1
|
Chen M, Liu CT, Tang Y. Discovery and Biocatalytic Application of a PLP-Dependent Amino Acid γ-Substitution Enzyme That Catalyzes C-C Bond Formation. J Am Chem Soc 2020; 142:10506-10515. [PMID: 32434326 DOI: 10.1021/jacs.0c03535] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes can catalyze transformations of l-amino acids at α, β, and γ positions. These enzymes are frequently involved in the biosynthesis of nonproteinogenic amino acids as building blocks of natural products and are attractive biocatalysts. Here, we report the discovery of a two-step enzymatic synthesis of (2S,6S)-6-methyl pipecolate 1, from the biosynthetic pathway of citrinadin. The key enzyme CndF is PLP-dependent and catalyzes the synthesis of (S)-2-amino-6-oxoheptanoate 3 that is in equilibrium with the cyclic Schiff base. The second enzyme CndE is a stereoselective imine reductase that gives 1. Biochemical characterization of CndF showed this enzyme performs γ-elimination of O-acetyl-l-homoserine to generate the vinylglycine ketimine, which is subjected to nucleophilic attack by acetoacetate to form the new Cγ-Cδ bond in 3 and complete the γ-substitution reaction. CndF displays promiscuity toward different β-keto carboxylate and esters. With use of an Aspergillus strain expressing CndF and CndE, feeding various alkyl-β-keto esters led to the biosynthesis of 6-substituted l-pipecolates. The discovery of CndF expands the repertoire of reactions that can be catalyzed by PLP-dependent enzymes.
Collapse
Affiliation(s)
- Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Chun-Ting Liu
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| |
Collapse
|
2
|
Ocal N, L’enfant M, Charmantray F, Pollegioni L, Martin J, Auffray P, Collin J, Hecquet L. d-Serine as a Key Building Block: Enzymatic Process Development and Smart Applications within the Cascade Enzymatic Concept. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nazim Ocal
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Mélanie L’enfant
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, Università degli Studi dell’Insubria, 21100 Varese, Italy
| | - Juliette Martin
- Protéus by Seqens, 70 Allée Graham Belln, F-30035 Nîmes, France
| | - Pascal Auffray
- Protéus by Seqens, 70 Allée Graham Belln, F-30035 Nîmes, France
| | - Jérôme Collin
- Protéus by Seqens, 70 Allée Graham Belln, F-30035 Nîmes, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| |
Collapse
|
3
|
Yu J, Li J, Gao X, Zeng S, Zhang H, Liu J, Jiao Q. Dynamic Kinetic Resolution for Asymmetric Synthesis of L-Noncanonical Amino Acids from D-Ser Using Tryptophan Synthase and Alanine Racemase. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jinhai Yu
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Jing Li
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Xia Gao
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Shuiyun Zeng
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Hongjuan Zhang
- School of Pharmacy; Nanjing Medical University; 211166 Nanjing China
| | - Junzhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Qingcai Jiao
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| |
Collapse
|
4
|
Xue YP, Cao CH, Zheng YG. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev 2018; 47:1516-1561. [DOI: 10.1039/c7cs00253j] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.
Collapse
Affiliation(s)
- Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Cheng-Hao Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| |
Collapse
|
5
|
Hirato Y, Tokuhisa M, Tanigawa M, Ashida H, Tanaka H, Nishimura K. Cloning and characterization of d-threonine aldolase from the green alga Chlamydomonas reinhardtii. PHYTOCHEMISTRY 2017; 135:18-23. [PMID: 28038776 DOI: 10.1016/j.phytochem.2016.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/07/2016] [Accepted: 12/14/2016] [Indexed: 06/06/2023]
Abstract
d-Threonine aldolase (DTA) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent interconversion of d-threonine and glycine plus acetaldehyde. The enzyme is a powerful tool for the stereospecific synthesis of various β-hydroxy amino acids in synthetic organic chemistry. In this study, DTA from the green alga Chlamydomonas reinhardtii was discovered and characterized, representing the first report to describe the existence of eukaryotic DTA. DTA was overexpressed in recombinant Escherichia coli BL21 (DE3) cells; the specific activity of the enzyme in the cell-free extract was 0.8 U/mg. The recombinant enzyme was purified to homogeneity by ammonium sulfate fractionation, DEAE-Sepharose, and Mono Q column chromatographies (purified enzyme 7.0 U/mg). For the cleavage reaction, the optimal temperature and pH were 70 °C and pH 8.4, respectively. The enzyme demonstrated 90% of residual activity at 50 °C for 1 h. The enzyme catalyzed the synthesis of d- and d-allo threonine from a mixture of glycine and acetaldehyde (the diastereomer excess of d-threonine was 18%). DTA was activated by several divalent metal ions, including manganese, and was inhibited by PLP enzyme inhibitors and metalloenzyme inhibitors.
Collapse
Affiliation(s)
- Yuki Hirato
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan
| | - Mayumi Tokuhisa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan
| | - Minoru Tanigawa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan
| | - Hiroyuki Ashida
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Nishikawatsu 1060, Matsue, Shimane, 690-8504, Japan
| | - Hiroyuki Tanaka
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Seta, Shiga, 520-2192, Japan
| | - Katsushi Nishimura
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan; Department of Biotechnology and Materials Chemistry, Junior College, Nihon University, 7-24-1Narashinodai, Funabashi, Chiba, 274-8501, Japan.
| |
Collapse
|
6
|
Hirato Y, Goto M, Tokuhisa M, Tanigawa M, Nishimura K. Crystallization and X-ray analysis of D-threonine aldolase from Chlamydomonas reinhardtii. Acta Crystallogr F Struct Biol Commun 2017; 73:86-89. [PMID: 28177318 PMCID: PMC5297928 DOI: 10.1107/s2053230x1602063x] [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: 11/15/2016] [Accepted: 12/29/2016] [Indexed: 11/10/2022] Open
Abstract
D-Threonine aldolase from the green alga Chlamydomonas reinhardtii (CrDTA) catalyzes the interconversion of several β-hydroxy-D-amino acids (e.g. D-threonine) and glycine plus the corresponding aldehydes. Recombinant CrDTA was overexpressed in Escherichia coli and purified to homogeneity; it was subsequently crystallized using the hanging-drop vapour-diffusion method at 295 K. Data were collected and processed at 1.85 Å resolution. Analysis of the diffraction pattern showed that the crystal belonged to space group P1, with unit-cell parameters a = 64.79, b = 74.10, c = 89.94 Å, α = 77.07, β = 69.34, γ = 71.93°. The asymmetric unit contained four molecules of CrDTA. The Matthews coefficient was calculated to be 2.12 Å3 Da-1 and the solvent content was 41.9%.
Collapse
Affiliation(s)
- Yuki Hirato
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo 101-8308, Japan
| | - Masaru Goto
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Mayumi Tokuhisa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo 101-8308, Japan
| | - Minoru Tanigawa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo 101-8308, Japan
| | - Katsushi Nishimura
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo 101-8308, Japan
- Department of Biotechnology and Material Chemistry, Junior College, Nihon University, 7-24-1 Narashinodai, Funabashi, Chiba 274-8501, Japan
| |
Collapse
|
7
|
Chen Q, Chen X, Cui Y, Ren J, Lu W, Feng J, Wu Q, Zhu D. A newd-threonine aldolase as a promising biocatalyst for highly stereoselective preparation of chiral aromatic β-hydroxy-α-amino acids. Catal Sci Technol 2017. [DOI: 10.1039/c7cy01774j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A newd-threonine aldolase was identified to tackle the “Cβ-stereoselectivity problem” in the enzymatic production of chiral aromatic β-hydroxy-α-amino acids.
Collapse
Affiliation(s)
- Qijia Chen
- University of Chinese Academy of Sciences
- Beijing
- China
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
| | - Xi Chen
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
- Tianjin
- China
| | - Yunfeng Cui
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
- Tianjin
- China
| | - Jie Ren
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
- Tianjin
- China
| | - Wei Lu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
- Tianjin
- China
| | - Jinhui Feng
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
- Tianjin
- China
| | - Qiaqing Wu
- University of Chinese Academy of Sciences
- Beijing
- China
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
| | - Dunming Zhu
- University of Chinese Academy of Sciences
- Beijing
- China
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
| |
Collapse
|
8
|
Kataoka M, Miyakawa T, Shimizu S, Tanokura M. Enzymes useful for chiral compound synthesis: structural biology, directed evolution, and protein engineering for industrial use. Appl Microbiol Biotechnol 2016; 100:5747-57. [DOI: 10.1007/s00253-016-7603-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
|
9
|
Threonine aldolases: perspectives in engineering and screening the enzymes with enhanced substrate and stereo specificities. Appl Microbiol Biotechnol 2016; 100:2579-90. [PMID: 26810201 PMCID: PMC4761611 DOI: 10.1007/s00253-015-7218-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/30/2015] [Accepted: 12/02/2015] [Indexed: 12/23/2022]
Abstract
Threonine aldolases have emerged as a powerful tool for asymmetric carbon-carbon bond formation. These enzymes catalyse the unnatural aldol condensation of different aldehydes and glycine to produce highly valuable β-hydroxy-α-amino acids with complete stereocontrol at the α-carbon and moderate specificity at the β-carbon. A range of microbial threonine aldolases has been recently recombinantly produced by several groups and their biochemical properties were characterized. Numerous studies have been conducted to improve the reaction protocols to enable higher conversions and investigate the substrate scope of enzymes. However, the application of threonine aldolases in organic synthesis is still limited due to often moderate yields and low diastereoselectivities obtained in the aldol reaction. This review briefly summarizes the screening techniques recently applied to discover novel threonine aldolases as well as enzyme engineering and mutagenesis studies which were accomplished to improve the catalytic activity and substrate specificity. Additionally, the results from new investigations on threonine aldolases including crystal structure determinations and structural-functional characterization are reviewed.
Collapse
|
10
|
Goldberg SL, Goswami A, Guo Z, Chan Y, Lo ET, Lee A, Truc VC, Natalie KJ, Hang C, Rossano LT, Schmidt MA. Preparation of β-hydroxy-α-amino Acid Using Recombinant d-Threonine Aldolase. Org Process Res Dev 2015. [DOI: 10.1021/acs.oprd.5b00191] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steven L. Goldberg
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Animesh Goswami
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Zhiwei Guo
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yeung Chan
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Ehrlic T. Lo
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Andrew Lee
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Vu Chi Truc
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Kenneth J. Natalie
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Chao Hang
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Lucius T. Rossano
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael A. Schmidt
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| |
Collapse
|
11
|
Uhl MK, Oberdorfer G, Steinkellner G, Riegler-Berket L, Mink D, van Assema F, Schürmann M, Gruber K. The crystal structure of D-threonine aldolase from Alcaligenes xylosoxidans provides insight into a metal ion assisted PLP-dependent mechanism. PLoS One 2015; 10:e0124056. [PMID: 25884707 PMCID: PMC4401734 DOI: 10.1371/journal.pone.0124056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/05/2015] [Indexed: 11/23/2022] Open
Abstract
Threonine aldolases catalyze the pyridoxal phosphate (PLP) dependent cleavage of threonine into glycine and acetaldehyde and play a major role in the degradation of this amino acid. In nature, L- as well as D-specific enzymes have been identified, but the exact physiological function of D-threonine aldolases (DTAs) is still largely unknown. Both types of enantio-complementary enzymes have a considerable potential in biocatalysis for the stereospecific synthesis of various β-hydroxy amino acids, which are valuable building blocks for the production of pharmaceuticals. While several structures of L-threonine aldolases (LTAs) have already been determined, no structure of a DTA is available to date. Here, we report on the determination of the crystal structure of the DTA from Alcaligenes xylosoxidans (AxDTA) at 1.5 Å resolution. Our results underline the close relationship of DTAs and alanine racemases and allow the identification of a metal binding site close to the PLP-cofactor in the active site of the enzyme which is consistent with the previous observation that divalent cations are essential for DTA activity. Modeling of AxDTA substrate complexes provides a rationale for this metal dependence and indicates that binding of the β-hydroxy group of the substrate to the metal ion very likely activates this group and facilitates its deprotonation by His193. An equivalent involvement of a metal ion has been implicated in the mechanism of a serine dehydratase, which harbors a metal ion binding site in the vicinity of the PLP cofactor at the same position as in DTA. The structure of AxDTA is completely different to available structures of LTAs. The enantio-complementarity of DTAs and LTAs can be explained by an approximate mirror symmetry of crucial active site residues relative to the PLP-cofactor.
Collapse
Affiliation(s)
- Michael K. Uhl
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Gustav Oberdorfer
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010, Graz, Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Lina Riegler-Berket
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010, Graz, Austria
| | - Daniel Mink
- DSM Chemical Technology R&D BV - Innovative Synthesis, 6167, Geleen, The Netherlands
| | - Friso van Assema
- DSM Chemical Technology R&D BV - Innovative Synthesis, 6167, Geleen, The Netherlands
| | - Martin Schürmann
- DSM Chemical Technology R&D BV - Innovative Synthesis, 6167, Geleen, The Netherlands
| | - Karl Gruber
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010, Graz, Austria
- * E-mail:
| |
Collapse
|
12
|
Liu G, Zhang M, Chen X, Zhang W, Ding W, Zhang Q. Evolution of Threonine Aldolases, a Diverse Family Involved in the Second Pathway of Glycine Biosynthesis. J Mol Evol 2015; 80:102-7. [DOI: 10.1007/s00239-015-9667-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/21/2015] [Indexed: 10/24/2022]
|
13
|
Ogawa J, Yamanaka H, Mano J, Doi Y, Horinouchi N, Kodera T, Nio N, Smirnov SV, Samsonova NN, Kozlov YI, Shimizu S. Synthesis of 4-Hydroxyisoleucine by the Aldolase–Transaminase Coupling Reaction and Basic Characterization of the Aldolase fromArthrobacter simplexAKU 626. Biosci Biotechnol Biochem 2014; 71:1607-15. [PMID: 17617727 DOI: 10.1271/bbb.60655] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Arthrobacter simplex AKU 626 was found to synthesize 4-hydroxyisoleucine from acetaldehyde, alpha-ketobutyrate, and L-glutamate in the presence of Escherichia coli harboring the branched chain amino acid transaminase gene (ilvE) from E. coli K12 substrain MG1655. By using resting cells of A. simplex AKU 626 and E. coli BL21(DE3)/pET-15b-ilvE, 3.2 mM 4-hydroxyisoleucine was produced from 250 mM acetaldehyde, 75 mM alpha-ketobutyrate, and 100 mM L-glutamate with a molar yield to alpha-ketobutyrate of 4.3% in 50 mM Tris-HCl buffer (pH 7.5) containing 2 mM MnCl(2) x 4H(2)O at 28 degrees C for 2 h. An aldolase that catalyzes the aldol condensation of acetaldehyde and alpha-ketobutyrate was purified from A. simplex AKU 626. Mn(2+) and pyridoxal 5'-monophosphate were effective in stabilizing the enzyme. The native and subunit molecular masses of the purified aldolase were about 180 and 32 kDa respectively. The N-terminal amino acid sequence of the purified enzyme showed no significant homology to known aldolases.
Collapse
Affiliation(s)
- Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
di Salvo ML, Remesh SG, Vivoli M, Ghatge MS, Paiardini A, D'Aguanno S, Safo MK, Contestabile R. On the catalytic mechanism and stereospecificity of Escherichia coli L-threonine aldolase. FEBS J 2013; 281:129-45. [PMID: 24165453 DOI: 10.1111/febs.12581] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/18/2013] [Accepted: 10/23/2013] [Indexed: 11/29/2022]
Abstract
L-threonine aldolases (L-TAs) represent a family of homologous pyridoxal 5'-phosphate-dependent enzymes found in bacteria and fungi, and catalyse the reversible cleavage of several L-3-hydroxy-α-amino acids. L-TAs have great biotechnological potential, as they catalyse the formation of carbon-carbon bonds, and therefore may be exploited for the bioorganic synthesis of L-3-hydroxyamino acids that are biologically active or constitute building blocks for pharmaceutical molecules. Many L-TAs, showing different stereospecificity towards the Cβ configuration, have been isolated. Because of their potential to carry out diastereoselective syntheses, L-TAs have been subjected to structural, functional and mechanistic studies. Nevertheless, their catalytic mechanism and the structural bases of their stereospecificity have not been elucidated. In this study, we have determined the crystal structure of low-specificity L-TA from Escherichia coli at 2.2-Å resolution, in the unliganded form and cocrystallized with L-serine and L-threonine. Furthermore, several active site mutants have been functionally characterized in order to elucidate the reaction mechanism and the molecular bases of stereospecificity. No active site catalytic residue was revealed, and a structural water molecule was assumed to act as the catalytic base in the retro-aldol cleavage reaction. Interestingly, the very large active site opening of E. coli L-TA suggests that much larger molecules than L-threonine isomers may be easily accommodated, and L-TAs may actually have diverse physiological functions in different organisms. Substrate recognition and reaction specificity seem to be guided by the overall microenvironment that surrounds the substrate at the enzyme active site, rather than by one ore more specific residues.
Collapse
Affiliation(s)
- Martino L di Salvo
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | | | | | | | | | | | | | | |
Collapse
|
15
|
|
16
|
Serine hydroxymethyltransferase: A model enzyme for mechanistic, structural, and evolutionary studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1489-96. [DOI: 10.1016/j.bbapap.2010.10.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 10/25/2010] [Accepted: 10/29/2010] [Indexed: 11/18/2022]
|
17
|
Baldassarre M, Scirè A, Tanfani F. Turning pyridoxal-5'-phosphate-dependent enzymes into thermostable binding proteins: D-Serine dehydratase from baker's yeast as a case study. Biochimie 2011; 94:479-86. [PMID: 21896305 DOI: 10.1016/j.biochi.2011.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 08/24/2011] [Indexed: 12/21/2022]
Abstract
D-serine dehydratase from Saccharomyces cerevisae is a recently discovered dimeric enzyme catalyzing the β-elimination of D-serine to pyruvate and ammonia. The reaction is highly enantioselective and depends on cofactor pyridoxal-5'-phosphate (PLP) and Zn(2+). In our work, the aldimine linkage tethering PLP to recombinant, tagged D-serine dehydratase (Dsd) has been reduced by treatment with NaBH(4) so as to yield an inactive form of the holoenzyme (DsdR), which was further treated with a protease in order to remove the amino-terminal purification tag. Fourier Transform infrared (FT-IR) spectroscopic analysis revealed that both the reduced form (DsdR) and the reduced/detagged form (DsdRD) maintain the overall secondary structure of Dsd, but featured a significant increased thermal stability. The observed T(m) values for DsdR and for DsdRD shifted to 71.5 °C and 73.3 °C, respectively, resulting in nearly 11 °C and 13 °C higher than the one measured for Dsd. Furthermore, the analysis of the FT-IR spectra acquired in the presence of D-serine and L-serine indicates that, though catalytically inert, DsdRD retains the ability to enantioselectively bind its natural substrate. Sequence analysis of D-serine dehydratase and other PLP-dependent enzymes also highlighted critical residues involved in PLP binding. In virtue of its intrinsic properties, DsdRD represents an ideal candidate for the design of novel platforms based on stable, non-consuming binding proteins aimed at measuring d-serine levels in biological fluids.
Collapse
Affiliation(s)
- Maurizio Baldassarre
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Ranieri, 60131 Ancona, Italy
| | | | | |
Collapse
|
18
|
Tanaka H, Senda M, Venugopalan N, Yamamoto A, Senda T, Ishida T, Horiike K. Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney. J Biol Chem 2011; 286:27548-58. [PMID: 21676877 PMCID: PMC3149347 DOI: 10.1074/jbc.m110.201160] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2010] [Revised: 05/30/2011] [Indexed: 12/30/2022] Open
Abstract
D-serine is a physiological co-agonist of the N-methyl-D-aspartate receptor. It regulates excitatory neurotransmission, which is important for higher brain functions in vertebrates. In mammalian brains, D-amino acid oxidase degrades D-serine. However, we have found recently that in chicken brains the oxidase is not expressed and instead a D-serine dehydratase degrades D-serine. The primary structure of the enzyme shows significant similarities to those of metal-activated D-threonine aldolases, which are fold-type III pyridoxal 5'-phosphate (PLP)-dependent enzymes, suggesting that it is a novel class of D-serine dehydratase. In the present study, we characterized the chicken enzyme biochemically and also by x-ray crystallography. The enzyme activity on D-serine decreased 20-fold by EDTA treatment and recovered nearly completely by the addition of Zn(2+). None of the reaction products that would be expected from side reactions of the PLP-D-serine Schiff base were detected during the >6000 catalytic cycles of dehydration, indicating high reaction specificity. We have determined the first crystal structure of the D-serine dehydratase at 1.9 Å resolution. In the active site pocket, a zinc ion that coordinates His(347) and Cys(349) is located near the PLP-Lys(45) Schiff base. A theoretical model of the enzyme-D-serine complex suggested that the hydroxyl group of D-serine directly coordinates the zinc ion, and that the ε-NH(2) group of Lys(45) is a short distance from the substrate Cα atom. The α-proton abstraction from D-serine by Lys(45) and the elimination of the hydroxyl group seem to occur with the assistance of the zinc ion, resulting in the strict reaction specificity.
Collapse
Affiliation(s)
- Hiroyuki Tanaka
- From the Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Seta, Ohtsu, Shiga 520-2192, Japan
| | - Miki Senda
- the Structure-guided Drug Development Project, JBIC Research Institute, Japan Biological Informatics Consortium, 2-4-7 Aomi Koto-ku, Tokyo 135-0064, Japan
| | - Nagarajan Venugopalan
- theNational Institute of General Medical Sciences and National Cancer Institute Collaborative Access Team, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, and
| | - Atsushi Yamamoto
- From the Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Seta, Ohtsu, Shiga 520-2192, Japan
| | - Toshiya Senda
- the Biomedicinal Information Research Center, National Institute of Advanced Industrial Sciences and Technology, 2-4-7 Aomi Koto-ku, Tokyo 135-0064, Japan
| | - Tetsuo Ishida
- From the Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Seta, Ohtsu, Shiga 520-2192, Japan
| | - Kihachiro Horiike
- From the Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Seta, Ohtsu, Shiga 520-2192, Japan
| |
Collapse
|
19
|
Friedman M, Levin CE. Nutritional and medicinal aspects of D-amino acids. Amino Acids 2011; 42:1553-82. [PMID: 21519915 DOI: 10.1007/s00726-011-0915-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/06/2011] [Indexed: 02/07/2023]
Abstract
This paper reviews and interprets a method for determining the nutritional value of D-amino acids, D-peptides, and amino acid derivatives using a growth assay in mice fed a synthetic all-amino acid diet. A large number of experiments were carried out in which a molar equivalent of the test compound replaced a nutritionally essential amino acid such as L-lysine (L-Lys), L-methionine (L-Met), L-phenylalanine (L-Phe), and L-tryptophan (L-Trp) as well as the semi-essential amino acids L-cysteine (L-Cys) and L-tyrosine (L-Tyr). The results show wide-ranging variations in the biological utilization of test substances. The method is generally applicable to the determination of the biological utilization and safety of any amino acid derivative as a potential nutritional source of the corresponding L-amino acid. Because the organism is forced to use the D-amino acid or amino acid derivative as the sole source of the essential or semi-essential amino acid being replaced, and because a free amino acid diet allows better control of composition, the use of all-amino-acid diets for such determinations may be preferable to protein-based diets. Also covered are brief summaries of the widely scattered literature on dietary and pharmacological aspects of 27 individual D-amino acids, D-peptides, and isomeric amino acid derivatives and suggested research needs in each of these areas. The described results provide a valuable record and resource for further progress on the multifaceted aspects of D-amino acids in food and biological samples.
Collapse
Affiliation(s)
- Mendel Friedman
- Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA.
| | | |
Collapse
|
20
|
Discovery and characterization of d-phenylserine deaminase from Arthrobacter sp. TKS1. Appl Microbiol Biotechnol 2010; 90:159-72. [DOI: 10.1007/s00253-010-3028-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 11/20/2010] [Accepted: 11/22/2010] [Indexed: 10/18/2022]
|
21
|
Maeda T, Takeda Y, Murakami T, Yokota A, Wada M. Purification, characterization and amino acid sequence of a novel enzyme, D-threo-3-hydroxyaspartate dehydratase, from Delftia sp. HT23. J Biochem 2010; 148:705-12. [PMID: 20843822 DOI: 10.1093/jb/mvq106] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
D-threo-3-hydroxyaspartate dehydratase (D-THA DH) was purified from the cell-free extract of the soil-isolated bacterium Delftia sp. HT23. The enzyme exhibited dehydratase activity towards D-threo-3-hydroxyaspartate, l-threo-3-hydroxyaspartate, l-erythro-3-hydroxyaspartate and d-serine. Absorption of the purified enzyme at 412 nm suggests that it contains pyridoxal 5'-phosphate (PLP) as a cofactor. The NH(2)-terminal and internal amino acid sequences showed significant similarity to hypothetical alanine racemase of genome-sequenced Delftia acidovorans SPH-1; however, the purified enzyme showed no alanine racemase activity. Using the sequence information of D. acidovorans SPH-1, the gene encoding d-THA DH was cloned. The deduced amino acid sequence, which belongs to the alanine racemase family, shows significant (26-36%) similarity to d-serine dehydratase of both Saccharomyces cerevisiae and chicken. In order to obtain purified d-THA DH efficiently, the gene was expressed in Escherichia coli. The recombinant enzyme was highly activated by divalent cations, such as Mn(2+), Co(2+) and Ni(2+). Site-directed mutagenesis experiment revealed that lysine 43 is an important residue involved in PLP binding and catalysis. This is the first reported enzyme that acts on d-THA. In addition, this enzyme is the first example of a prokaryotic dehydratase belonging to the fold-type III PLP-dependent enzyme family.
Collapse
Affiliation(s)
- Takayuki Maeda
- Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, Japan
| | | | | | | | | |
Collapse
|
22
|
Threonine aldolases—screening, properties and applications in the synthesis of non-proteinogenic β-hydroxy-α-amino acids. Appl Microbiol Biotechnol 2010; 88:409-24. [DOI: 10.1007/s00253-010-2751-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Revised: 06/23/2010] [Accepted: 06/23/2010] [Indexed: 11/26/2022]
|
23
|
López C, Ríos SD, López-Santín J, Caminal G, Álvaro G. Immobilization of PLP-dependent enzymes with cofactor retention and enhanced stability. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2010.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
24
|
Fesko K, Giger L, Hilvert D. Synthesis of β-hydroxy-α-amino acids with a reengineered alanine racemase. Bioorg Med Chem Lett 2008; 18:5987-90. [DOI: 10.1016/j.bmcl.2008.08.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 08/08/2008] [Accepted: 08/11/2008] [Indexed: 10/21/2022]
|
25
|
Four types of threonine aldolases: Similarities and differences in kinetics/thermodynamics. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcatb.2007.10.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
26
|
Abstract
YGL196W of Saccharomyces cerevisiae encodes a putative protein that is unidentified but is predicted to have a motif similar to that of the N-terminal domain of the bacterial alanine racemase. In the present study we found that YGL196W encodes a novel D-serine dehydratase, which belongs to a different protein family from that of the known bacterial enzyme. The yeast D-serine dehydratase purified from recombinant Escherichia coli cells depends on pyridoxal 5′-phosphate and zinc, and catalyses the conversion of D-serine into pyruvate and ammonia with the Km and kcat values of 0.39 mM and 13.1 s−1 respectively. D-Threonine and β-Cl-D-alanine also serve as substrates with catalytic efficiencies which are approx. 3 and 2% of D-serine respectively. L-Serine, L-threonine and β-Cl-L-alanine are inert as substrates. Atomic absorption analysis revealed that the enzyme contains one zinc atom per enzyme monomer. The enzyme activities toward D-serine and D-threonine were decreased by EDTA treatment and recovered by the addition of Zn2+. Little recovery was observed with Mg2+, Mn2+, Ca2+, Ni2+, Cu2+, K+ or Na+. In contrast, the activity towards β-Cl-D-alanine was retained after EDTA treatment. These results suggest that zinc is involved in the elimination of the hydroxy group of D-serine and D-threonine. D-Serine dehydratase of S. cerevisiae is probably the first example of a eukaryotic D-serine dehydratase and that of a specifically zinc-dependent pyridoxal enzyme as well.
Collapse
|
27
|
Toscano MD, Woycechowsky KJ, Hilvert D. Minimalist active-site redesign: teaching old enzymes new tricks. Angew Chem Int Ed Engl 2007; 46:3212-36. [PMID: 17450624 DOI: 10.1002/anie.200604205] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although nature evolves its catalysts over millions of years, enzyme engineers try to do it a bit faster. Enzyme active sites provide highly optimized microenvironments for the catalysis of biologically useful chemical transformations. Consequently, changes at these centers can have large effects on enzyme activity. The prediction and control of these effects provides a promising way to access new functions. The development of methods and strategies to explore the untapped catalytic potential of natural enzyme scaffolds has been pushed by the increasing demand for industrial biocatalysts. This Review describes the use of minimal modifications at enzyme active sites to expand their catalytic repertoires, including targeted mutagenesis and the addition of new reactive functionalities. Often, a novel activity can be obtained with only a single point mutation. The many successful examples of active-site engineering through minimal mutations give useful insights into enzyme evolution and open new avenues in biocatalyst research.
Collapse
Affiliation(s)
- Miguel D Toscano
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, Switzerland
| | | | | |
Collapse
|
28
|
Kato Y, Tsuda T, Asano Y. Purification and partial characterization of N-hydroxy-l-phenylalanine decarboxylase/oxidase from Bacillus sp. strain OxB-1, an enzyme involved in aldoxime biosynthesis in the “aldoxime–nitrile pathway”. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:856-65. [PMID: 17544345 DOI: 10.1016/j.bbapap.2007.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 03/27/2007] [Accepted: 04/25/2007] [Indexed: 11/22/2022]
Abstract
An enzyme that catalyzes the conversion of N-hydroxy-l-phenylalanine to phenylacetaldoxime was shown to be present in the Z-phenylacetaldoxime-degrading bacterium, Bacillus sp. strain OxB-1. The aldoxime-forming enzyme, which is induced by L-phenylalanine, was purified 8,050-fold to apparent homogeneity with a yield of 15.2%. The enzyme has a subunit M(r) of about 86,000. The enzyme converts N-hydroxy-L-phenylalanine (K(m) 0.99 mM) to only one geometrical isomer, namely Z-phenylacetaldoxime. Relatively large amounts of pyridoxal 5'-phosphate (PLP) are required to be present in the reaction mixture because PLP reacts non-enzymatically with the N-hydroxy amino acid substrate to form a nitrone. Several characteristics of the enzyme were compared with those of other PLP-dependent aromatic amino acid-converting enzymes described in the literature. The enzyme is tentatively named "N-hydroxy-L-phenylalanine decarboxylase/oxidase". Finally, the possible biosynthesis and metabolism of phenylacetaldoxime in Bacillus sp. strain OxB-1 is discussed.
Collapse
Affiliation(s)
- Yasuo Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | | | | |
Collapse
|
29
|
Toscano MD, Müller MM, Hilvert D. Enhancing Activity and Controlling Stereoselectivity in a Designed PLP-Dependent Aldolase. Angew Chem Int Ed Engl 2007; 46:4468-70. [PMID: 17486616 DOI: 10.1002/anie.200700710] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Miguel D Toscano
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg HCI F339, 8093 Zürich, Switzerland
| | | | | |
Collapse
|
30
|
Toscano M, Müller M, Hilvert D. Enhancing Activity and Controlling Stereoselectivity in a Designed PLP-Dependent Aldolase. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
31
|
Toscano M, Woycechowsky K, Hilvert D. Minimale Umgestaltung aktiver Enzymtaschen – wie man alten Enzymen neue Kunststücke beibringt. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604205] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
32
|
Misono H, Maeda H, Tuda K, Ueshima S, Miyazaki N, Nagata S. Characterization of an inducible phenylserine aldolase from Pseudomonas putida 24-1. Appl Environ Microbiol 2005; 71:4602-9. [PMID: 16085854 PMCID: PMC1183316 DOI: 10.1128/aem.71.8.4602-4609.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An inducible phenylserine aldolase (L-threo-3-phenylserine benzaldehyde-lyase, EC 4.1.2.26), which catalyzes the cleavage of L-3-phenylserine to yield benzaldehyde and glycine, was purified to homogeneity from a crude extract of Pseudomonas putida 24-1 isolated from soil. The enzyme was a hexamer with the apparent subunit molecular mass of 38 kDa and contained 0.7 mol of pyridoxal 5' phosphate per mol of the subunit. The enzyme exhibited absorption maxima at 280 and 420 nm. The maximal activity was obtained at about pH 8.5. The enzyme acted on L-threo-3-phenylserine (Km, 1.3 mM), l-erythro-3-phenylserine (Km, 4.6 mM), l-threonine (Km, 29 mM), and L-allo-threonine (Km, 22 mM). In the reverse reaction, threo- and erythro- forms of L-3-phenylserine were produced from benzaldehyde and glycine. The optimum pH for the reverse reaction was 7.5. The structural gene coding for the phenylserine aldolase from Pseudomonas putida 24-1 was cloned and overexpressed in Escherichia coli cells. The nucleotide sequence of the phenylserine aldolase gene encoded a peptide containing 357 amino acids with a calculated molecular mass of 37.4 kDa. The recombinant enzyme was purified and characterized. Site-directed mutagenesis experiments showed that replacement of K213 with Q resulted in a loss of the enzyme activity, with a disappearance of the absorption maximum at 420 nm. Thus, K213 of the enzyme probably functions as an essential catalytic residue, forming a Schiff base with pyridoxal 5'-phosphate.
Collapse
Affiliation(s)
- Haruo Misono
- Department of Bioresources Science, Kochi University, Nankoku, Kochi 783-8502, Japan.
| | | | | | | | | | | |
Collapse
|
33
|
Wada M, Nakamori S, Takagi H. Serine racemase homologue of Saccharomyces cerevisiae has L-threo-3-hydroxyaspartate dehydratase activity. FEMS Microbiol Lett 2003; 225:189-93. [PMID: 12951240 DOI: 10.1016/s0378-1097(03)00484-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The NH(2)-terminal amino acid sequence of L-threo-3-hydroxyaspartate dehydratase from Pseudomonas sp. T62 showed significant similarity to that of the SRY1 gene product of Saccharomyces cerevisiae (serine racemase in yeast). SRY1 was cloned and expressed in Escherichia coli, and the gene product was purified and partially characterized. The SRY1 gene product exhibited dehydratase activity specific for L-threo-3-hydroxyaspartate (K(m)=3.9 mM, V(max)=110 micromol min(-1) (mg protein)(-1)) but not for D-threo- or DL-erythro-3-hydroxyaspartate. The purified enzyme showed no detectable serine racemase activity. The activity of the enzyme was inhibited by hydroxylamine and EDTA, and was activated by Mg(2+), Ca(2+), and Mn(2+), suggesting that pyridoxal-5'-phosphate and divalent cations participate in the enzyme reaction. Gene disruption and overexpression indicated that SRY1 is responsible for the 3-hydroxyaspartate resistance of S. cerevisiae. To our knowledge, this is the first report of 3-hydroxyaspartate dehydratase activity in eukaryotic cells.
Collapse
Affiliation(s)
- Masaru Wada
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka-cho, Fukui 910-1195, Japan.
| | | | | |
Collapse
|
34
|
Paiardini A, Contestabile R, D'Aguanno S, Pascarella S, Bossa F. Threonine aldolase and alanine racemase: novel examples of convergent evolution in the superfamily of vitamin B6-dependent enzymes. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1647:214-9. [PMID: 12686135 DOI: 10.1016/s1570-9639(03)00050-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vitamin B(6)-dependent enzymes may be grouped into five evolutionarily unrelated families, each having a different fold. Within fold type I enzymes, L-threonine aldolase (L-TA) and fungal alanine racemase (AlaRac) belong to a subgroup of structurally and mechanistically closely related proteins, which specialised during evolution to perform different functions. In a previous study, a comparison of the catalytic properties and active site structures of these enzymes suggested that they have a catalytic apparatus with the same basic features. Recently, recombinant D-threonine aldolases (D-TAs) from two bacterial organisms have been characterised, their predicted amino acid sequences showing no significant similarities to any of the known B(6) enzymes. In the present work, a comparative structural analysis suggests that D-TA has an alpha/beta barrel fold and therefore is a fold type III B(6) enzyme, as eukaryotic ornithine decarboxylase (ODC) and bacterial AlaRac. The presence of both TA and AlaRac in two distinct evolutionary unrelated families represents a novel and interesting example of convergent evolution. The independent emergence of the same catalytic properties in families characterised by completely different folds may have not been determined by chance, but by the similar structural features required to catalyse pyridoxal phosphate-dependent aldolase and racemase reactions.
Collapse
Affiliation(s)
- Alessandro Paiardini
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università degli Studi di Roma La Sapienza, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | | | | | | | | |
Collapse
|
35
|
Cook SP, Galve-Roperh I, Martínez del Pozo A, Rodríguez-Crespo I. Direct calcium binding results in activation of brain serine racemase. J Biol Chem 2002; 277:27782-92. [PMID: 12021263 DOI: 10.1074/jbc.m111814200] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Serine racemase (SR) is a brain enzyme present in glial cells, where it isomerizes L-serine into D-serine that, in turn, diffuses and coactivates the N-methyl-D-aspartate receptor through the binding to the so-called "glycine site." We have developed a method for the slow expression of SR in a eukaryotic vector that permits the correct insertion of the prosthetic group into the active site, rendering functional SR with a K(m) toward L-serine of 4.8 mm. Divalent cations such as calcium or manganese were necessary for complete enzyme activity, whereas the presence of chelators such as EDTA completely inhibited the enzyme. Moreover, direct binding of calcium to SR was evidenced using (45)Ca(2+). Gel filtration of the recombinant SR revealed the protein to be in a dimer-tetramer equilibrium. The addition of EDTA to a calcium-saturated serine racemase evokes a profound conformational change, as monitored by both fluorescence and circular dichroism techniques. Fluorescence titration allowed us to calculate a binding constant for calcium of 6.2 microm. Reagents that react with sulfhydryl groups, such as cystamine, were potent inhibitors of SR, in a clear reflection that one or more cysteine residues are important for enzyme activity. Additionally, 16 serine analogues were tested as a putative SR substrate or inhibitors. Significant inhibition was only observed for L-Ser-O-sulfate, L-cycloserine, and L-cysteine. Finally, activation of brain SR as a result of the changes in calcium concentration was studied in primary astrocytes. Treatment of astrocytes with the calcium ionophore, as well as with compounds that augment the intracellular calcium levels such as glutamate or kainate led to an increase in the amount of d-serine present in the extracellular medium. These results suggest that there might be a glutamatergic-mediated regulation of SR activity by intracellular calcium concentration.
Collapse
Affiliation(s)
- Silas P Cook
- Departamento de Bioquímica y Biología Molecular, Fac. CC. Químicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | | | | | | |
Collapse
|
36
|
Metzler DE, Metzler CM, Sauke DJ. The Metabolism of Nitrogen and Amino Acids. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
37
|
Liu JQ, Dairi T, Itoh N, Kataoka M, Shimizu S, Yamada H. Diversity of microbial threonine aldolases and their application. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(00)00118-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
38
|
Mehta PK, Christen P. The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2000; 74:129-84. [PMID: 10800595 DOI: 10.1002/9780470123201.ch4] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The pyridoxal-5-phosphate-dependent enzymes (B6 enzymes) that act on amino acid substrates are of multiple evolutionary origin. The numerous common mechanistic features of B6 enzymes thus are not historical traits passed on from a common ancestor enzyme but rather reflect evolutionary or chemical necessities. Family profile analysis of amino acid sequences supported by comparison of the available three-dimensional (3-D) crystal structures indicates that the B6 enzymes known to date belong to four independent evolutionary lineages of homologous (or more precisely paralogous) proteins, of which the alpha family is by far the largest. The alpha family (with aspartate aminotransferase as the prototype enzyme) includes enzymes that catalyze, with several exceptions, transformations of amino acids in which the covalency changes are limited to the same carbon atom that carries the amino group forming the imine linkage with the coenzyme (i.e., Calpha in most cases). Enzymes of the beta family (tryptophan synthase beta as the prototype enzyme) mainly catalyze replacement and elimination reactions at Cbeta. The D-alanine aminotransferase family and the alanine racemase family are the two other independent lineages, both with relatively few member enzymes. The primordial pyridoxal-5-phosphate-dependent enzymes apparently were regio-specific catalysts that first diverged into reaction-specific enzymes and then specialized for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages. Comparison of sequences from eukaryotic, archebacterial, and eubacterial species indicates that the functional specialization of most B6 enzymes has occurred already in the universal ancestor cell. The cofactor pyridoxal-5-phosphate must have emerged very early in biological evolution; conceivably, organic cofactors and metal ions were the first biological catalysts. In attempts to stimulate particular steps of molecular evolution, oligonucleotide-directed mutagenesis of active-site residues and directed molecular evolution have been applied to change both the substrate and reaction specificity of existent B6 enzymes. Pyridoxal-5-phosphate-dependent catalytic antibodies were elicited with a screening protocol that applied functional selection criteria as they might have been operative in the evolution of protein-assisted pyridoxal catalysis.
Collapse
Affiliation(s)
- P K Mehta
- Biochemisches Institut, Universität Zürich, Switzerland
| | | |
Collapse
|
39
|
Ogawa H, Gomi T, Fujioka M. Serine hydroxymethyltransferase and threonine aldolase: are they identical? Int J Biochem Cell Biol 2000; 32:289-301. [PMID: 10716626 DOI: 10.1016/s1357-2725(99)00113-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serine hydroxymethyltransferase, a pyridoxal phosphate-dependent enzyme, catalyses the interconversion of serine and glycine, both of which are major sources of one-carbon units necessary for the synthesis of purine, thymidylate, methionine, and so on. Threonine aldolase catalyzes the pyridoxal phosphate-dependent, reversible reaction between threonine and acetaldehyde plus glycine. No extensive studies have been carried out on threonine aldolase in animal tissues, and it has long been believed that serine hydroxymethyltransferase and threonine aldolase are the same, i.e. one entity. This is based on the finding that rabbit liver serine hydroxymethyltransferase possesses some threonine aldolase activity. Recently, however, many kinds of threonine aldolase and corresponding genes were isolated from micro-organisms, and these enzymes were shown to be distinct from serine hydroxymethyltransferase. The experiments with isolated hepatocytes and cell-free extracts from various animals revealed that threonine is degraded mainly through the pathway initiated by threonine 3-dehydrogenase, and there is little or no contribution by threonine aldolase. Thus, although serine hydroxymethyltransferase from some mammalian livers exhibits a low threonine aldolase activity, the two enzymes are distinct from each other and mammals lack the "genuine" threonine aldolase.
Collapse
Affiliation(s)
- H Ogawa
- Department of Biochemistry, Faculty of Medicine, Toyama Medical and Pharmaceutical University, Japan.
| | | | | |
Collapse
|
40
|
Wada M, Matsumoto T, Nakamori S, Sakamoto M, Kataoka M, Liu JQ, Itoh N, Yamada H, Shimizu S. Purification and characterization of a novel enzyme, L-threo-3-hydroxyaspartate dehydratase, from Pseudomonas sp. T62. FEMS Microbiol Lett 1999; 179:147-51. [PMID: 10481099 DOI: 10.1111/j.1574-6968.1999.tb08720.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
L-threo-3-Hydroxyaspartate dehydratase (L-threo-3-hydroxyaspartate hydro-lyase), which exhibited specificity for L-threo-3-hydroxyaspartate (K(m)=0.74 mM, V(max)=37.5 micromol min(-1) (mg protein)(-1)) but not for D-threo or D, L-erythro-3-hydroxyaspartate, was purified from a cell-free extract of Pseudomonas sp. T62. The activity of the enzyme was inhibited by hydroxylamine and EDTA, which suggests that pyridoxal 5'-phosphate and divalent cations participate in the enzyme reaction. The NH(2)-terminal amino acid sequence showed significant similarity to the Saccharomyces cerevisiae YKL218c gene product, a hypothetical threonine dehydratase. However, the purified enzyme showed no threonine dehydratase activity.
Collapse
Affiliation(s)
- M Wada
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Kenjyojima, Matsuoka-cho, Fukui, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|