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Thirumalai A, Ganapathy Raman P, Jayavelu T, Subramanian R. Bridging the gap between maleate hydratase, citraconase and isopropylmalate isomerase: Insights into the single broad-specific enzyme. Enzyme Microb Technol 2023; 162:110140. [DOI: 10.1016/j.enzmictec.2022.110140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/23/2022] [Accepted: 10/08/2022] [Indexed: 11/13/2022]
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2
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Identification of a Specific Maleate Hydratase in the Direct Hydrolysis Route of the Gentisate Pathway. Appl Environ Microbiol 2015; 81:5753-60. [PMID: 26070679 DOI: 10.1128/aem.00975-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/09/2015] [Indexed: 11/20/2022] Open
Abstract
In contrast to the well-characterized and more common maleylpyruvate isomerization route of the gentisate pathway, the direct hydrolysis route occurs rarely and remains unsolved. In Pseudomonas alcaligenes NCIMB 9867, two gene clusters, xln and hbz, were previously proposed to be involved in gentisate catabolism, and HbzF was characterized as a maleylpyruvate hydrolase converting maleylpyruvate to maleate and pyruvate. However, the complete degradation pathway of gentisate through direct hydrolysis has not been characterized. In this study, we obtained from the NCIMB culture collection a Pseudomonas alcaligenes spontaneous mutant strain that lacked the xln cluster and designated the mutant strain SponMu. The hbz cluster in strain SponMu was resequenced, revealing the correct location of the stop codon for hbzI and identifying a new gene, hbzG. HbzIJ was demonstrated to be a maleate hydratase consisting of large and small subunits, stoichiometrically converting maleate to enantiomerically pure d-malate. HbzG is a glutathione-dependent maleylpyruvate isomerase, indicating the possible presence of two alternative pathways of maleylpyruvate catabolism. However, the hbzF-disrupted mutant could still grow on gentisate, while disruption of hbzG prevented this ability, indicating that the direct hydrolysis route was not a complete pathway in strain SponMu. Subsequently, a d-malate dehydrogenase gene was introduced into the hbzG-disrupted mutant, and the engineered strain was able to grow on gentisate via the direct hydrolysis route. This fills a gap in our understanding of the direct hydrolysis route of the gentisate pathway and provides an explanation for the high yield of d-malate from maleate by this d-malate dehydrogenase-deficient natural mutant.
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Chen BS, Otten LG, Hanefeld U. Stereochemistry of enzymatic water addition to C=C bonds. Biotechnol Adv 2015; 33:526-46. [PMID: 25640045 DOI: 10.1016/j.biotechadv.2015.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 12/20/2022]
Abstract
Water addition to carbon-carbon double bonds using hydratases is attracting great interest in biochemistry. Most of the known hydratases are involved in primary metabolism and to a lesser extent in secondary metabolism. New hydratases have recently been added to the toolbox, both from natural sources or artificial metalloenzymes. In order to comprehensively understand how the hydratases are able to catalyse the water addition to carbon-carbon double bonds, this review will highlight the mechanistic and stereochemical studies of the enzymatic water addition to carbon-carbon double bonds, focusing on the syn/anti-addition and stereochemistry of the reaction.
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Affiliation(s)
- Bi-Shuang Chen
- Biokatalyse, Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Linda G Otten
- Biokatalyse, Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Ulf Hanefeld
- Biokatalyse, Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628 BL Delft, The Netherlands.
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Abstract
Water is omnipresent and unreactive. How to speed up water addition and even make it selective are highlighted in this perspective.
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Affiliation(s)
- Verena Resch
- Gebouw voor Scheikunde
- Biokatalyse
- Afdeling Biotechnologie
- Technische Universiteit Delft
- 2628BL Delft
| | - Ulf Hanefeld
- Gebouw voor Scheikunde
- Biokatalyse
- Afdeling Biotechnologie
- Technische Universiteit Delft
- 2628BL Delft
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Jin J, Hanefeld U. The selective addition of water to CC bonds; enzymes are the best chemists. Chem Commun (Camb) 2011; 47:2502-10. [DOI: 10.1039/c0cc04153j] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Michielsen MJF, Frielink C, Meijer EA, van der Werf MJ, Wijffels RH, Tramper J, Beeftink HH. Stabilization of Maleate-Hydratase Activity of PermeabilizedPseudomonas Pseudoalcaligenes. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242429909015227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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7
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Chen L, Vitkup D. Distribution of orphan metabolic activities. Trends Biotechnol 2007; 25:343-8. [PMID: 17580095 DOI: 10.1016/j.tibtech.2007.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 04/17/2007] [Accepted: 06/01/2007] [Indexed: 10/23/2022]
Abstract
A significant fraction (30-40%) of known metabolic activities is currently orphan. Although orphan activities have been biochemically characterized, we do not know a single gene responsible for these reactions in any organism. The problem of orphan activities represents one of the major challenges of modern biochemistry. We analyze the distribution of orphans across biochemical space, through years of enzymatic characterization, and by biological organisms. We find that orphan metabolic activities have been accumulating for many decades. They are widely distributed across enzymatic functional space and metabolic network neighborhoods. Although orphans are relatively more abundant in less studied species, over half of orphan reactions have been experimentally characterized in more than one organism. Shrinking the space of orphan activities will likely require a close collaboration between computational and experimental laboratories.
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Affiliation(s)
- Lifeng Chen
- Center for Computational Biology and Bioinformatics and Department of Biomedical Informatics, Columbia University, 1130 Nicholas Ave., Irving Cancer Research Center, New York, NY 10032, USA
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8
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Drevland RM, Waheed A, Graham DE. Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii. J Bacteriol 2007; 189:4391-400. [PMID: 17449626 PMCID: PMC1913355 DOI: 10.1128/jb.00166-07] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The archaeon Methanocaldococcus jannaschii uses three different 2-oxoacid elongation pathways, which extend the chain length of precursors in leucine, isoleucine, and coenzyme B biosyntheses. In each of these pathways an aconitase-type hydrolyase catalyzes an hydroxyacid isomerization reaction. The genome sequence of M. jannaschii encodes two homologs of each large and small subunit that forms the hydrolyase, but the genes are not cotranscribed. The genes are more similar to each other than to previously characterized isopropylmalate isomerase or homoaconitase enzyme genes. To identify the functions of these homologs, the four combinations of subunits were heterologously expressed in Escherichia coli, purified, and reconstituted to generate the iron-sulfur center of the holoenzyme. Only the combination of MJ0499 and MJ1277 proteins catalyzed isopropylmalate and citramalate isomerization reactions. This pair also catalyzed hydration half-reactions using citraconate and maleate. Another broad-specificity enzyme, isopropylmalate dehydrogenase (MJ0720), catalyzed the oxidative decarboxylation of beta-isopropylmalate, beta-methylmalate, and d-malate. Combined with these results, phylogenetic analysis suggests that the pyruvate pathway to 2-oxobutyrate (an alternative to threonine dehydratase in isoleucine biosynthesis) evolved several times in bacteria and archaea. The enzymes in the isopropylmalate pathway of leucine biosynthesis facilitated the evolution of 2-oxobutyrate biosynthesis through the introduction of a citramalate synthase, either by gene recruitment or gene duplication and functional divergence.
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Affiliation(s)
- Randy M Drevland
- Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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Alberty RA. Calculation of Thermodynamic Properties of Species of Biochemical Reactants Using the Inverse Legendre Transform. J Phys Chem B 2005; 109:9132-9. [PMID: 16852086 DOI: 10.1021/jp044162j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The determination of apparent equilibrium constants and heats of enzyme-catalyzed reactions provides a way to determine Delta(f)G degrees and Delta(f)H degrees of species of biochemical reactants. These calculations are more difficult than the calculation of transformed thermodynamic properties from species properties, and they are an application of the inverse Legendre transform. The Delta(f)G degrees values of species of a reactant can be calculated from an apparent equilibrium constant if the Delta(f)G degrees values are known for all the species of all the other reactants and the pKs of the reactant of interest are known. The Delta(f)H degrees of species of a reactant can be calculated from the heat of reaction if the Delta(f)H degrees values are known for all species of the other reactants and Delta(f)G degrees values are known for all species in the reaction. The standard enthalpies of acid dissociation of the reactant of interest are also needed. The inverse Legendre transformation is accomplished by using computer programs to set up the simultaneous equations that involve the Delta(f)H degrees of the species and solving them. Thirty two new species matrixes providing Delta(f)G degrees values and eight new species matrixes providing Delta(f)H degrees values are calculated. It is the specificity and speed of enzyme-catalyzed reactions that make it possible to determine standard thermodynamic properties of complicated species in aqueous solution that could never have been obtained classically.
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Affiliation(s)
- Robert A Alberty
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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He BF, Nakajima-Kambe T, Ozawa T, Nakahara T. Production of d-malate and d-citramalate by Arthrobacter pascens DMDC12 having stable citraconase. Process Biochem 2000. [DOI: 10.1016/s0032-9592(00)00219-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Michielsen MJ, Frielink C, Wijffels RH, Tramper J, Beeftink HH. Modeling solid-to-solid biocatalysis: integration of six consecutive steps. Biotechnol Bioeng 2000; 69:597-606. [PMID: 10918134 DOI: 10.1002/1097-0290(20000920)69:6<597::aid-bit3>3.0.co;2-c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A quantitative model for the conversion of a solid-substrate salt to a solid-product salt in a batch bioreactor seeded with product crystals is presented. The overall process consists of six serial steps (with dissolution and crystallization each in themselves complex multistep processes): solid-salt dissolution, salt dissociation into an ionic substrate and a counter-ion, bioconversion accompanied by biocatalyst inactivation, complexation of the ionic product with the counter-ion, and salt crystal growth. In the model, the consecutive steps are integrated, including biocatalyst inactivation and assuming that salt dissociation and complexation of ions are at equilibrium. Model parameters were determined previously in separate independent experiments. To validate the model, either dissolved or solid Ca-maleate was converted to solid Ca-D-malate by permeabilized Pseudomonas pseudoalcaligenes in a batch bioreactor seeded with Ca-D-malate crystals. The model very well predicted the concentrations of all components in the liquid phase (Ca-maleate, Ca(2+), maleate(2-), D-malate(2-), and Ca-D-malate) and the amounts of the solid phases (Ca-maleate. H(2)O and Ca-D-malate. 3H(2)O), especially when high initial amounts of Ca-maleate. H(2)O and Ca-D-malate. 3H(2)O were present.
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Affiliation(s)
- M J Michielsen
- Wageningen University, Food and Bioprocess Engineering Group, Department of Food Technology and Nutritional Sciences, Biotechnion/Dreijencomplex, P.O. Box 8129/6700 EV Wageningen, The
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Van Der Werf MJ. Purification and characterization of a Baeyer-Villiger mono-oxygenase from Rhodococcus erythropolis DCL14 involved in three different monocyclic monoterpene degradation pathways. Biochem J 2000; 347 Pt 3:693-701. [PMID: 10769172 PMCID: PMC1221005 DOI: 10.1042/0264-6021:3470693] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A Baeyer-Villiger mono-oxygenase (BVMO), catalysing the NADPH- and oxygen-dependent oxidation of the monocyclic monoterpene ketones 1-hydroxy-2-oxolimonene, dihydrocarvone and menthone, was purified to homogeneity from Rhodococcus erythropolis DCL14. Monocyclic monoterpene ketone mono-oxygenase (MMKMO) is a monomeric enzyme of molecular mass 60 kDa. It contains 1 mol of FAD/monomer as the prosthetic group. The N-terminal amino acid sequence showed homology with many other NADPH-dependent and FAD-containing (Type 1) BVMOs. Maximal enzyme activity was measured at pH 9 and 35 degrees C. MMKMO has a broad substrate specificity, catalysing the lactonization of a large number of monocyclic monoterpene ketones and substituted cyclohexanones. The natural substrates 1-hydroxy-2-oxolimonene, dihydrocarvone and menthone were converted stoichiometrically into 3-isopropenyl-6-oxoheptanoate (the spontaneous rearrangement product of the lactone formed by MMKMO), 4-isopropenyl-7-methyl-2-oxo-oxepanone and 7-isopropyl-4-methyl-2-oxo-oxepanone respectively. The MMKMO-catalysed conversion of iso-dihydrocarvone showed an opposite regioselectivity to that of dihydrocarvone; in this case, 6-isopropenyl-3-methyl-2-oxo-oxepanone was formed as the product. MMKMO converted all enantiomers of the natural substrates with almost equal efficiency. MMKMO is involved in the conversion of the monocyclic monoterpene ketone intermediates formed in the degradation pathways of all stereoisomers of three different monocyclic monoterpenes, i.e. limonene, (dihydro)carveol and menthol.
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Affiliation(s)
- M J Van Der Werf
- Division of Industrial Microbiology, Department of Food Technology and Nutritional Sciences, Wageningen University, 6700 EV Wageningen, The Netherlands.
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Michielsen MJ, Frielink C, Wijffels RH, Tramper J, Beeftink HH. D-malate production by permeabilized Pseudomonas pseudoalcaligenes; optimization of conversion and biocatalyst productivity. J Biotechnol 2000; 79:13-26. [PMID: 10817338 DOI: 10.1016/s0168-1656(00)00220-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
For the development of a continuous process for the production of solid D-malate from a Ca-maleate suspension by permeabilized Pseudomonas pseudoalcaligenes, it is important to understand the effect of appropriate process parameters on the stability and activity of the biocatalyst. Previously, we quantified the effect of product (D-malate2 -) concentration on both the first-order biocatalyst inactivation rate and on the biocatalytic conversion rate. The effects of the remaining process parameters (ionic strength, and substrate and Ca2 + concentration) on biocatalyst activity are reported here. At (common) ionic strengths below 2 M, biocatalyst activity was unaffected. At high substrate concentrations, inhibition occurred. Ca2+ concentration did not affect biocatalyst activity. The kinetic parameters (both for conversion and inactivation) were determined as a function of temperature by fitting the complete kinetic model, featuring substrate inhibition, competitive product inhibition and first-order irreversible biocatalyst inactivation, at different temperatures simultaneously through three extended data sets of substrate concentration versus time. Temperature affected both the conversion and inactivation parameters. The final model was used to calculate the substrate and biocatalyst costs per mmol of product in a continuous system with biocatalyst replenishment and biocatalyst recycling. Despite the effect of temperature on each kinetic parameter separately, the overall effect of temperature on the costs was found to be negligible (between 293 and 308 K). Within pertinent ranges, the sum of the substrate and biocatalyst costs per mmol of product was calculated to decrease with the influent substrate concentration and the residence time. The sum of the costs showed a minimum as a function of the influent biocatalyst concentration.
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Affiliation(s)
- M J Michielsen
- Department of Food Technology and Nutritional Sciences, Wageningen Agricultural University, The Netherlands
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14
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van der Werf MJ, van der Ven C, Barbirato F, Eppink MH, de Bont JA, van Berkel WJ. Stereoselective carveol dehydrogenase from Rhodococcus erythropolis DCL14. A novel nicotinoprotein belonging to the short chain dehydrogenase/reductase superfamily. J Biol Chem 1999; 274:26296-304. [PMID: 10473585 DOI: 10.1074/jbc.274.37.26296] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel nicotinoprotein, catalyzing the dichlorophenolindophenol-dependent oxidation of carveol to carvone, was purified to homogeneity from Rhodococcus erythropolis DCL14. The enzyme is specifically induced after growth on limonene and carveol. Dichlorophenolindophenol-dependent carveol dehydrogenase (CDH) is a homotetramer of 120 kDa with each subunit containing a tightly bound NAD(H) molecule. The enzyme is optimally active at pH 5.5 and 50 degrees C and displays a broad substrate specificity with a preference for substituted cyclohexanols. When incubated with a diastereomeric mixture of (4R)- or (4S)-carveol, CDH stereoselectively catalyzes the conversion of the (6S)-carveol stereoisomers only. Kinetic studies with pure stereoisomers showed that this is due to large differences in V(max)/K(m) values and simultaneous product inhibition by (R)- or (S)-carvone. The R. erythropolis CDH gene (limC) was identified in an operon encoding the enzymes involved in limonene degradation. The CDH nucleotide sequence revealed an open reading frame of 831 base pairs encoding a 277-amino acid protein with a deduced mass of 29,531 Da. The CDH primary structure shares 10-30% sequence identity with members of the short chain dehydrogenase/reductase superfamily. Structure homology modeling with trihydroxynaphthalene reductase from Magnaporthe grisea suggests that CDH from R. erythropolis DCL14 is an alpha/beta one-domain protein with an extra loop insertion involved in NAD binding and a flexible C-terminal part involved in monoterpene binding.
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Affiliation(s)
- M J van der Werf
- Division of Industrial Microbiology, Department of Food Technology and Nutritional Sciences, Wageningen University, Bomenweg 2, 6703 HD Wageningen, The Netherlands.
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Michielsen M, Meijer E, Wijffels R, Tramper J, Beeftink H. Kinetics of d-Malate Production by Permeabilized Pseudomonas Pseudoalcaligenes. Enzyme Microb Technol 1998. [DOI: 10.1016/s0141-0229(97)00266-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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van der Werf MJ, Hartmans S, van den Tweel WJJ. Permeabilization and lysis of Pseudomonas pseudoalcaligenes cells by Triton X-100 for efficient production of d-malate. Appl Microbiol Biotechnol 1995. [DOI: 10.1007/bf00164759] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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van der Werf MJ, Hartmans S, van den Tweel WJ. Effect of maleate counterion on malease activity: Production of d-malate in a crystal-liquid two-phase system. Enzyme Microb Technol 1995. [DOI: 10.1016/0141-0229(94)00070-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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van der Werf MJ, van den Tweel WJ, Kamphuis J, Hartmans S, de Bont JA. The potential of lyases for the industrial production of optically active compounds. Trends Biotechnol 1994; 12:95-103. [PMID: 7764830 DOI: 10.1016/0167-7799(94)90112-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Lyases catalyse the cleavage of C-C, C-N, C-O and other bonds by elimination to produce double bonds or, conversely, catalyse the addition of groups to double bonds. These enzymes do not require cofactor recycling, show an absolute stereospecificity and can give a theoretical yield of 100%, compared with only 50% for enantiomeric resolutions. Lyases are therefore attracting considerable interest as biocatalysts for the production of optically active compounds, and have already found application in several large commercial processes.
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Affiliation(s)
- M J van der Werf
- Department of Food Science, Wageningen Agricultural University, The Netherlands
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