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Hélaine V, Gastaldi C, Lemaire M, Clapés P, Guérard-Hélaine C. Recent Advances in the Substrate Selectivity of Aldolases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Virgil Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Cédric Gastaldi
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Marielle Lemaire
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Pere Clapés
- Biological Chemistry Department, Institute for Advanced Chemistry of Catalonia, IQAC−CSIC, 08034 Barcelona, Spain
| | - Christine Guérard-Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
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2
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Abstract
Formation of carbon-carbon bonds is central to synthetic chemistry. The aldol reaction provides the chemistry to fuse a nucleophilic enolate with an electrophilic aldehyde to form a new CC bond between two newly formed asymmetric centers. A major challenge in the reaction is steering the stereochemistry of the product. Aldolases are lyases that catalyze aldol reactions as well as the retro-aldol cleavage, and are abundant in cellular metabolism. Due to the often exquisite stereoselectivity in aldolase catalyzed carboligation reactions, these enzymes are gaining increased interest as potentially important tools in asymmetric synthesis of new useful compounds. Fructose 6-phosphate aldolase from Escherichia coli (FSA) is of special interest because of its very unusual independence of phosphorylated reactant substrates. The current text describes the protein engineering of FSA, applying principles of directed evolution, for the generation, production and characterization of new aldolase variants. A range of new enantiopure polyhydroxylated compounds were produced applying isolated FSA variants.
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Affiliation(s)
- Mikael Widersten
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.
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3
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Marín-Valls R, Hernández K, Bolte M, Joglar J, Bujons J, Clapés P. Chemoenzymatic Hydroxymethylation of Carboxylic Acids by Tandem Stereodivergent Biocatalytic Aldol Reaction and Chemical Decarboxylation. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01646] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Roser Marín-Valls
- Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Karel Hernández
- Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Michael Bolte
- Institut für Anorganische Chemie, J.-W.-Goethe-Universität, D-60438 Frankfurt/Main, Germany
| | - Jesús Joglar
- Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Jordi Bujons
- Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Pere Clapés
- Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
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4
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Laurent V, Uzel A, Hélaine V, Nauton L, Traïkia M, Gefflaut T, Salanoubat M, de Berardinis V, Lemaire M, Guérard‐Hélaine C. Exploration of Aldol Reactions Catalyzed by Stereoselective Pyruvate Aldolases with 2‐Oxobutyric Acid as Nucleophile. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900128] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- V. Laurent
- Université Clermont AuvergneCNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand 63000 Clermont-Ferrand France
| | - A. Uzel
- Université Clermont AuvergneCNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand 63000 Clermont-Ferrand France
| | - V. Hélaine
- Université Clermont AuvergneCNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand 63000 Clermont-Ferrand France
| | - L. Nauton
- Université Clermont AuvergneCNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand 63000 Clermont-Ferrand France
| | - M. Traïkia
- Université Clermont AuvergneCNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand 63000 Clermont-Ferrand France
| | - T. Gefflaut
- Université Clermont AuvergneCNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand 63000 Clermont-Ferrand France
| | - M. Salanoubat
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Univ. EvryUniversité Paris-Saclay 91057 Evry France
| | - V. de Berardinis
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Univ. EvryUniversité Paris-Saclay 91057 Evry France
| | - M. Lemaire
- Université Clermont AuvergneCNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand 63000 Clermont-Ferrand France
| | - C. Guérard‐Hélaine
- Université Clermont AuvergneCNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand 63000 Clermont-Ferrand France
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5
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Nigro MJ, Palazzolo MA, Colasurdo D, Iribarren AM, Lewkowicz ES. N-Acetylneuraminic acid aldolase-catalyzed synthesis of acyclic nucleoside analogues carrying a 4-hydroxy-2-oxoacid moiety. CATAL COMMUN 2019. [DOI: 10.1016/j.catcom.2018.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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6
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Hernández K, Szekrenyi A, Clapés P. Nucleophile Promiscuity of Natural and Engineered Aldolases. Chembiochem 2018; 19:1353-1358. [DOI: 10.1002/cbic.201800135] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Karel Hernández
- Department of Chemical Biology and Molecular Modelling; Catalonia Institute for Advanced Chemistry IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Anna Szekrenyi
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Pere Clapés
- Department of Chemical Biology and Molecular Modelling; Catalonia Institute for Advanced Chemistry IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
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7
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Hernández K, Gómez A, Joglar J, Bujons J, Parella T, Clapés P. 2-Keto-3-Deoxy-l-Rhamnonate Aldolase (YfaU) as Catalyst in Aldol Additions of Pyruvate to Amino Aldehyde Derivatives. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700360] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Karel Hernández
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Ariadna Gómez
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jesús Joglar
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Bujons
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear; Facultat de Ciències; Universitat Autònoma de Barcelona; 08193 Cerdanyola del Vallès Barcelona Spain
| | - Pere Clapés
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
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Nishiyama R, Inoue A, Ojima T. Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01. Mar Drugs 2017; 15:md15020037. [PMID: 28216576 PMCID: PMC5334617 DOI: 10.3390/md15020037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/26/2017] [Accepted: 02/08/2017] [Indexed: 01/21/2023] Open
Abstract
Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-d-gluconate (KDG) kinase and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase genes, i.e., flkin and flald, still remained uncharacterized. The amino acid sequences deduced from flkin and flald showed low identities with those of corresponding enzymes of Saccharophagus degradans 2-40T, a member of Proteobacteria (Kim et al., Process Biochem., 2016). This led us to consider that the DEH-assimilating enzymes of Bacteroidetes species are somewhat deviated from those of Proteobacteria species. Thus, in the present study, we first assessed the characteristics in the primary structures of KDG kinase and KDG aldolase of the strain UMI-01, and then investigated the enzymatic properties of recombinant enzymes, recFlKin and recFlAld, expressed by an Escherichia coli expression system. Multiple-sequence alignment among KDG kinases and KDG aldolases from several Proteobacteria and Bacteroidetes species indicated that the strain UMI-01 enzymes showed considerably low sequence identities (15%-25%) with the Proteobacteria enzymes, while they showed relatively high identities (47%-68%) with the Bacteroidetes enzymes. Phylogenetic analyses for these enzymes indicated the distant relationship between the Proteobacteria enzymes and the Bacteroidetes enzymes, i.e., they formed distinct clusters in the phylogenetic tree. recFlKin and recFlAld produced with the genes flkin and flald, respectively, were confirmed to show KDG kinase and KDPG aldolase activities. Namely, recFlKin produced 1.7 mM KDPG in a reaction mixture containing 2.5 mM KDG and 2.5 mM ATP in a 90-min reaction, while recFlAld produced 1.2 mM pyruvate in the reaction mixture containing 5 mM KDPG at the equilibrium state. An in vitro alginate-metabolizing system constructed from recFlKin, recFlAld, and previously reported alginate lyases and DEH reductase of the strain UMI-01 could convert alginate to pyruvate and glyceraldehyde-3-phosphate with an efficiency of 38%.
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Affiliation(s)
- Ryuji Nishiyama
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
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9
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Schmidt NG, Eger E, Kroutil W. Building Bridges: Biocatalytic C-C-Bond Formation toward Multifunctional Products. ACS Catal 2016; 6:4286-4311. [PMID: 27398261 PMCID: PMC4936090 DOI: 10.1021/acscatal.6b00758] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/13/2016] [Indexed: 12/12/2022]
Abstract
Carbon-carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. The review gives a selection of biocatalytic C-C-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. In most cases, the reactions lead to products functionalized at the site of C-C-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow to decorate aromatic and heteroaromatic molecules. Furthermore, examples for cyclization of (non)natural precursors leading to saturated carbocycles are given as well as the stereoselective cyclopropanation of olefins affording cyclopropanes. Although many tools are already available, recent research also makes it clear that nature provides an even broader set of enzymes to perform specific C-C coupling reactions. The possibilities are without limit; however, a big library of variants for different types of reactions is required to have the specific enzyme for a desired specific (stereoselective) reaction at hand.
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Affiliation(s)
- Nina G. Schmidt
- ACIB
GmbH c/o, Department of Chemistry, University
of Graz, Heinrichstrasse
28, 8010 Graz, Austria
| | - Elisabeth Eger
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- ACIB
GmbH c/o, Department of Chemistry, University
of Graz, Heinrichstrasse
28, 8010 Graz, Austria
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
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10
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Cheriyan M, Chan SH, Perler F. Traceless splicing enabled by substrate-induced activation of the Nostoc punctiforme Npu DnaE intein after mutation of a catalytic cysteine to serine. J Mol Biol 2014; 426:4018-4029. [PMID: 25451033 DOI: 10.1016/j.jmb.2014.10.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/15/2014] [Accepted: 10/26/2014] [Indexed: 11/24/2022]
Abstract
Inteins self-catalytically cleave out of precursor proteins while ligating the surrounding extein fragments with a native peptide bond. Much attention has been lavished on these molecular marvels with the hope of understanding and harnessing their chemistry for novel biochemical transformations including coupling peptides from synthetic or biological origins and controlling protein function. Despite an abundance of powerful applications, the use of inteins is still hampered by limitations in our understanding of their specificity (defined as flanking sequences that permit splicing) and the challenge of inserting inteins into target proteins. We examined the frequently used Nostoc punctiforme Npu DnaE intein after the C-extein cysteine nucleophile (Cys+1) was mutated to serine or threonine. Previous studies demonstrated reduced rates and/or splicing yields with the Npu DnaE intein after mutation of Cys+1 to Ser+1. In this study, genetic selection identified extein sequences with Ser+1 that enabled the Npu DnaE intein to splice with only a 5-fold reduction in rate compared to the wild-type Cys+1 intein and without mutation of the intein itself to activate Ser+1 as a nucleophile. Three different proteins spliced efficiently after insertion of the intein flanked by the selected sequences. We then used this selected specificity to achieve traceless splicing in a targeted enzyme at a location predicted by primary sequence similarity to only the selected C-extein sequence. This study highlights the latent catalytic potential of the Npu DnaE intein to splice with an alternative nucleophile and enables broader intein utility by increasing insertion site choices.
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Affiliation(s)
- Manoj Cheriyan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Francine Perler
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
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11
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Bowers CM, Carlson DA, Rivera M, Clark RL, Toone EJ. Effect of compressive force on unbinding specific protein-ligand complexes with force spectroscopy. J Phys Chem B 2013; 117:4755-62. [PMID: 23537272 DOI: 10.1021/jp309393s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Atomic force microscopy (AFM) is used extensively for the investigation of noncovalent molecular association. Although the technique is used to derive various types of information, in almost all instances the frequency of complex formation, the magnitude of rupture forces, and the shape of the force-distance curve are used to determine the behavior of the system. We have used AFM to consider the effect of contact force on the unbinding profiles of lactose-galectin-3, as well as the control pairs lactose-KDPG aldolase, and mannose-galectin-3, where the interacting species show negligible solution-phase affinity. Increased contact forces (>250 pN) resulted in increased probabilitites of binding and decreased blocking efficiencies for the cognate ligand-receptor pair lactose-G3. Increased contact force applied to two control systems with no known affinity, mannose-G3 and lactose-KDPG aldolase, resulted in nonspecific ruptures that were indistinguishable from those of specific lactose-G3 interactions. These results demonstrate that careful experimental design is vital to the production of interpretable data, and suggest that contact force minimization is an effective technique for probing the unbinding forces and rupture lengths of only specific ligand-receptor interactions.
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Affiliation(s)
- Carleen M Bowers
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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12
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13
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Cheriyan M, Toone EJ, Fierke CA. Improving upon nature: active site remodeling produces highly efficient aldolase activity toward hydrophobic electrophilic substrates. Biochemistry 2012; 51:1658-68. [PMID: 22316217 DOI: 10.1021/bi201899b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The substrate specificity of enzymes is frequently narrow and constrained by multiple interactions, limiting the use of natural enzymes in biocatalytic applications. Aldolases have important synthetic applications, but the usefulness of these enzymes is hampered by their narrow reactivity profile with unnatural substrates. To explore the determinants of substrate selectivity and alter the specificity of Escherichia coli 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, we employed structure-based mutagenesis coupled with library screening of mutant enzymes localized to the bacterial periplasm. We identified two active site mutations (T161S and S184L) that work additively to enhance the substrate specificity of this aldolase to include catalysis of retro-aldol cleavage of (4S)-2-keto-4-hydroxy-4-(2'-pyridyl)butyrate (S-KHPB). These mutations improve the value of k(cat)/K(M)(S-KHPB) by >450-fold, resulting in a catalytic efficiency that is comparable to that of the wild-type enzyme with the natural substrate while retaining high stereoselectivity. Moreover, the value of k(cat)(S-KHPB) for this mutant enzyme, a parameter critical for biocatalytic applications, is 3-fold higher than the maximal value achieved by the natural aldolase with any substrate. This mutant also possesses high catalytic efficiency for the retro-aldol cleavage of the natural substrate, KDPG, and a >50-fold improved activity for cleavage of 2-keto-4-hydroxy-octonoate, a nonfunctionalized hydrophobic analogue. These data suggest a substrate binding mode that illuminates the origin of facial selectivity in aldol addition reactions catalyzed by KDPG and 2-keto-3-deoxy-6-phosphogalactonate aldolases. Furthermore, targeting mutations to the active site provides a marked improvement in substrate selectivity, demonstrating that structure-guided active site mutagenesis combined with selection techniques can efficiently identify proteins with characteristics that compare favorably to those of naturally occurring enzymes.
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Affiliation(s)
- Manoj Cheriyan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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Baker P, Seah SYK. Rational Design of Stereoselectivity in the Class II Pyruvate Aldolase BphI. J Am Chem Soc 2011; 134:507-13. [DOI: 10.1021/ja208754r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Perrin Baker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Stephen Y. K. Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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15
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Cheriyan M, Walters MJ, Kang BD, Anzaldi LL, Toone EJ, Fierke CA. Directed evolution of a pyruvate aldolase to recognize a long chain acyl substrate. Bioorg Med Chem 2011; 19:6447-53. [PMID: 21944547 DOI: 10.1016/j.bmc.2011.08.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 08/19/2011] [Accepted: 08/26/2011] [Indexed: 11/29/2022]
Abstract
The use of biological catalysts for industrial scale synthetic chemistry is highly attractive, given their cost effectiveness, high specificity that obviates the need for protecting group chemistry, and the environmentally benign nature of enzymatic procedures. Here we evolve the naturally occurring 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolases from Thermatoga maritima and Escherichia coli, into enzymes that recognize a nonfunctionalized electrophilic substrate, 2-keto-4-hydroxyoctonoate (KHO). Using an in vivo selection based on pyruvate auxotrophy, mutations were identified that lower the K(M) value up to 100-fold in E. coli KDPG aldolase, and that enhance the efficiency of retro-aldol cleavage of KHO by increasing the value of k(cat)/K(M) up to 25-fold in T. maritima KDPG aldolase. These data indicate that numerous mutations distal from the active site contribute to enhanced 'uniform binding' of the substrates, which is the first step in the evolution of novel catalytic activity.
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Affiliation(s)
- Manoj Cheriyan
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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16
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17
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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18
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Royer SF, Haslett L, Crennell SJ, Hough DW, Danson MJ, Bull SD. Structurally Informed Site-Directed Mutagenesis of a Stereochemically Promiscuous Aldolase To Afford Stereochemically Complementary Biocatalysts. J Am Chem Soc 2010; 132:11753-8. [DOI: 10.1021/ja104412a] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sylvain F. Royer
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - Luke Haslett
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - Susan J. Crennell
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - David W. Hough
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - Michael J. Danson
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - Steven D. Bull
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
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19
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Bolt A, Berry A, Nelson A. Directed evolution of aldolases for exploitation in synthetic organic chemistry. Arch Biochem Biophys 2008; 474:318-30. [PMID: 18230325 PMCID: PMC2431125 DOI: 10.1016/j.abb.2008.01.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Revised: 01/03/2008] [Accepted: 01/06/2008] [Indexed: 02/03/2023]
Abstract
This review focuses on the directed evolution of aldolases with synthetically useful properties. Directed evolution has been used to address a number of limitations associated with the use of wild-type aldolases as catalysts in synthetic organic chemistry. The generation of aldolase enzymes with a modified or expanded substrate repertoire is described. Particular emphasis is placed on the directed evolution of aldolases with modified stereochemical properties: such enzymes can be useful catalysts in the stereoselective synthesis of biologically active small molecules. The review also describes some of the fundamental insights into mechanistic enzymology that directed evolution can provide.
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Affiliation(s)
- Amanda Bolt
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Adam Nelson
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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20
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Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ. Characterization and crystal structure of Escherichia coli KDPGal aldolase. Bioorg Med Chem 2008; 16:710-20. [PMID: 17981470 PMCID: PMC3326530 DOI: 10.1016/j.bmc.2007.10.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 10/05/2007] [Accepted: 10/12/2007] [Indexed: 11/29/2022]
Abstract
2-Keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolases catalyze an identical reaction differing in substrate specificity in only the configuration of a single stereocenter. However, the proteins show little sequence homology at the amino acid level. Here we investigate the determinants of substrate selectivity of these enzymes. The Escherichia coli KDPGal aldolase gene, cloned into a T7 expression vector and overexpressed in E. coli, catalyzes retro-aldol cleavage of the natural substrate, KDPGal, with values of k(cat)/K(M) and k(cat) of 1.9x10(4)M(-1)s(-1) and 4s(-1), respectively. In the synthetic direction, KDPGal aldolase efficiently catalyzes an aldol addition using a limited number of aldehyde substrates, including d-glyceraldehyde-3-phosphate (natural substrate), d-glyceraldehyde, glycolaldehyde, and 2-pyridinecarboxaldehyde. A preparative scale reaction between 2-pyridinecarboxaldehyde and pyruvate catalyzed by KDPGal aldolase produced the aldol adduct of the R stereochemistry in >99.7% ee, a result complementary to that observed using the related KDPG aldolase. The native crystal structure has been solved to a resolution of 2.4A and displays the same (alpha/beta)(8) topology, as KDPG aldolase. We have also determined a 2.1A structure of a Schiff base complex between the enzyme and its substrate. This model predicts that a single amino acid change, T161 in KDPG aldolase to V154 in KDPGal aldolase, plays an important role in determining the stereochemical course of enzyme catalysis and this prediction was borne out by site-directed mutagenesis studies. However, additional changes in the enzyme sequence are required to prepare an enzyme with both high catalytic efficiency and altered stereochemistry.
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Affiliation(s)
- Matthew J Walters
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Cheriyan M, Toone EJ, Fierke CA. Mutagenesis of the phosphate-binding pocket of KDPG aldolase enhances selectivity for hydrophobic substrates. Protein Sci 2008; 16:2368-77. [PMID: 17962400 DOI: 10.1110/ps.073042907] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Narrow substrate specificities often limit the use of enzymes in biocatalysis. To further the development of Escherichia coli 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase as a biocatalyst, the molecular determinants of substrate specificity were probed by mutagenesis. Our data demonstrate that S184 is located in the substrate-binding pocket and interacts with the phosphate moiety of KDPG, providing biochemical support for the binding model proposed on the basis of crystallographic data. An analysis of the substrate selectivity of the mutant enzymes indicates that alterations to the phosphate-binding site of KDPG aldolase changes the substrate selectivity. We report mutations that enhance catalysis of aldol cleavage of substrates lacking a phosphate moiety and demonstrate that electrophile reactivity correlates with the hydrophobicity of the substituted side chain. These mutations improve the selectivity for unnatural substrates as compared to KDPG by up to 2000-fold. Furthermore, the S184L KDPG aldolase mutant improves the catalytic efficiency for the synthesis of a precursor for nikkomycin by 40-fold, making it a useful biocatalyst for the preparation of fine chemicals.
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Affiliation(s)
- Manoj Cheriyan
- Department of Chemistry, University of Michigan, Ann Arbor 48109, USA
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Wolterink-van Loo S, van Eerde A, Siemerink MAJ, Akerboom J, Dijkstra BW, van der Oost J. Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases. Biochem J 2007; 403:421-30. [PMID: 17176250 PMCID: PMC1876368 DOI: 10.1042/bj20061419] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aldolases are enzymes with potential applications in biosynthesis, depending on their activity, specificity and stability. In the present study, the genomes of Sulfolobus species were screened for aldolases. Two new KDGA [2-keto-3-deoxygluconate (2-oxo-3-deoxygluconate) aldolases] from Sulfolobus acidocaldarius and Sulfolobus tokodaii were identified, overexpressed in Escherichia coli and characterized. Both enzymes were found to have biochemical properties similar to the previously characterized S. solfataricus KDGA, including the condensation of pyruvate and either D,L-glyceraldehyde or D,L-glyceraldehyde 3-phosphate. The crystal structure of S. acidocaldarius KDGA revealed the presence of a novel phosphate-binding motif that allows the formation of multiple hydrogen-bonding interactions with the acceptor substrate, and enables high activity with glyceraldehyde 3-phosphate. Activity analyses with unnatural substrates revealed that these three KDGAs readily accept aldehydes with two to four carbon atoms, and that even aldoses with five carbon atoms are accepted to some extent. Water-mediated interactions permit binding of substrates in multiple conformations in the spacious hydrophilic binding site, and correlate with the observed broad substrate specificity.
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Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ. Mechanism of the Class I KDPG aldolase. Bioorg Med Chem 2006; 14:3002-10. [PMID: 16403639 PMCID: PMC3315828 DOI: 10.1016/j.bmc.2005.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 12/04/2005] [Accepted: 12/09/2005] [Indexed: 11/17/2022]
Abstract
In vivo, 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase catalyzes the reversible, stereospecific retro-aldol cleavage of KDPG to pyruvate and D-glyceraldehyde-3-phosphate. The enzyme is a lysine-dependent (Class I) aldolase that functions through the intermediacy of a Schiff base. Here, we propose a mechanism for this enzyme based on crystallographic studies of wild-type and mutant aldolases. The three dimensional structure of KDPG aldolase from the thermophile Thermotoga maritima was determined to 1.9A. The structure is the standard alpha/beta barrel observed for all Class I aldolases. At the active site Lys we observe clear density for a pyruvate Schiff base. Density for a sulfate ion bound in a conserved cluster of residues close to the Schiff base is also observed. We have also determined the structure of a mutant of Escherichia coli KDPG aldolase in which the proposed general acid/base catalyst has been removed (E45N). One subunit of the trimer contains density suggesting a trapped pyruvate carbinolamine intermediate. All three subunits contain a phosphate ion bound in a location effectively identical to that of the sulfate ion bound in the T. maritima enzyme. The sulfate and phosphate ions experimentally locate the putative phosphate binding site of the aldolase and, together with the position of the bound pyruvate, facilitate construction of a model for the full-length KDPG substrate complex. The model requires only minimal positional adjustments of the experimentally determined covalent intermediate and bound anion to accommodate full-length substrate. The model identifies the key catalytic residues of the protein and suggests important roles for two observable water molecules. The first water molecule remains bound to the enzyme during the entire catalytic cycle, shuttling protons between the catalytic glutamate and the substrate. The second water molecule arises from dehydration of the carbinolamine and serves as the nucleophilic water during hydrolysis of the enzyme-product Schiff base. The second water molecule may also mediate the base-catalyzed enolization required to form the carbon nucleophile, again bridging to the catalytic glutamate. Many aspects of this mechanism are observed in other Class I aldolases and suggest a mechanistically and, perhaps, evolutionarily related family of aldolases distinct from the N-acetylneuraminate lyase (NAL) family.
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Affiliation(s)
- Matthew J. Walters
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Andrew R. McEwan
- Centre for Biomolecular Sciences, The University of St. Andrews, St. Andrews KY169ST, UK
| | - James H. Naismith
- Centre for Biomolecular Sciences, The University of St. Andrews, St. Andrews KY169ST, UK
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103, USA
| | - Eric J. Toone
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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Samland AK, Sprenger GA. Microbial aldolases as C-C bonding enzymes--unknown treasures and new developments. Appl Microbiol Biotechnol 2006; 71:253-64. [PMID: 16614860 DOI: 10.1007/s00253-006-0422-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 03/10/2006] [Accepted: 03/10/2006] [Indexed: 11/26/2022]
Abstract
Aldolases are a specific group of lyases that catalyze the reversible stereoselective addition of a donor compound (nucleophile) onto an acceptor compound (electrophile). Whereas most aldolases are specific for their donor compound in the aldolization reaction, they often tolerate a wide range of aldehydes as acceptor compounds. C-C bonding by aldolases creates stereocenters in the resulting aldol products. This makes aldolases interesting tools for asymmetric syntheses of rare sugars or sugar-derived compounds as iminocyclitols, statins, epothilones, and sialic acids. Besides the well-known fructose 1,6-bisphosphate aldolase, other aldolases of microbial origin have attracted the interest of synthetic bio-organic chemists in recent years. These are either other dihydroxyacetone phosphate aldolases or aldolases depending on pyruvate/phosphoenolpyruvate, glycine, or acetaldehyde as donor substrate. Recently, an aldolase that accepts dihydroxyacetone or hydroxyacetone as a donor was described. A further enlargement of the arsenal of available chemoenzymatic tools can be achieved through screening for novel aldolase activities and directed evolution of existing aldolases to alter their substrate- or stereospecifities. We give an update of work on aldolases, with an emphasis on microbial aldolases.
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Affiliation(s)
- Anne K Samland
- Institut für Mikrobiologie, Universität Stuttgart, Germany
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26
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Directed Evolution of Enantioselective Enzymes as Catalysts for Organic Synthesis. ADVANCES IN CATALYSIS 2006. [DOI: 10.1016/s0360-0564(05)49001-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Lamble HJ, Theodossis A, Milburn CC, Taylor GL, Bull SD, Hough DW, Danson MJ. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett 2005; 579:6865-9. [PMID: 16330030 DOI: 10.1016/j.febslet.2005.11.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 11/03/2005] [Accepted: 11/03/2005] [Indexed: 11/25/2022]
Abstract
The hyperthermophilic archaeon Sulfolobus solfataricus metabolises glucose and galactose by a 'promiscuous' non-phosphorylative variant of the Entner-Doudoroff pathway, in which a series of enzymes have sufficient substrate promiscuity to permit the metabolism of both sugars. Recently, it has been proposed that the part-phosphorylative Entner-Doudoroff pathway occurs in parallel in S. solfataricus as an alternative route for glucose metabolism. In this report we demonstrate, by in vitro kinetic studies of D-2-keto-3-deoxygluconate (KDG) kinase and KDG aldolase, that the part-phosphorylative pathway in S. solfataricus is also promiscuous for the metabolism of both glucose and galactose.
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Affiliation(s)
- Henry J Lamble
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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28
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Elshafei AM, Elsayed MA, Abdel-Fatah OM, Ali NH, Mohamed LA. Some properties of two aldolases in extracts ofAspergillus oryzae. J Basic Microbiol 2005; 45:31-40. [PMID: 15678561 DOI: 10.1002/jobm.200410440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fructose 1,6-diphosphate (FDP) aldolase and 2-keto-3-deoxy-D-gluconate (KDG) aldolase the two key enzymes of Embden-Meyerhof-Parnas (EMP) and the nonphosphorolytic Entner-Doudoroff (ED) pathways respectively, were identified in cell-free extracts of four Aspergillus oryzae strains grown on D-glucose as sole source of carbon. A. oryzae NRRL 3435 gave the highest enzymatic activity for the two enzymes and selected for further studies. Studies on the properties of the two key enzymes indicated that the optimum conditions for the activities of FDP aldolase and KDG aldolases occurred at pH 8.5, 45 degrees C and pH 8.0, 55 degrees C, respectively. Tris-acetate buffer and phosphate buffer showed the highest enzymatic activity for these two enzymes respectively. KDG aldolase was stable at 55 degrees C for 60 minutes however FDP aldolase was found to be less stable above 45 degrees C. On the other hand the two aldolases showed a high degree of stability towards frequent freezing and thawing. Dialysis of the extracts caused a decrease in the enzymatic activity of KDG aldolase, and an increase in FDP aldolase activity. The addition of ethylene diamine tetraacetate to the crude extracts caused an inhibition of KDG aldolase, whileas FDP aldolase was not affected. Addition of MnCl(2), CoSO(4), MgCl(2) and ZnSO(4) to the dialyzed extracts increased the activity of KDG aldolase by 67%, 54%, 61% and 37%, respectively. On the other hand the addition of some metal salts caused an inhibition of FDP aldolase. The results obtained indicate the absence of evidence for the involvement of sulfhydryl groups in the catalytic sites of the two aldolases.
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Affiliation(s)
- Ali M Elshafei
- Department of Microbial Chemistry, National Research Centre, El-Tahrir Street, Dokki, Cairo, Egypt.
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29
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Affiliation(s)
- Dirk Franke
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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García-Junceda E, García-García JF, Bastida A, Fernández-Mayoralas A. Enzymes in the synthesis of bioactive compounds: the prodigious decades. Bioorg Med Chem 2004; 12:1817-34. [PMID: 15051051 DOI: 10.1016/j.bmc.2004.01.032] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Accepted: 01/16/2004] [Indexed: 11/16/2022]
Abstract
The growing demand for enantiomerically pure pharmaceuticals has impelled research on enzymes as catalysts for asymmetric synthetic transformations. However, the use of enzymes for this purpose was rather limited until the discovery that enzymes can work in organic solvents. Since the advent of the PCR the number of available enzymes has been growing rapidly and the tailor-made biocatalysts are becoming a reality. Thus, it has been possible the use of enzymes for the synthesis of new innovative medicines such as carbohydrates and their incorporation to modern methods for drug development, such as combinatorial chemistry. Finally, the genomic research is allowing the manipulation of whole genomes opening the door to the combinatorial biosynthesis of compounds. In this review, our intention is to highlight the main landmarks that have led to transfer the chemical efficiency shown by the enzymes in the cell to the synthesis of bioactive molecules in the lab during the last 20 years.
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Affiliation(s)
- Eduardo García-Junceda
- Departamento de Química Orgánica Biológica, Instituto de Química Orgánica General, CSIC, C/ Juan de la Cierva 3. Madrid 28006, Spain.
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31
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Braga R, Hecquet L, Blonski C. Slow-binding inhibition of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase. Bioorg Med Chem 2004; 12:2965-72. [PMID: 15142555 DOI: 10.1016/j.bmc.2004.03.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2003] [Accepted: 03/16/2004] [Indexed: 11/22/2022]
Abstract
2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase is a key enzyme in the Entner-Doudoroff pathway of bacteria. It catalyzes the reversible production of KDPG from pyruvate and D-glyceraldehyde 3-phosphate through a class I Schiff base mechanism. On the basis of aldolase mechanistic pathway, various pyruvate analogues bearing beta-diketo structures were designed and synthesized as potential inhibitors. Their capacity to inhibit aldolase catalyzed reaction by forming stabilized iminium ion or conjugated enamine were investigated by enzymatic kinetics and UV-vis difference spectroscopy. Depending of the substituent R (methyl or aromatic ring), a competitive or a slow-binding inhibition takes place. These results were examined on the basis of the three-dimensional structure of the enzyme.
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Affiliation(s)
- Rémi Braga
- Université Paul Sabatier, LSPCMIB, UMR 5068, Groupe de Chimie Organique Biologique, Bât IIR1, 118 Route de Narbonne, 31062 Toulouse Cedex 4, France
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32
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Lamble HJ, Heyer NI, Bull SD, Hough DW, Danson MJ. Metabolic pathway promiscuity in the archaeon Sulfolobus solfataricus revealed by studies on glucose dehydrogenase and 2-keto-3-deoxygluconate aldolase. J Biol Chem 2003; 278:34066-72. [PMID: 12824170 DOI: 10.1074/jbc.m305818200] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic Archaeon Sulfolobus solfataricus metabolizes glucose by a non-phosphorylative variant of the Entner-Doudoroff pathway. In this pathway glucose dehydrogenase and gluconate dehydratase catalyze the oxidation of glucose to gluconate and the subsequent dehydration of gluconate to 2-keto-3-deoxygluconate. 2-Keto-3-deoxygluconate (KDG) aldolase then catalyzes the cleavage of 2-keto-3-deoxygluconate to glyceraldehyde and pyruvate. The gene encoding glucose dehydrogenase has been cloned and expressed in Escherichia coli to give a fully active enzyme, with properties indistinguishable from the enzyme purified from S. solfataricus cells. Kinetic analysis revealed the enzyme to have a high catalytic efficiency for both glucose and galactose. KDG aldolase from S. solfataricus has previously been cloned and expressed in E. coli. In the current work its stereoselectivity was investigated by aldol condensation reactions between D-glyceraldehyde and pyruvate; this revealed the enzyme to have an unexpected lack of facial selectivity, yielding approximately equal quantities of 2-keto-3-deoxygluconate and 2-keto-3-deoxygalactonate. The KDG aldolase-catalyzed cleavage reaction was also investigated, and a comparable catalytic efficiency was observed with both compounds. Our evidence suggests that the same enzymes are responsible for the catabolism of both glucose and galactose in this Archaeon. The physiological and evolutionary implications of this observation are discussed in terms of catalytic and metabolic promiscuity.
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Affiliation(s)
- Henry J Lamble
- Centre for Extremophile Research, the Department of Biology and Biochemistry, University of Bath, United Kingdom
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33
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Affiliation(s)
- Rosa M de Lederkremer
- CIHIDECAR, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Ciudad Universitaria, 1428 Buenos Aires, Argentina
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34
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Griffiths JS, Wymer NJ, Njolito E, Niranjanakumari S, Fierke CA, Toone EJ. Cloning, isolation and characterization of the Thermotoga maritima KDPG aldolase. Bioorg Med Chem 2002; 10:545-50. [PMID: 11814840 DOI: 10.1016/s0968-0896(01)00307-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Thermotoga maritima aldolase gene has been cloned into a T7 expression vector and overexpressed in Escherichia coli. The preparation yields 470 UL(-1) of enzyme at a specific activity of 9.4 U mg(-1). During retroaldol cleavage of KDPG, the enzyme shows a k(cat) that decreases with decreasing temperature. A more than offsetting decrease in K(m) yields an enzyme that is more efficient at 40 degrees C than at 70 degrees C. The substrate specificity of the enzyme was evaluated in the synthetic direction with a range of aldehyde substrates. Although the protein shows considerable structural homology to KDPG aldolases from mesophilic sources, significant differences in substrate specificity exist. A preparative scale reaction between 2-pyridine carboxaldehyde and pyruvate provided product of the same absolute configuration as mesophilic enzymes, but with diminished stereoselectivity.
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35
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Allard J, Grochulski P, Sygusch J. Covalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-A resolution. Proc Natl Acad Sci U S A 2001; 98:3679-84. [PMID: 11274385 PMCID: PMC31111 DOI: 10.1073/pnas.071380898] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2000] [Indexed: 11/18/2022] Open
Abstract
2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. The enzyme is a class I aldolase whose reaction mechanism involves formation of Schiff base intermediates between Lys-133 and a keto substrate. A covalent adduct was trapped by flash freezing KDPG aldolase crystals soaked with 10 mM pyruvate in acidic conditions at pH 4.6. Structure determination to 1.95-A resolution showed that pyruvate had undergone nucleophilic attack with Lys-133, forming a protonated carbinolamine intermediate, a functional Schiff base precursor, which was stabilized by hydrogen bonding with active site residues. Carbinolamine interaction with Glu-45 indicates general base catalysis of several rate steps. Stereospecific addition is ensured by aromatic interaction of Phe-135 with the pyruvate methyl group. In the native structure, Lys-133 donates all of its hydrogen bonds, indicating the presence of an epsilon-ammonium salt group. Nucleophilic activation is postulated to occur by proton transfer in the monoprotonated zwitterionic pair (Glu-45/Lys-133). Formation of the zwitterionic pair requires prior side chain rearrangement by protonated Lys-133 to displace a water molecule, hydrogen bonded to the zwitterionic residues.
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Affiliation(s)
- J Allard
- Département de Biochimie, Université de Montréal, Montreal, QC, H3C 3J7 Canada
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36
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Sundaram AK, Woodard RW. Neisseria gonorrhoeae 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase does not catalyze the formation of the ribo analogue. Org Lett 2001; 3:21-4. [PMID: 11429861 DOI: 10.1021/ol0066126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[figure: see text] Neisseria gonorrhoeae 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH 7-P) synthase catalyzes an aldol-type condensation between D-erythrose 4-phosphate and phosphoenolpyruvate (PEP) to form 3-deoxy-D-arabino-heptulosonate 7-phosphate and not 3-deoxy-D-riboheptulosonate 7-phosphate. Similar to the Escherichia coli enzyme, N. gonorrhoeae DAH 7-P synthase condenses D-arabinose 5-phosphate with PEP to give 3-deoxy-D-manno-octulosonate 8-phosphate. Therefore, the stereochemistry of the reaction catalyzed by N. gonorrhoeae DAH 7-P synthase at C1 of the phosphorylated monosaccharide is the same as that for the E. coli enzyme, namely, re face attack.
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Affiliation(s)
- A K Sundaram
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
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37
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Abstract
New catalytic synthetic methods in organic chemistry that satisfy increasingly stringent environmental constraints are in great demand by the pharmaceutical and chemical industries. In addition, novel catalytic procedures are necessary to produce the emerging classes of organic compounds that are becoming the targets of molecular and biomedical research. Enzyme-catalysed chemical transformations are now widely recognized as practical alternatives to traditional (non-biological) organic synthesis, and as convenient solutions to certain intractable synthetic problems.
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Affiliation(s)
- K M Koeller
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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38
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Wymer N, Buchanan LV, Henderson D, Mehta N, Botting CH, Pocivavsek L, Fierke CA, Toone EJ, Naismith JH. Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli. Structure 2001; 9:1-9. [PMID: 11342129 DOI: 10.1016/s0969-2126(00)00555-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Aldolases are carbon bond-forming enzymes that have long been identified as useful tools for the organic chemist. However, their utility is limited in part by their narrow substrate utilization. Site-directed mutagenesis of various enzymes to alter their specificity has been performed for many years, typically without the desired effect. More recently directed evolution has been employed to engineer new activities onto existing scaffoldings. This approach allows random mutation of the gene and then selects for fitness to purpose those proteins with the desired activity. To date such approaches have furnished novel activities through multiple mutations of residues involved in recognition; in no instance has a key catalytic residue been altered while activity is retained. RESULTS We report a double mutant of E. coli 2-keto-3-deoxy-6-phosphogluconate aldolase with reduced but measurable enzyme activity and a synthetically useful substrate profile. The mutant was identified from directed-evolution experiments. Modification of substrate specificity is achieved by altering the position of the active site lysine from one beta strand to a neighboring strand rather than by modification of the substrate recognition site. The new enzyme is different to all other existing aldolases with respect to the location of its active site to secondary structure. The new enzyme still displays enantiofacial discrimination during aldol addition. We have determined the crystal structure of the wild-type enzyme (by multiple wavelength methods) to 2.17 A and the double mutant enzyme to 2.7 A resolution. CONCLUSIONS These results suggest that the scope of directed evolution is substantially larger than previously envisioned in that it is possible to perturb the active site residues themselves as well as surrounding loops to alter specificity. The structure of the double mutant shows how catalytic competency is maintained despite spatial reorganization of the active site with respect to substrate.
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Affiliation(s)
- N Wymer
- Department of Chemistry, LSRC, Duke University, Durham, NC 27708, USA
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39
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Fong S, Machajewski TD, Mak CC, Wong C. Directed evolution of D-2-keto-3-deoxy-6-phosphogluconate aldolase to new variants for the efficient synthesis of D- and L-sugars. CHEMISTRY & BIOLOGY 2000; 7:873-83. [PMID: 11094340 DOI: 10.1016/s1074-5521(00)00035-1] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Exploitation and improvement of enzymes as catalysts for organic synthesis is of current interest in biocatalysis. A representative enzyme for investigation is the Escherichia coli D-2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, which catalyzes the highly specific reversible aldol reaction using the D-configurated KDPG as substrate. RESULTS Using in vitro evolution, the aldolase has been converted into aldolases with improved catalytic efficiency, altered substrate specificity and stereoselectivity. In particular, some evolved aldolases capable of accepting both D- and L- glyceraldehyde in the non-phosphorylated form as substrates for reversible aldol reaction have been obtained, providing a new direction to the enzymatic synthesis of both D- and L-sugars. CONCLUSIONS This research has demonstrated the effectiveness of using in vitro evolution to rapidly alter the properties of an aldolase to improve its utility in asymmetric synthesis. The evolved aldolases, differing from the native enzyme which is highly phosphate- and D-sugar-dependent, catalyze the efficient synthesis of both D- and L-sugars from non-phosphorylated aldehydes and pyruvate. The principles and strategies described in this study should be applicable to other aldolases to further expand the scope of their synthetic utility.
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Affiliation(s)
- S Fong
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Sheflyan GY, Sundaram AK, Taylor WP, Woodard RW. Substrate ambiguity of 3-deoxy-D-manno-octulosonate 8-phosphate synthase from Neisseria gonorrhoeae revisited. J Bacteriol 2000; 182:5005-8. [PMID: 10940049 PMCID: PMC111385 DOI: 10.1128/jb.182.17.5005-5008.2000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Homogeneous, recombinant 3-deoxy-D-manno-octulosonate 8-phosphate synthase from Neisseria gonorrhoeae is shown to catalyze the formation of 3-deoxy-D-manno-octulosonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate as determined from (1)H-nuclear magnetic resonance analysis of the product. This enzyme does not catalyze the condensation of D-erythrose 4-phosphate and phosphoenolpyruvate to form 3-deoxy-D-ribo-heptulosonate 7-phosphate, as was previously reported (P. S. Subramaniam, G. Xie, T. Xia, and R. A. Jensen, J. Bacteriol. 180:119-127, 1998).
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Affiliation(s)
- G Y Sheflyan
- Interdepartmental Program in Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
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Sheflyan GY, Howe DL, Wilson TL, Woodard RW. Enzymatic Synthesis of 3-Deoxy-d-manno-octulosonate 8-Phosphate, 3-Deoxy-d-altro-octulosonate 8-Phosphate, 3,5-Dideoxy-d-gluco(manno)-octulosonate 8-Phosphate by 3-Deoxy-d-arabino-heptulosonate 7-Phosphate Synthase. J Am Chem Soc 1998. [DOI: 10.1021/ja9816281] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Galina Ya. Sheflyan
- Contribution from the Interdepartmental Program in Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
| | - David L. Howe
- Contribution from the Interdepartmental Program in Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
| | - Trudy L. Wilson
- Contribution from the Interdepartmental Program in Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
| | - Ronald W. Woodard
- Contribution from the Interdepartmental Program in Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
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Cotterill IC, Henderson DP, Shelton MC, Toone EJ. The synthetic utility of KDPGal aldolase. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1381-1177(98)00087-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Henderson DP, Cotterill IC, Shelton MC, Toone EJ. 2-Keto-3-deoxy-6-phosphogalactonate Aldolase as a Catalyst for Stereocontrolled Carbon−Carbon Bond Formation. J Org Chem 1998. [DOI: 10.1021/jo9718814] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ian C. Cotterill
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | | | - Eric J. Toone
- Department of Chemistry, Duke University, Durham, North Carolina 27708
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Abstract
A number of significant biocatalysts have been investigated over the past year to improve accessibility, functional knowledge and use in developing synthetic applications. In particular, accumulating protein structural information has facilitated major advances in the detailed understanding of catalytic events and has, therefore, set the stage for rational protein engineering. This will have important implications for the future scope of practical applications, the first of which are currently being industrialized.
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Affiliation(s)
- W D Fessner
- Department of Organic Chemistry, Rheinisch-Westfälische Technische Hochschule Aachen, Professor-Pirlet-Str. 1, D-52056, Aachen, Germany.
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Henderson DP, Shelton MC, Cotterill IC, Toone EJ. Stereospecific Preparation of the N-Terminal Amino Acid Moiety of Nikkomycins K(X) and K(Z) via a Multiple Enzyme Synthesis. J Org Chem 1997; 62:7910-7911. [PMID: 11671888 DOI: 10.1021/jo971549s] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Takayama S, McGarvey GJ, Wong CH. Microbial aldolases and transketolases: new biocatalytic approaches to simple and complex sugars. Annu Rev Microbiol 1997; 51:285-310. [PMID: 9343352 DOI: 10.1146/annurev.micro.51.1.285] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Enzymes have become exceedingly valuable tools in organic synthesis as the reactions they catalyze generally proceed under mild conditions and in high stereo- and regioselectivity. Advances in microbiology and genetic engineering have greatly increased the availability of various enzymes. One of the most useful applications of enzyme-catalyzed chemical transformations is in the synthesis of water-soluble, polyfunctional organic molecules such as carbohydrates. As the pivotal roles that carbohydrates play in biological processes become more evident, access to these compounds becomes increasingly important. This review gives a brief overview of the use of aldolases and transketolases in the synthesis of sugars, sugar analogs, and related compounds.
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Affiliation(s)
- S Takayama
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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McGarvey GJ, Wong CH. Chemical, Enzymatic and Structural Studies in Molecular Glycobiology. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/jlac.199719970604] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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