloned and overexpressed in Escherichia coli. The purified recombinant enzyme was isolated as a mixture of dimer (90%) and tetramer (10%). This is the first report demonstrating the existence of SHMT as a dimer and tetramer in the same organism. The specific activities at 37 C of the dimeric and tetrameric forms were 6 7 U/mg and 4 1 U/mg, respectively. The purified dimer was extremely thermostable with a T(m) of 85 degrees C in the presence of PLP and L-Ser. The temperature optimum of the dimer was 80 degrees C with a specific activity of 32 4 U/mg at this temperature. The enzyme catalyzed tetrahydrofolate-independent reactions at a slower rate compared to the tetrahydrofolate-dependent retro-aldol cleavage of L-Ser. The interaction with substrates and their analogues indicated that the orientation of PLP ring of B. stearothermophilus SHMT was probably different from sheep liver cytosolic recombinant SHMT (scSHMT).
Collapse
|
18
|
Yoon HG, Yang SW, Kim HY, Kim HK, Shin DH, Hong BS, Cho HY. Analysis of essential leucine residue for catalytic activity of novel thermostable chitosanase by site-directed mutagenesis. JOURNAL OF PROTEIN CHEMISTRY 2000; 19:621-30. [PMID: 11233177 DOI: 10.1023/a:1007147214796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Bacterial chitosanases share weak amino acid sequence similarities at certain regions of each enzyme. These regions have been assumed to be important for catalytic activities of the enzyme. To verify this assumption, the functional importance of the conserved region in a novel thermostable chitosanase (TCH-2) from Bacillus coagulans CK108 was investigated. Each of the conserved amino acid residues (Leu64, Glu80, Glu94, Asp98, and Gly108) was changed to aspartate and glutamine or asparagine and glutamate by site-directed mutagenesis, respectively. Kinetic parameters for colloidal chitosan hydrolysis were determined with wild-type and 10 mutant chitosanases. The Leu64 --> Arg and Leu64 --> Gln mutations were essentially inactive and kinetic parameters such as Vmax and kcat were approximately 1/10(7) of those of the wild-type enzyme. The Asp98 --> Asn mutation did not affect the Km value significantly, but decreased kcat to 15% of that of wild-type chitosanase. On the other hand, the Asp98 --> Glu mutation affected neither Km nor kcat. The observation that approximately 15% of activity remained after the substitution of Asp98 by Asn indicated that the carboxyl side chain of Asp98 is not absolutely required for catalytic activity. These results indicate that the Leu64 residue is directly involved in the catalytic activity of TCH-2.
Collapse
Affiliation(s)
- H G Yoon
- Department of Food and Biotechnology, Graduate School of Biotechnology, Korea University, Seoul
| | | | | | | | | | | | | |
Collapse
|
19
|
Yoon HG, Kim HY, Lim YH, Kim HK, Shin DH, Hong BS, Cho HY. Thermostable chitosanase from Bacillus sp. Strain CK4: cloning and expression of the gene and characterization of the enzyme. Appl Environ Microbiol 2000; 66:3727-34. [PMID: 10966383 PMCID: PMC92213 DOI: 10.1128/aem.66.9.3727-3734.2000] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A thermostable chitosanase gene from the environmental isolate Bacillus sp. strain CK4, which was identified on the basis of phylogenetic analysis of the 16S rRNA gene sequence and phenotypic analysis, was cloned, and its complete DNA sequence was determined. The thermostable chitosanase gene was composed of an 822-bp open reading frame which encodes a protein of 242 amino acids and a signal peptide corresponding to a 30-kDa enzyme. The deduced amino acid sequence of the chitosanase from Bacillus sp. strain CK4 exhibits 76.6, 15.3, and 14.2% similarities to those from Bacillus subtilis, Bacillus ehemensis, and Bacillus circulans, respectively. C-terminal homology analysis shows that Bacillus sp. strain CK4 belongs to cluster III with B. subtilis. The gene was similar in size to that of the mesophile B. subtilis but showed a higher preference for codons ending in G or C. The enzyme contains 2 additional cysteine residues at positions 49 and 211. The recombinant chitosanase has been purified to homogeneity by using only two steps with column chromatography. The half-life of the enzyme was 90 min at 80 degrees C, which indicates its usefulness for industrial applications. The enzyme had a useful reactivity and a high specific activity for producing functional oligosaccharides as well, with trimers through hexamers as the major products.
Collapse
Affiliation(s)
- H G Yoon
- Graduate School of Biotechnology, Korea University, Seoul 136-701, Korea
| | | | | | | | | | | | | |
Collapse
|
20
|
Brunhuber NM, Blanchard JS. The biochemistry and enzymology of amino acid dehydrogenases. Crit Rev Biochem Mol Biol 1994; 29:415-67. [PMID: 7705101 DOI: 10.3109/10409239409083486] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This review is an exhaustive description of the biochemistry and enzymology of all 17 known NAD(P)(+)-amino acid dehydrogenases. These enzymes catalyze the oxidative deamination of an amino acid to its keto acid and ammonia, with the concomitant reduction of either NAD+ or NADP+. These enzymes have many important applications in industrial and medical settings and have been the object of prodigious enzymological research. This article describes all that is known about the poorly characterized members of the family and contains detailed information on the better characterized enzymes, including valine, phenylalanine, leucine, alanine, and glutamate dehydrogenases. The latter three enzymes have been the subject of extensive enzymological experimentation, and, consequently, their chemical mechanisms are discussed. The three-dimensional structure of the Clostridium symbiosum glutamate dehydrogenase has been determined recently and remains the only structure known of any amino acid dehydrogenase. The three-dimensional structure and its implications to the chemical mechanisms and rate-limiting steps of the amino acid dehydrogenase family are discussed.
Collapse
Affiliation(s)
- N M Brunhuber
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | | |
Collapse
|
21
|
|
22
|
Schultes V, Deutzmann R, Jaenicke R. Complete amino-acid sequence of glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 192:25-31. [PMID: 2401296 DOI: 10.1111/j.1432-1033.1990.tb19190.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
1. The complete amino-acid sequence of D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the extreme thermophilic eubacterium Thermotoga maritima has been determined by classical automated sequence analysis of peptides derived by chemical fragmentation with cyanogen bromide and enzymatic cleavages with specific proteases. 2. The protein contains 332 amino acids per subunit. Its sequence is as follows: (sequence; see text) 3. Comparing the given sequence with those of the enzymes from the moderate and extreme thermophilic bacteria Bacillus stearothermophilus and Thermus aquaticus, 63% and 59% identity are observed. Alignment of the sequences of GAPDHs from a variety of sources yields one deletion (one amino acid) and one insertion (two amino acids). 4. Thermal stability is caused by minute adjustments of the local three-dimensional structure. Previous 'strategies of thermal adaptation' in terms of preferred amino-acid exchanges are not in accordance with the present sequence data.
Collapse
Affiliation(s)
- V Schultes
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Federal Republic of Germany
| | | | | |
Collapse
|
23
|
Wrba A, Schweiger A, Schultes V, Jaenicke R, Závodszky P. Extremely thermostable D-glyceraldehyde-3-phosphate dehydrogenase from the eubacterium Thermotoga maritima. Biochemistry 1990; 29:7584-92. [PMID: 2271518 DOI: 10.1021/bi00485a007] [Citation(s) in RCA: 173] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Thermotoga maritima, a hyperthermophilic eubacterium, has been isolated in pure crystalline form. The enzyme is a homotetramer with a subunit molecular mass of 37 kDa. The sedimentation coefficient of the native enzyme is 7.3 X 10(-13)s, the isoelectric point is 4.6, and the specific absorption coefficient A1%, 1cm 280nm = 8.4. The enzyme shows extreme thermal stability: differential scanning calorimetry yields a transition temperature (Tm) of 109 degrees C for the NAD-saturated enzyme. Thermal deactivation occurs at T greater than 90 degrees C. The physicochemical characteristics of the enzyme suggest that its gross structure must be very similar to the structure of GAPDHs from mesophilic sources. The amino acid composition does not confirm the known "traffic rules" of thermal adaptation, apart from the Lys----Arg exchange. One reactive and at least two buried SH groups can be titrated with 5,5'-dithiobis(2-nitrobenzoate). The highly reactive SH group is probably the active-site cysteine residue common to all known GAPDHs. The activation energy of the glyceraldehyde 3-phosphate oxidation reaction decreases with increasing temperature. This functional behavior can be correlated with the temperature-dependent changes of both the intrinsic fluorescence and the near-UV circular dichroism; both indicate a temperature-dependent structural reorganization of the enzyme. Hydrogen-deuterium exchange reveals significantly increased rigidity of the thermophilic enzyme if compared to mesophilic GAPDHs at 25 degrees C, thus indicating that the conformational flexibility is similar at the corresponding physiological temperatures.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- A Wrba
- Institut für Biophysik und Physikalische Biochemie, Universität-Regensburg, FRG
| | | | | | | | | |
Collapse
|
24
|
Ohshima T, Sakane M, Yamazaki T, Soda K. Thermostable alanine dehydrogenase from thermophilic Bacillus sphaericus DSM 462. Purification, characterization and kinetic mechanism. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 191:715-20. [PMID: 2390993 DOI: 10.1111/j.1432-1033.1990.tb19180.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alanine dehydrogenase (L-alanine: NAD+ oxidoreductase, deaminating) was simply purified to homogeneity from a thermophile, Bacillus sphaericus DSM 462, by ammonium sulfate fractionation, red-Sepharose 4B chromatography and preparative slab gel electrophoresis. The enzyme had a molecular mass of about 230 kDa and consisted of six subunits with an identical molecular mass of 38 kDa. The enzyme was much more thermostable than that from a mesophile, B. sphaericus, and retained its full activity upon heating at 75 degrees C for at least 60 min and with incubation in pH 5.5-9.5 at 75 degrees C for 10 min. The enzyme can be stored without loss of its activity in a frozen state (-20 degrees C, at pH 7.2) for over 5 months. The optimum pH for the L-alanine deamination and pyruvate amination were around 10.5 and 8.2, respectively. The enzyme exclusively catalyzed the oxidative deamination of L-alanine in the presence of NAD+, but showed low amino acceptor specificity; hydroxypyruvate, oxaloacetate, 2-oxobutyrate and 3-fluoropyruvate are also aminated as well as pyruvate in the presence of NADH and ammonia. Initial velocity and product inhibition studies showed that the reductive amination proceeded through a sequential mechanism containing partially random binding. NADH binds first to the enzyme, and then pyruvate and ammonia bind in a random fashion. The products are sequentially released from the enzyme in the order L-alanine then NAD+. A dead-end inhibition by the formation of an abortive ternary complex which consists of the enzyme, NAD+ and pyruvate was included in the reaction. A possible role of the dead-end inhibition is to prevent the enzyme from functioning in the L-alanine synthesis. The Michaelis constants for the substrates were as follows: NADH, 0.10 mM; pyruvate, 0.50 mM; ammonia, 38.0 mM; L-alanine, 10.5 mM and NAD+, 0.26 mM.
Collapse
Affiliation(s)
- T Ohshima
- Department of Chemistry, Kyoto University of Education, Japan
| | | | | | | |
Collapse
|
25
|
Abstract
Life on earth is ubiquitous within the limits from -5 to 110 degrees C for temperature, 0.1 to 120 MPa for hydrostatic pressure, 1.0 to 0.6 for water activity and pH 1 to 12. In general, mutative adaptation of proteins to changing environmental conditions tends to maintain 'corresponding states' regarding overall topology, flexibility and hydration. Due to the minute changes in the free energy of stabilization responsible for enhanced stability, nature provides a wide variety of different adaptative strategies. In the case of thermophilic proteins, improved packing densities are crucial. In halophilic proteins, decreased hydrophobicity and clustered surface charges serve to increase water and salt binding required for solubilization at high salt concentration. In the case of barophiles, high-pressure adaptation is expected to be less important than adaptation to low temperatures governing the deep sea. Nothing is known with respect to the mechanisms underlying psychrophilic and acidophilic/alkalophilic adaptation.
Collapse
Affiliation(s)
- R Jaenicke
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, FRG
| | | |
Collapse
|
26
|
Kuroda S, Tanizawa K, Sakamoto Y, Tanaka H, Soda K. Alanine dehydrogenases from two Bacillus species with distinct thermostabilities: molecular cloning, DNA and protein sequence determination, and structural comparison with other NAD(P)(+)-dependent dehydrogenases. Biochemistry 1990; 29:1009-15. [PMID: 2340274 DOI: 10.1021/bi00456a025] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The gene encoding alanine dehydrogenase (EC 1.4.1.1) from a mesophile, Bacillus sphaericus, was cloned, and its complete DNA sequence was determined. In addition, the same gene from a moderate thermophile, B. stearothermophilus, was analyzed in a similar manner. Large parts of the two translated amino acid sequences were confirmed by automated Edman degradation of tryptic peptide fragments. Each alanine dehydrogenase gene consists of a 1116-bp open reading frame and encodes 372 amino acid residues corresponding to the subunit (Mr = 39,500-40,000) of the hexameric enzyme. The similarity of amino acid sequence between the two alanine dehydrogenases with distinct thermostabilities is very high (greater than 70%). The nonidentical residues are clustered in a few regions with relatively short length, which may correlate with the difference in thermal stability of the enzymes. Homology search of the primary structures of both alanine dehydrogenases with those of other pyridine nucleotide-dependent oxidoreductases revealed significant sequence similarity in the regions containing the coenzyme binding domain. Interestingly, several catalytically important residues in lactate and malate dehydrogenases are conserved in the primary structure of alanine dehydrogenases at matched positions with similar mutual distances.
Collapse
Affiliation(s)
- S Kuroda
- Institute for Chemical Research, Kyoto University, Japan
| | | | | | | | | |
Collapse
|
27
|
Gene cloning, purification and characterization of thermostable alanine dehydrogenase of Bacillus stearothermophilus. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/0922-338x(90)90038-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
28
|
Asano Y, Nakazawa A, Endo K. Novel phenylalanine dehydrogenases from Sporosarcina ureae and Bacillus sphaericus. Purification and characterization. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61119-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
29
|
Porumb H, Vancea D, Mureşan L, Presecan E, Lascu I, Petrescu I, Porumb T, Pop R, Bârzu O. Structural and catalytic properties of L-alanine dehydrogenase from Bacillus cereus. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61237-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
30
|
Ohshima T, Nagata S, Soda K. Purification and characterization of thermostable leucine dehydrogenase from Bacillus stearothermophilus. Arch Microbiol 1985. [DOI: 10.1007/bf00428857] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
31
|
Mureşan L, Vancea D, Presecan E, Porumb H, Lascu I, Oargă M, Matinca D, Abrudan I, Bârzu O. Catalytic properties of Sepharose-bound L-alanine dehydrogenase from Bacillus cereus. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 742:617-22. [PMID: 6404304 DOI: 10.1016/0167-4838(83)90280-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
(1) L-Alanine dehydrogenase from Bacillus cereus was purified by a two-step chromatographic procedure involving Cibacron-Blue 3G-A Sepharose 4B-CL, and Sepharose 6B-CL, and immobilized on CNBr-activated Sepharose 4B. (2) Following immobilization via two of the six subunits, L-alanine dehydrogenase retained 66% of the specific activity of the soluble enzyme. The affinity of the immobilized enzyme for NH4+, pyruvate and L-alanine, was not different to that of the soluble form. The Km of the Sepharose-bound L-alanine dehydrogenase for pyridine coenzymes was 6-8-times higher than in the soluble case. (3) The stability of L-alanine dehydrogenase towards urea or thermal denaturation was increased by immobilization. (4) The incubation at 37 degrees C for 24 h of the immobilized L-alanine dehydrogenase with 3 M NH4Cl/NH4OH buffer (pH 9) released 70% of the enzyme. The specific activity and the affinity of the 'solubilized' L-alanine dehydrogenase for the pyridine coenzymes was the same as that obtained with the original, soluble L-alanine dehydrogenase.
Collapse
|
32
|
Mocanu A, Niac G, Ivanof A, Gorun V, Palibroda N, Vargha E, Bologa M, Bârzu O. Preparation of 15N-labeled L-alanine by coupling the alanine dehydrogenase and alcohol dehydrogenase reactions. FEBS Lett 1982; 143:153-6. [PMID: 6811316 DOI: 10.1016/0014-5793(82)80294-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|